Genome and Genomics From Archaea to Eukaryotes

K. V. Chaitanya install download

https://textbookfull.com/product/genome-and-genomics-from-
archaea-to-eukaryotes-k-v-chaitanya/

Download more ebook instantly today - get yours now at textbookfull.com

We believe these products will be a great fit for you. Click
the link to download now, or visit textbookfull.com
to discover even more!

Plant Responses to Environmental Stresses From

Phytohormones to Genome Reorganization From
Phytohormones to Genome Reorganization First Edition
Lerner
https://textbookfull.com/product/plant-responses-to-
environmental-stresses-from-phytohormones-to-genome-
reorganization-from-phytohormones-to-genome-reorganization-first-
edition-lerner/

Genome Plasticity in Health and Disease (Translational

and Applied Genomics) 1st Edition Diego A. Forero
(Editor)

https://textbookfull.com/product/genome-plasticity-in-health-and-
disease-translational-and-applied-genomics-1st-edition-diego-a-
forero-editor/

Geospatial Technologies for Agriculture Case Studies

from India K. V. Raju

https://textbookfull.com/product/geospatial-technologies-for-
agriculture-case-studies-from-india-k-v-raju/

Introduction To Embedded Systems 2nd Edition K. V Shibu

https://textbookfull.com/product/introduction-to-embedded-
systems-2nd-edition-k-v-shibu/
The Human Mitochondrial Genome: From Basic Biology to
Disease 1st Edition Giuseppe Gasparre

https://textbookfull.com/product/the-human-mitochondrial-genome-
from-basic-biology-to-disease-1st-edition-giuseppe-gasparre/

Precision Medicine CRISPR and Genome Engineering Moving

from Association to Biology and Therapeutics 1st
Edition Stephen H. Tsang (Eds.)

https://textbookfull.com/product/precision-medicine-crispr-and-
genome-engineering-moving-from-association-to-biology-and-
therapeutics-1st-edition-stephen-h-tsang-eds/

Practical Civil Engineering 1st Edition P K Jayasree K

Balan V Rani

https://textbookfull.com/product/practical-civil-engineering-1st-
edition-p-k-jayasree-k-balan-v-rani/

Practical Civil Engineering 1st Edition Jayasree P K

Balan K Rani V

https://textbookfull.com/product/practical-civil-engineering-1st-
edition-jayasree-p-k-balan-k-rani-v/

Endo symbiotic Methanogenic Archaea Johannes H. P.

Hackstein

https://textbookfull.com/product/endo-symbiotic-methanogenic-
archaea-johannes-h-p-hackstein/
K. V. Chaitanya

Genome and
Genomics
From Archaea to Eukaryotes
Genome and Genomics
K. V. Chaitanya

Genome and Genomics

From Archaea to Eukaryotes
K. V. Chaitanya
Department of Biotechnology
GITAM University
Visakhapatnam, Andhra Pradesh, India

ISBN 978-981-15-0701-4 ISBN 978-981-15-0702-1 (eBook)

https://doi.org/10.1007/978-981-15-0702-1

# Springer Nature Singapore Pte Ltd. 2019

This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the
material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,
broadcasting, reproduction on microfilms or in any other physical way, and transmission or information
storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology
now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication
does not imply, even in the absence of a specific statement, that such names are exempt from the relevant
protective laws and regulations and therefore free for general use.
The publisher, the authors, and the editors are safe to assume that the advice and information in this
book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or
the editors give a warranty, expressed or implied, with respect to the material contained herein or for any
errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd.
The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721,
Singapore
Knowledge of Sequences Could Contribute
Much to Our Understanding of Living
Matter
Frederick Sanger
Dedicated to My Teachers
Preface

A genome encodes all the necessary information for the function of both single cell
and highly complex organisms. Genome comprises a cluster of genes, regulated in a
wide variety of cells, whose division makes an organism. Apart from the genes, a
genome is also composed of noncoding regions, regulatory regions, etc. whose
coordinated function will make the process of life. A lot of advancement has been
made in the field of genomics with the genomes of all model organisms and
economically important organisms being sequenced and deposited in the databases.
This book addresses the new tools, technologies, and approaches that were made
to sequence a variety of genomes belonging to various organisms for both the
students and experienced, practicing biologists. The achievement of long-sought
decoding a genome sequence was possible through the development of instrumenta-
tion and computational technologies with user-friendly softwares and tools, which
has irrevocably changed the perspective and provided a new direction for the a better
understanding of biology. The development of other omics technologies such as
proteomics, transcriptomics, and metabolomics has also provided a comprehensive
scope of understanding a living system in detail.
Genome and Genomics: From Archaea to Eukaryotes is the most updated book,
which mentions about the components of the genomes of all three major life forms
along with the organelles. This book covers the concepts of the genomes, how
various components in the genome are operating for the life of an organism, how
the genomes and different life forms have evolved, what are other “omics” which
provides a better understanding of genome functions, and what are the major
applications of the genomics in providing a healthy, hunger-free, and disease-free
human society.
This book is divided into nine chapters. Chapter 1 describes the variations in the
viral genomes and their evolution. In Chap. 2, archaeal genomes and their relation-
ship with the prokaryote and eukaryote genomes were discussed. Chapter 3 explains
about the bacterial genomes. Chapter 4 mentions the organellar genomes and their
evolution from the bacteria. Chapter 5 describes the eukaryotic genomes with model
organisms including the human genome. Chapter 6 explains the sequencing
technologies that are applied for sequencing the genomes of various organisms
including fossils, their annotation, and assembly mechanisms. The role of other
omics technology that has helped in the better understanding of the life processes

ix
x Preface

such as proteomics, transcriptomics, metabolomics, and exposomics was discussed

in Chap. 7. Applications of genome sequencing were described in Chap. 8. Chapter 9
consists of the genome databases and their URLs.
I owe my profound gratitude to Late Dr. M.V.V.S. Murthy, Founder President,
GITAM Deemed to be University whose vision, dynamism, and motivation have
deeply inspired me. I am indebted to Dr. Utpal Nath, Associate Professor, MCB
Department, Indian Institute of Science, Bengaluru, Professor Ch. Ramakrishna,
Professor Sk. Khasim Beebi, and Professor T. Sekhar, GITAM University, for their
unstinting support. I thank Dr. Nageswara Rao Reddy for sparing his time to read the
drafts and provide invaluable suggestions and comments. I thank my wife Lalita and
my children Abhiram and Aamukta for their patience and constant support.
I express my deep sense of gratefulness to all authors, whose works have been
consulted for writing this book. I shall highly appreciate any valuable suggestions
for further improvement of this work.

Visakhapatnam, Andhra Pradesh, India K. V. Chaitanya

Contents

1 Structure and Organization of Virus Genomes . . . . . . . . . . . . . . . . . 1

1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 General Features of Viral Genomes and their Classification . . . . . 3
1.2.1 Classification of Viral Genomes . . . . . . . . . . . . . . . . . 3
1.3 Size, Structure, and Composition of Double Stranded DNA
Virus Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.1 Analysis of Adenovirus 2(AD2) Genome . . . . . . . . . . . 7
1.3.2 Herpesviridae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4 Genomes of Single Stranded DNA Viruses and their
Mosaicism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.4.1 Genomes of Bacteriophages . . . . . . . . . . . . . . . . . . . . 12
1.4.2 Phage Genome Sequence Diversity . . . . . . . . . . . . . . . 13
1.4.3 Genome Mosaicism of Phages . . . . . . . . . . . . . . . . . . . 14
1.4.4 Genomes of Enterobacteria Phage M13
and λ Phages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.4.5 The Genome of T4 Phage . . . . . . . . . . . . . . . . . . . . . . 15
1.5 Positive and Negative Stranded RNA Viral Genomes . . . . . . . . . 17
1.5.1 Positive Stranded RNA Viral Genomes . . . . . . . . . . . . 18
1.5.2 Negative Stranded RNA Viral Genomes . . . . . . . . . . . 20
1.6 Segmentation in Viral Genomes . . . . . . . . . . . . . . . . . . . . . . . . . 23
1.6.1 Influenza Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.7 Multipartite Viral Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
1.7.1 The Genome of Gemini Virus . . . . . . . . . . . . . . . . . . . 28
1.8 Evolution of Viral Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
1.9 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2 Archeal Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.2 Archaea, the Third Main Domain of Life . . . . . . . . . . . . . . . . . . 32
2.3 Unique Features of Archaea . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.3.1 Cell Envelopes and Cell Structure . . . . . . . . . . . . . . . . 33
2.3.2 Unusual Appendages . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.3.3 Exosome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

xi
xii Contents

2.3.4 Archaeal Virus Families . . . . . . . . . . . . . . . . . . . . . . . 34

2.3.5 Archaea and Extra Terrestrial Life . . . . . . . . . . . . . . . . 35
2.4 Archaea and Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
2.5 Archaeal Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.5.1 Structure and Organization of Archaeal Genomes . . . . . 37
2.6 Plasmids of Archaea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.7 Horizontal Gene Transfer (HGT) . . . . . . . . . . . . . . . . . . . . . . . . 42
2.8 Integrase-Mediated Insertion and Deletion of Archaeal DNA . . . . 43
2.9 Genome of Methanogenic Archeon Methanococcus
Jannaschii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
2.9.1 The Methodology of Genome Sequencing . . . . . . . . . . 44
2.9.2 Properties of the Genome . . . . . . . . . . . . . . . . . . . . . . 44
2.9.3 Identification of Proteins by Shotgun Proteomics . . . . . 47
2.10 Genome of Archaeoglobus Fulgidus . . . . . . . . . . . . . . . . . . . . . 49
2.10.1 Genome Sequencing and Assembly . . . . . . . . . . . . . . . 49
2.10.2 ORF Prediction and Gene Identification . . . . . . . . . . . . 50
2.10.3 Features of the Genome . . . . . . . . . . . . . . . . . . . . . . . 50
2.11 Comparative Genomics of A. Fulgidus and M. Jannaschii . . . . . . 54
2.12 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3 Structure, Function, and Evolution of Bacterial Genomes . . . . . . . . . 55
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
3.2 Structure and Organization of Bacterial Genomes . . . . . . . . . . . . 56
3.2.1 Bacterial Chromosomes and Plasmids . . . . . . . . . . . . . 56
3.2.2 Bacterial Genomes with Primary and Secondary
Chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.2.3 Insertion Sequence (IS) Elements . . . . . . . . . . . . . . . . 57
3.2.4 Conjugative Transposons . . . . . . . . . . . . . . . . . . . . . . 58
3.2.5 Invertrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.2.6 Integrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.2.7 Integratable Plasmids and Phages . . . . . . . . . . . . . . . . 61
3.3 Genome Rearrangements in Bacteria . . . . . . . . . . . . . . . . . . . . . 62
3.3.1 Rearrangements Due to Mobile Genetic Elements . . . . . 62
3.3.2 Transposons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.3.3 Genomic Islands in Bacteria . . . . . . . . . . . . . . . . . . . . 64
3.3.4 Inteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.3.5 Introns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.3.6 Homing Endonucleases . . . . . . . . . . . . . . . . . . . . . . . . 66
3.3.7 Retro Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.4 Evolution of Bacterial Genomes . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.4.1 Role of Mutations in Bacterial Genome Evolution . . . . 68
3.4.2 Role of Recombinations in Bacterial Genome
Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.4.3 Evolution of Bacterial Pathogens . . . . . . . . . . . . . . . . . 69
Contents xiii

3.5 Genetic Diversity of Pathogenic Bacteria . . . . . . . . . . . . . . . . . . 70

3.5.1 Mechanisms of Genetic Diversity . . . . . . . . . . . . . . . . 70
3.5.2 Horizontal Gene Transfer . . . . . . . . . . . . . . . . . . . . . . 71
3.5.3 Pathogenicity Islands . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.5.4 Genetic Diversity and Origin of New Bacterial
Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.5.5 Techniques Used for Studying the Genetic Diversity
of Pathogenic Bacteria . . . . . . . . . . . . . . . . . . . . . . . . 73
3.6 Genome of Escherichia coli K-12 Strain . . . . . . . . . . . . . . . . . . . 73
3.6.1 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . 74
3.6.2 Annotation of the Genome . . . . . . . . . . . . . . . . . . . . . 75
3.6.3 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
3.6.4 Compositional Organization of the Genome . . . . . . . . . 77
3.6.5 Open Reading Frames and Gene Function . . . . . . . . . . 78
3.6.6 Operons, Promoters and Protein Binding Sites . . . . . . . 79
3.6.7 Repeated Sequences and Insertion Sequences . . . . . . . . 80
3.6.8 Cryptic Prophage and Phage Remnants . . . . . . . . . . . . 80
3.7 Genome of Enterohaemorrhagic E. coli O157: H7 . . . . . . . . . . . . 81
3.7.1 Genome Sequencing and Annotation . . . . . . . . . . . . . . 81
3.7.2 Outline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
3.7.3 Comparison Between E. coli O157 and E. coli K-12
Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
3.8 Genome of Mycoplasma genitalium . . . . . . . . . . . . . . . . . . . . . . 83
3.8.1 Genome Sequencing, Assembly and Annotation . . . . . . 83
3.8.2 Overview of the Genome . . . . . . . . . . . . . . . . . . . . . . 84
3.9 Synthetic Genome of Mycoplasma genitalium . . . . . . . . . . . . . . . 85
3.9.1 Strategy for Synthesis and Assembly . . . . . . . . . . . . . . 85
3.9.2 Minimal Number of Genes . . . . . . . . . . . . . . . . . . . . . 87
3.10 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
4 Orgenellar Genome Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
4.2 Resemblances of Chloroplast and Mitochondria with Bacteria . . . 90
4.3 Architecture of Organelle Genomes . . . . . . . . . . . . . . . . . . . . . . 90
4.3.1 Genome Size and Structure . . . . . . . . . . . . . . . . . . . . . 91
4.3.2 Nucleotide Composition . . . . . . . . . . . . . . . . . . . . . . . 91
4.3.3 Chromosome Number . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.3.4 Non-coding DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.3.5 Coding Regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.3.6 Genome Loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
4.3.7 Gene Fragmentation . . . . . . . . . . . . . . . . . . . . . . . . . . 94
4.3.8 Non-Canonical Genetic Codes and RNA Editing . . . . . 95
4.3.9 Horizontal Gene Transfer and Acquisition of Foreign
DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
xiv Contents

4.4 Evolution of Organelle Genomes . . . . . . . . . . . . . . . . . . . . . . . . 95

4.4.1 Evolution of Traits and Characteristics in Organelle
Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
4.5 Chloroplast Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
4.5.1 Sequencing Technologies for Chloroplast Genomes . . . 98
4.5.2 Chloroplast Genome Sequencing . . . . . . . . . . . . . . . . . 98
4.5.3 Structure of Chloroplast Genome . . . . . . . . . . . . . . . . . 99
4.5.4 Phylogeny of Chloroplast Genomes . . . . . . . . . . . . . . . 99
4.5.5 Chloroplast Genome Engineering . . . . . . . . . . . . . . . . 101
4.5.6 Chloroplast Genome of Euglena gracilis . . . . . . . . . . . 102
4.6 Mitochondrial Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.6.1 Sequencing Technologies for Mitochondrial
Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.6.2 Structure of Mitochondrial Genome . . . . . . . . . . . . . . . 109
4.6.3 Mutations in the Human Mitochondrial DNA
and Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
4.6.4 Mitochondrial Genome of Neandertal Fossil . . . . . . . . . 115
4.6.5 Structure and Organization of Plant Mitochondrial
Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.7 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
5 Eukaryotic Genome Organization, Regulation, Evolution
and Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.2 Organisation of Eukaryotic Genomes . . . . . . . . . . . . . . . . . . . . . 122
5.2.1 Organization of Chromosomes . . . . . . . . . . . . . . . . . . 122
5.2.2 Centromeres of Eukaryotic Chromosomes . . . . . . . . . . 123
5.2.3 Telomeres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
5.2.4 Spatial Organisation of Eukaryotic Genomes . . . . . . . . 124
5.2.5 Whole Genome Duplications and Segmental
Duplications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.2.6 Transposable Elements . . . . . . . . . . . . . . . . . . . . . . . . 127
5.2.7 Satellite DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.3 Complexity of the Eukaryotic Genomes . . . . . . . . . . . . . . . . . . . 132
5.4 Yeast Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
5.4.1 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . 134
5.4.2 Genome Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.4.3 Chromosomal Organization . . . . . . . . . . . . . . . . . . . . . 135
5.4.4 Organellar, Plasmid, and Viruses in Yeast Genome . . . . 136
5.4.5 Genome Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
5.4.6 Comparative Genomics of Yeast . . . . . . . . . . . . . . . . . 137
5.4.7 Yeast Proteome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
5.4.8 Future Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Contents xv

5.5 Caenorhabditis elegans Genome . . . . . . . . . . . . . . . . . . . . . . . . 139

5.5.1 Importance of C. elegans as a Model Organism . . . . . . 139
5.5.2 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.5.3 Overview of the Genome . . . . . . . . . . . . . . . . . . . . . . 141
5.6 The Genome of Drosophila melanogaster . . . . . . . . . . . . . . . . . 144
5.6.1 Drosophila melanogaster as a Model Organism . . . . . . 144
5.6.2 Genetic Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.6.3 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.6.4 Gene Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.6.5 Gene Similarity with Humans . . . . . . . . . . . . . . . . . . . 148
5.7 Genome of Arabidopsis thaliana . . . . . . . . . . . . . . . . . . . . . . . . 148
5.7.1 Arabidopsis thaliana as a Model Organism . . . . . . . . . 149
5.7.2 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . 149
5.7.3 Gene Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
5.7.4 Genome Organization and Duplication . . . . . . . . . . . . . 151
5.7.5 Telomeres and Centromeres . . . . . . . . . . . . . . . . . . . . 152
5.7.6 Transposable Elements . . . . . . . . . . . . . . . . . . . . . . . . 153
5.7.7 Gene Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
5.7.8 Developmental Regulation . . . . . . . . . . . . . . . . . . . . . 154
5.7.9 Photomorphogenesis and Photosynthesis . . . . . . . . . . . 155
5.7.10 Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
5.7.11 Comparative Genomics with B. oleracea . . . . . . . . . . . 157
5.8 The Soybean Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
5.8.1 Soybean and its Importance . . . . . . . . . . . . . . . . . . . . 157
5.8.2 Genome Sequencing and Assembly . . . . . . . . . . . . . . . 158
5.8.3 Gene Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
5.8.4 Repetitive Elements . . . . . . . . . . . . . . . . . . . . . . . . . . 160
5.8.5 Structural Organization of the Genome . . . . . . . . . . . . 161
5.8.6 Importance of Soybean Genome . . . . . . . . . . . . . . . . . 162
5.8.7 Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.9 The Rice Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.9.1 Importance of Rice Crop to the World . . . . . . . . . . . . . 163
5.9.2 International Rice Genome Sequencing Project
(IRGSP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.9.3 Physical Map and Sequencing of the Rice Genome . . . . 164
5.9.4 Genome Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . 165
5.9.5 Components of Rice Genome . . . . . . . . . . . . . . . . . . . 165
5.9.6 Outcomes of the Rice Genome Project . . . . . . . . . . . . . 169
5.10 The Human Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
5.10.1 Sources of DNA and Sequencing Methods . . . . . . . . . . 170
5.10.2 Genome Assembly Strategy and Characterization . . . . . 171
5.10.3 Whole-Genome Assembly . . . . . . . . . . . . . . . . . . . . . 172
5.10.4 Gene Prediction and Annotation . . . . . . . . . . . . . . . . . 173
5.10.5 Genome Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
xvi Contents

5.10.6 Evolution of Human Genome . . . . . . . . . . . . . . . . . . . 176

5.10.7 Sequence Variations in the Human Genome . . . . . . . . . 177
5.10.8 Analysis of Predicted Protein-Coding Genes . . . . . . . . 177
5.10.9 Evolutionary Studies and Comparative Genomics . . . . . 178
5.10.10 80% of the Human Genome has an Active
Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
5.11 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
6 Genome Sequencing, Assembly, and Annotation . . . . . . . . . . . . . . . . 181
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.2 Sequencing Technologies and Genome Sequencing . . . . . . . . . . . 182
6.2.1 First-Generation DNA Sequencing . . . . . . . . . . . . . . . 182
6.2.2 Second Generation DNA Sequencing . . . . . . . . . . . . . 183
6.2.3 Third Generation DNA Sequencing . . . . . . . . . . . . . . . 186
6.2.4 Sequencing of Fungal Genomes . . . . . . . . . . . . . . . . . 188
6.2.5 Sequencing of Plant Genomes . . . . . . . . . . . . . . . . . . . 189
6.2.6 Sequencing of Animal Genomes . . . . . . . . . . . . . . . . . 190
6.2.7 Sequencing of Degraded and Ancient Fossil DNA . . . . 191
6.2.8 Structural Variations in the Drosophila Genome . . . . . . 191
6.3 Whole Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
6.3.1 Major Strategies for Whole Genome Sequencing . . . . . 191
6.4 Genome Sequencing by Mass Spectrometry . . . . . . . . . . . . . . . . 192
6.4.1 Mass Analysis of Sanger Sequencing Reaction
Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
6.4.2 DNA Ladder Sequencing . . . . . . . . . . . . . . . . . . . . . . 194
6.4.3 Gas-Phase Fragmentation . . . . . . . . . . . . . . . . . . . . . . 195
6.4.4 Mass Spectrometry and SNP Genotyping . . . . . . . . . . . 195
6.5 Mapping of Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
6.5.1 Genetic Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
6.5.2 Physical Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
6.6 Genome Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
6.6.1 Overlap Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.6.2 Layout Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.6.3 Derivation of a Consensus Sequence . . . . . . . . . . . . . . 201
6.6.4 Repeats and Sequencing Errors in the Genome
Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.6.5 Assembly Algorithms and Notable Assembly
Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
6.7 Scaffolding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
6.8 Finishing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
6.9 Genome Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
6.9.1 Nucleotide Annotation . . . . . . . . . . . . . . . . . . . . . . . . 204
6.9.2 Protein-Level Annotation . . . . . . . . . . . . . . . . . . . . . . 206
6.9.3 Process-Level Annotation . . . . . . . . . . . . . . . . . . . . . . 206
Contents xvii

6.10 Applications of Next Generation Sequencing Systems . . . . . . . . . 207

6.10.1 Transcriptome Sequencing . . . . . . . . . . . . . . . . . . . . . 207
6.10.2 The Resurrection of Ancient Genomes . . . . . . . . . . . . . 208
6.10.3 Analysis of Epigenetic Modifications of Histones
and DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
6.10.4 Sequencing of Cancer Genome . . . . . . . . . . . . . . . . . . 208
6.10.5 Diagnosis of Rare Diseases and Exome
Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
6.11 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
7 Other ‘Omics’ Integrated into Biosciences . . . . . . . . . . . . . . . . . . . . 211
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
7.2 Transcriptomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
7.2.1 Categories of RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
7.2.2 Transcriptome Sequencing and Analysis . . . . . . . . . . . 213
7.3 Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
7.3.1 Life and Death of a Protein . . . . . . . . . . . . . . . . . . . . . 217
7.3.2 Types of Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . 218
7.3.3 Gene Expression and Codon Bias Affecting
the Protein Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
7.3.4 Techniques that are Involved in the Proteomics
Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
7.3.5 Applications of Proteomics . . . . . . . . . . . . . . . . . . . . . 227
7.4 Metabolomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
7.4.1 Approaches for Metabolomics . . . . . . . . . . . . . . . . . . . 229
7.5 Exposomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
7.5.1 External Exposome . . . . . . . . . . . . . . . . . . . . . . . . . . 235
7.5.2 Internal Expsome . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
7.6 Connectomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
7.6.1 Need for the Connectome . . . . . . . . . . . . . . . . . . . . . . 237
7.6.2 Measurement of Regional Connections in the Living
Human Brain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
7.7 Microbiomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
7.7.1 Human Microbiome . . . . . . . . . . . . . . . . . . . . . . . . . . 239
7.8 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
8 Applications of Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
8.2 Application of Genomics in Agriculture . . . . . . . . . . . . . . . . . . . 244
8.2.1 Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
8.2.2 Genome Wide SNP Studies . . . . . . . . . . . . . . . . . . . . . 245
8.2.3 Construction of Genetic Maps . . . . . . . . . . . . . . . . . . . 246
8.2.4 Identification of QTL Related Markers . . . . . . . . . . . . . 247
8.2.5 Association Mapping . . . . . . . . . . . . . . . . . . . . . . . . . 247
8.2.6 Abiotic Stress Tolerance . . . . . . . . . . . . . . . . . . . . . . . 248
xviii Contents

8.3 Application of Genomics in Genetic Testing and Molecular

Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
8.3.1 Single Gene Disorders . . . . . . . . . . . . . . . . . . . . . . . . 249
8.3.2 Multifactorial Gene Disorders . . . . . . . . . . . . . . . . . . . 250
8.4 Epigenetics and Epigenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
8.5 Genomic Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
8.6 Genomics and Cancer Therapy . . . . . . . . . . . . . . . . . . . . . . . . . 253
8.7 Cytogenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
8.7.1 Cytogenomics of Brain Diseases . . . . . . . . . . . . . . . . . 255
8.7.2 Cytogenomics of Plants . . . . . . . . . . . . . . . . . . . . . . . 255
8.8 Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
8.8.1 Genomic Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . 256
8.9 Comparative Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
8.9.1 Comparative Genomics of Human and Mouse . . . . . . . 258
8.9.2 Evolution of Sex-Chromosomes in Humans . . . . . . . . . 259
8.9.3 Language Adaptation in Humans . . . . . . . . . . . . . . . . . 259
8.10 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
9 Important Databases Related to Genomes . . . . . . . . . . . . . . . . . . . . . 261
9.1 Virus Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
9.2 Archaeal Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
9.3 Bacterial Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
9.4 Cell Organelle Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
9.5 In-Vertebrate Genome Databases . . . . . . . . . . . . . . . . . . . . . . . . 264
9.6 Vertebrate Genome Databases . . . . . . . . . . . . . . . . . . . . . . . . . . 265
9.7 Human Genome Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
9.8 Plant Genome Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
9.9 Genomes of Economically Important and Model Plants . . . . . . . . 269

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
About the Author

K. V. Chaitanya is an Associate Professor at the Department of Biotechnology,

GITAM University, Visakhapatnam. He completed his Ph.D. in Life Sciences at
Pondicherry University and then received a fellowship from DBT to pursue post-
doctoral studies at the Indian Institute of Science, Bengaluru. He has over 15 years of
experience in research in the fields of genomics, molecular biology, and plant
biotechnology. He has worked in various capacities in internationally respected
academic and research institutes and has published a number of articles in leading
international journals. He has published one book on cell and molecular biology and
has filed five patents. Dr. Chaitanya has received numerous academic awards and
fellowships.

xix
Structure and Organization of Virus
Genomes 1

Abstract
This chapter provides an in depth study on the structure, composition, and
organization of viral genomes, their classification into double stranded and single
stranded DNA viruses, positive and negative stranded RNA viruses with and their
genome diversity. Segmentation and re-assortment of viral genomes have been
discussed along with the multipartite virus genomes. Genome details of 13 differ-
ent viruses have been provided as type studies for better understanding of these
topics. Concepts of viral genome evolution have also been discussed.

1.1 Introduction

A Virus is a small electron microscopic parasite, incapable of reproducing by its

own, survives by directing the host cell machinery for the production of more
viruses, which emerges from their respective host cell through lysis. Most of these
viral organisms contain either double stranded or single stranded DNA as well as
RNA in their genomes, which may be either single stranded or double stranded.
After the purification and partial crystallization of Tobacco Mosiac Virus in 1935 by
Wendell Stanley, the study of viruses has inspired many scientists, which lead to
identification and characterization of plant, bacteria, archaea, and animal viruses.
Since viruses are capable of infecting a large number of various cell types, geneti-
cally modified viruses are being considered for the gene therapy. All these factors
and applications make the virus an important organism for its capability to infect any
living organism on this planet.
Viruses are small submicroscopic, obligate intracellular parasites, which contains
either DNA or RNA as genome protected by a virus-encoded protein coat called
capsid. Viruses are mobile genetic elements, depends on metabolic and biosynthetic
machinery of host cells for their propagation. Viruses cannot carry out their life
sustaining functions outside the host cell. They cannot synthesize proteins as they
lack ribosomes and uses the host cell ribosome machinery for translating their

# Springer Nature Singapore Pte Ltd. 2019 1

K. V. Chaitanya, Genome and Genomics,
https://doi.org/10.1007/978-981-15-0702-1_1
2 1 Structure and Organization of Virus Genomes

mRNA into proteins. Viruses can neither generate nor store ATP but derive the
necessary energy and other metabolic functions by parasitizing the host cell for the
basic materials such as amino acids, nucleotides, and lipids. Even though the viruses
are speculated as a form of proto-life, their inability to survive outside living
organisms does not make them as living organisms in the strict sense and it is highly
unlikely that they preceded cellular life during the evolution of the earth. Some
scientists even speculate that viruses have begun as rogue segments of genetic code
which got adapted to a parasitic form of existence. Virions are the complete virus
particles that are produced by the assembly of the pre-formed viral components,
whose main function is to deliver its genome into the host cell for its expression
(transcription and translation). The icosahedral virion belonging to the icosahedral
or quasi-spherical structural class of viruses is made of 20 identical triangular faces,
each face is constructed with three identical capsid protein units making 60 subunits
per capsid, with five subunits symmetrically contacting each of the 12 vertices, thus
making all proteins in equivalent interaction with each other. The viral genome is
packed inside a symmetric protein capsid, composed of either a single or multiple
proteins, each of them is encoding a single viral gene. Due to this symmetric
structure, viruses could encode all the necessary information for constructing a
large capsid using a small set of genes. A capsid along with the enclosed nucleic
acid is called a nucleocapsid. In enveloped viruses, the nucleocapsid is surrounded
by a lipid bilayer and is studded with a layer of glycoproteins. Often, the nucleic acid
is associated with a protein called nucleoprotein. Viruses possess a great diversity
with respect to their size. Mimivirus is the largest virus reported with 400 nm in
diameter, bigger than the Mycoplasma bacteria, which is ~200 to 300 nm long. They
also exhibit a wide diversity in shapes and forms, such as spherical, rod-like, etc.
There are few subviral entities which are highly similar, pathogenic and are
possessing the properties similar to that of viruses. These entities are viroids,
virusoids, and prions. Viroids are a short stretch of highly complementary, single
stranded (200–400 nucleotides), circular RNA molecules possessing a rod-like
secondary structure without any capsid or envelope. These viroids are associated
with plant and human diseases such as hepatitis D. They are obligate intracellular
parasites, with replication strategies similar to viruses. Virusoids are a satellite,
circular single-stranded RNAs (1000 nucleotides) dependent on plant viruses for
replication and encapsidation. They are packed into virus capsids as passengers.
Their genome encodes only structural proteins. Prions are anomalous infectious
agents that cause fatal neurodegenerative diseases mediated by contemporary
mechanisms. Prions consist of a single type of protein molecule without any nucleic
acid component. The protein is a modified isoform of prion protein (PrP) designated
PrPSc. The normal cellular PrPC is converted into PrPSc by a structural transition of
its α-helical and coil structure is refolded into β-sheet. The prion protein and its
encoding gene are often found in normal uninfected cells and are associated with
viral diseases such as Creutzfeldt–Jakob disease in humans, scrapie in sheep and
bovine spongiform encephalopathy (BSE) in cattle.
1.2 General Features of Viral Genomes and their Classification 3

1.2 General Features of Viral Genomes and their Classification

It has been estimated that there are 1031–1032 viruses in the earth’s atmosphere,
which exceeds the number of host cells fairly by an order of magnitude. As a
consequence, every organism on the planet or even every living cell is under
constant attack from viruses, even viruses are highly responsible for the greatest
selection pressure on the living organisms. In spite of their small size, viruses play an
important role as obligate intracellular parasites, modulating their host cells for
energy and reproduction leading to adverse effects. The main emphasis of virology
is focused on the identification and control of pathogenic viruses that invade
humans, domestic animals, and plants. But, origin and organization of viruses,
their evolution is the deep questions which are fundamental to molecular virology.
The comparative genomics has allowed closely related viruses to be compared and
classified. In addition, the sequencing of eukaryotic genomes has revealed that
5–10% of their DNA encodes information for these organisms. A large fraction of
the remainder is thought to be composed of mobile retrovirus-like elements (retro-
transposons), which may have played a considerable role in shaping these complex
genomes. Bacterial genomes do not have such extra genetic material. But, the
genomes of certain bacteriophages have a close resemblance with bacterial plasmids
in their structure and in the way of their replication, revealing that the relationship
between viruses and other living organisms is perhaps more complex than what was
previously thought.

1.2.1 Classification of Viral Genomes

Currently, over 4000 viruses have been described, classified into 71 families. Even
though viruses possess small genomes, they exhibit enormous diversity compared
with plants, animals and even bacteria. With respect to the genome, viruses are
broadly divided into DNA viruses and RNA viruses. Both DNA and RNA viruses
can either single stranded or double stranded, with a circular, linear or segmented
arrangement. DNA and RNA viruses are distinguished by their features, such as
monopartite or multipartite. In monopartite, their genome is having a single nucleic
acid molecule. All double stranded DNA genomes contain only a single nucleic acid
molecule and few of the viruses with single stranded genomes are reported to have
multiple segments. In contrast, RNA viral genomes are generally multipartite, with
more frequency for single stranded RNA viruses. Additionally, single stranded virus
genomes may be either positive sense (+) where the RNA present in the genome will
of the same polarity as mRNA and will encode the genes or negative sense (
),
where the entire ssRNA genome must be copied and the copied strand is transcribed.
Some single stranded viruses are ambisense (a mixture of + and
sense).
Bacteriophages such as MS2, Qb, and Mimivirus belonging to family Leviviridae
consists of ambisense viral genomes. Size of the DNA viruses is larger than that of
RNA viruses. Few DNA viruses can be as large as 305,000 nucleotides. DNA
viruses are called large viruses and RNA viruses are small. Size of a few single
4 1 Structure and Organization of Virus Genomes

stranded RNA genomes is up to 31,000 nucleotides. The small size of the single-
stranded virus might be limited due to the fragility of the RNA, which provides the
tendency of the large RNA strands to break and also due to the fact that RNA viruses
are more susceptible to mutations than DNA viruses. Single stranded DNA and RNA
viruses are fragile than double stranded viruses.
The genomes of the largest double-stranded DNA viruses such as herpesviruses
and poxviruses are quite complex, resembling their host cells. Genomes of Poly-
omavirus are complexed with cellular histone proteins, which form a chromatin-like
structure inside the virus particle. After infecting the host cell, these genomes behave
like miniature satellite chromosomes inside the host cell following the dictates of
cellular enzymes and the cell cycle. mRNAs of Vaccinia virus were polyadenylated
at their 3¢. The genome of Adenovirus consists of split genes with non-coding
introns, protein-coding exons, and spliced mRNAs. In order to streamline the
replication cycle, the Adenovirus takes control of many biological processes in the
cell, such as alternative RNA splicing and polyadenylation for expanding the coding
potential of the limited viral genome.
Phage genomes are simple and least complex. Introns in prokaryotes were first
discovered in the genome of T4 phage in 1984. The genome of T4 phage is 160 kbp
double-stranded DNA, highly compressed with promoters and sequences that con-
trol translation are nested within the coding regions of overlapping upstream genes.
It consists of three self-splicing group I introns, located in the genes that codes for
thymidylate synthase (td), aerobic ribonucleotide reductase (nrdB) small subunit and
the anaerobic ribonucleotide reductase (nrdD). Like any other group I introns, the td
and nrdD introns each contain an open reading frame encodes for a homing
endonuclease that renders the introns mobile and they can be inserted into new
phage genomes. The nrdB intron is non-mobile due to a deletion in the intron-borne
homing endonuclease gene. It was speculated that the presence of in these introns
may confer a selective advantage to the phage by offering the possibility of
regulating the expression of the intron-containing genes by the regulation of splic-
ing. It was also believed that horizontal transfer of the introns between phages
through homing has played a significant role in the evolution of group I introns in
T-like phages.
The size of viral genomes also depends on the type of host cell. Viruses with
prokaryotic host cells tend to replicate quickly to keep up with their host cells, which
are reflected in the compact nature with overlapping genes of many bacteriophages,
leading to the minimum genome size. Viruses with eukaryotic cells as hosts show
tremendous compression while the core is getting packed into the capsid so that only
optimum amount of genome can be packed. Viruses pack their genomes into
protective protein contained capsids. Packaging strategies of viruses are related to
the type of genome. Viruses with double stranded DNA genomes use a molecular
motor with a spool like structure to pack their genomes into the capsid. In contrast,
viruses with single stranded DNA or RNA genomes employ a co-operative mecha-
nism, in which package and assembly of the genome into the capsid will occur
simultaneously, enhancing the assembly efficiency of the capsid. In bacteriophage
MS2, genomic RNA sequence will form a short term loop, for its interaction with the
1.3 Size, Structure, and Composition of Double Stranded DNA Virus Genomes 5

Table 1.1 General features of viral genomes sequenced

S. No. Class Sequenced genomes Size (Nt) Proteins
1 DsDNA 414 4697–335,593 6–240
2 SsDNA 230 1360–10,958 6–11
3 DsRNA 61 3090–29,174 2–13
4 SsRNA (+) 421 2343–31,357 1–11
5 SsRNA (
) 81 8910–25,142 5–6

capsid proteins. This interaction will trigger conformational changes that convert
symmetric protein dimers into asymmetric form, needed to build the capsid. Some
bacteriophages of the family Myoviridae, such as T4 contain relatively large
genomes, up to 170 kbp. The largest viral genome currently is known that of
Mimivirus, ~1.2 Mbp, consisting of 1200 open reading frames, with only 10% of
them showing the similarity with proteins of known function. Among the eukaryotic
viruses, herpesviruses and poxviruses possess relatively large genomes, up to
235 kbp. These genomes contain genes involved in their own replication, particu-
larly enzymes concerned with nucleic acid metabolism. Therefore, these viruses can
partially escape the restrictions of the host cell biochemistry by encoding additional
biochemical apparatus with the penalty of encoding all information necessary for a
genome to pack into the capsid, which also causes upward pressure on its size.
Whatever might be the composition of a genome, all viruses are obligate intracellular
parasites, which can replicate only inside the appropriate host cells, their encoded
genomes must be recognized by a specific host cell, which is getting parasitized. For
that, the genetic code employed by the virus must either match or recognized by the
host cell. Similarly, the signals that regulate the expression of viral genes must be
inappropriate to the host. The general features of viral genomes sequenced are
displayed in Table 1.1.

1.3 Size, Structure, and Composition of Double Stranded DNA

Virus Genomes

Cellular life forms of all categories possess genomes with double stranded DNA and
utilize the same as a standard scheme for their replication and expression. In contrast,
viruses and other pathogenic and selfish elements exploit all possible inter-
conversions of nucleic acids, with their genomes that can be either DNA or RNA,
which are single-stranded or double-stranded. Viral genomes that have been
sequenced and annotated are compared with genomes of cellular life forms, which
were small with unknown gene functions. But, in the past few years, discovery of
giant viruses has rapidly expanded the size of viral genomes whose range spans up to
3 orders of their magnitude, from 2 kb to 2 Mb. Surprisingly, the genomes of
giant viruses are larger than the genomes of many bacteria and archaea, obliterating
the gulf between cells and viruses in terms of genome size and complexity. A
number of viral groups possess double-stranded DNA as their genomes are of
6 1 Structure and Organization of Virus Genomes

considerable complexity, classified into small and large genomes depending on the
type of replication. Small genomes use a host DNA polymerase for replication, In
contrast, large genomes encode a virus-specific DNA polymerase, responsible for
their genome replication. These viruses are genetically similar to the host cells they
infect. Large DNA viruses encode more proteins than small DNA viruses.
There are two major viral groups representing the double stranded DNA genomes
ie. members of the Adenoviridae and Herpesviridae families. Human adenovirus is
one of the most common pathogens that causes minor, self-limiting illness to most of
the patients. Adenovirus is one of the very well understood viruses, whose basic
biology has been extensively studied over the past 60 years. Human Adenovirus has
been isolated in the early 1950s from the adenoid tissue causing respiratory
infections. This virus has a remarkable capacity to spread among patients contacting
from as few as five virus particles. Adenovirus-induced acute respiratory disease is
the most common infection in confined populations of daycare centers, hospitals,
retirement homes, and military training venues, accounting for ~8% of all childhood
respiratory tract infections, which can lead to bronchitis, bronchiolitis, or pneumo-
nia, requiring hospitalization in ~25% of diagnosed cases. It also causes other
localized diseases, such as colitis, hemorrhagic cystitis, hepatitis, nephritis, enceph-
alitis, myocarditis and disseminated disease with multiorgan failure. A few such
diseases can be more serious in pediatric and geriatric populations, especially in the
individuals with suppressed immune systems, such as transplant recipients or
patients suffering from AIDS. Many aspects of Adenoviral life cycle have been
completely elucidated in great detail, which has allowed the development of adeno-
viral vectors that are highly efficient in delivering genes into the mammalian
systems, especially human cells for the transgene expression and for delivering
therapeutic genes in human gene therapy. Adeno viruses specifically consist of a
nucleoprotein core with a 30–40 kb linear double-stranded DNA, surrounded by an
icosahedral, non-enveloped capsid of 70 to 100 nm diameter. These viral genomes
contain 30–40 genes. The terminal sequence of each DNA strand has an inverted
repeat of 100–140 bp. The denatured single strands form a ‘panhandle’ like
structures, which are important for the DNA replication. A 55 kDa protein known
as the terminal protein is covalently attached to the 5¢ end of each strand. During the
genome replication, this protein might acts as a primer, for initiating the synthesis of
new DNA strands. The expression of the genes is rather more complex in
Adenoviruses with clusters of genes expressed from a limited number of shared
promoters. Multiply spliced mRNAs and alternative splicing patterns are used to
express a variety of polypeptides from each promoter.
Apart from the differences in host and tissue tropism, a very less amount of
variation is found in the Adenoviral genomes and their structural parameters. Human
adenoviral serotype 5, is one of the highly characterized adenovirus, consisting of
~36 kb genome. Its coding region is divided into early (E1–E4) and late (L1–L5)
transcripts based on their stage of expression. Essential early E1 region is deleted in
most adenoviral vectors, rendering their incapability of replicating in most cell lines.
Numerous studies have shown that after the deletion of E1, Adenoviral vectors are
more ideal for the in vivo and in vitro studies requiring short-term transgene
1.3 Size, Structure, and Composition of Double Stranded DNA Virus Genomes 7

expression. The Second generation Adenoviral vector constructs are made after
deletions in the essential E2 or E4 regions, facilitating the prolonged transgene
expression. Helper-dependent Adenoviral vectors (hdAd) are generated by deleting
all genes that code for viral proteins for increased cloning capacity. Removal of
protein coding sequences in these vectors allows the overall reduction in their
genome size from 36 kb for the wildtype to 30 kb in E1/E3-deleted Adenoviruses
and ~500 bp for helper-dependent Adenoviral vectors.

1.3.1 Analysis of Adenovirus 2(AD2) Genome

The genome of adenovirus 2(Ad2) was the first adenoviral genome to be fully
sequenced, which is of the size ~36 kb, encoding over 40 proteins. Adenoviral
coding regions are designated as early or late depending on their expression before or
after the DNA replication. The early genes E1A, E1B, E2, E3, and E4 are the first
ones to get transcribed. They encode for the proteins involved in activating tran-
scription of other viral regions, altering the cellular environment to promote viral
production. E1A proteins also induce mitogenic activity in the host cell, which
stimulates the expression of other viral genes. E2 proteins regulate viral DNA
replication, while E3 and E4 proteins are involved in altering the host immune
responses and cell signaling. Activation of the major late promoter (MLP) followed
by the start of viral DNA synthesis, allowing the expression of late genes encoding
primarily virion structural proteins. L1–L5 of the late regions are transcribed from an
alternatively spliced transcript. The regions encoding the L4-22 K and L4-33 K
proteins are initially expressed at low levels from a novel promoter located within
the L4 region and these proteins functions in fully activating the major late promoter
(MLP). Four small proteins including the structural protein IX (pIX) and the IVa2
protein produced at intermediate/late stages of infection, helps in packing of viral
DNA into immature virions. The late products VA RNA I and II inhibits the
activation of the interferon response, impede cellular micro-RNA processing and
also influence the expression of host genes. There are 100 bp inverted terminal
repeats (ITRs), located at both ends of the genome, which act as the sites for the
origin of replication, with the ~200 bp viral packaging sequence positioned next to
the left ITR (Fig. 1.1). Even though Adenovirus is being studied in great detail for
more than 60 years, our knowledge of the genes encoded by this virus is still
expanding. In 2007, a new open reading frame (ORF) has been identified to be
located between the fiber ORF and E3, which is termed as U exon. The U exon
protein (UXP) is expressed from a unique promoter during later stages of infection
and is hypothesized to play a significant role in the transcription.
Most of the transcription processes in the adenovirus result in more than two
alternatively spliced mRNAs. Keeping the compactness of the adenovirus genome,
regulatory events that take place at the level of RNA processing are of great
importance for controlling the lytic cycle of the virus. Splicing of large introns
results in the production and accumulation of shorter mRNAs, at the later stages of
viral infection. Except for E1A, L4-33Kand the U exon protein, viral introns do not
8 1 Structure and Organization of Virus Genomes

Fig. 1.1 Organisation of the Adenovirus genome (Courtesy Russel WC, School of Biology,
University of St Andrews, UK)

interrupt the ORF of the gene. Further, Adenoviral genes contain very few introns
compared to that of cellular genes. Viral mRNAs mature by removing one to three
introns. As the virus has to compress much of its genetic information into a small
genome, the selection pressure appears to have favored few and small introns. Deep
cDNA sequencing of Adenovirus genome has identified many novel alternatively
spliced transcripts, suggesting that there may be numerous new or altered
polypeptides produced by this virus in the infected host cell, reflecting that this
genome still has many secrets that remain to be uncovered.

1.3.2 Herpesviridae

Herpesviridae belongs to a large family of ~100 members with at least one for each
of the animal species that have been examined till date. There are eight human
herpesviruses, all of them share a common overall genome structure, but differs in
the fine details of genome organization and at the level of the nucleotide sequence.
Herpesviridae is a family of enveloped, DNA viruses with complex genomes. They
replicate in the nucleus of a wide range of vertebrate and invertebrate hosts, such as
humans, horses, cattle, mice, pigs, chickens, turtles, lizards, fish, and invertebrates
such as oysters. There are eight human Herpesviruses divided into three subfamilies.
Herpesviruses possess very large complex genomes composed of large complex
virus particles up to 235 kbp of linear, double-stranded DNA and 35 virion
polypeptides. Members of Herpesviridae are highly diversified in terms of their
genome sequence and protein synthesis but show a great similarity in terms of
1.3 Size, Structure, and Composition of Double Stranded DNA Virus Genomes 9

structure, genome organization and almost all of their genomes encode the enzymes
involved in nucleic acid metabolism, DNA synthesis, and protein processing. Few
Herpesviral genomes consist of two covalently joined sections named as a unique
long (UL) and a unique short (US) regions, each bounded by inverted repeats. These
repeats allow structural rearrangements of the unique regions, facilitating the exis-
tence of genomes as a mixture of four functionally equivalent isomers. These
genomes also reported contain multiple repeated sequences and depending on their
number, size of the genome may vary up to 10 kbp.
Integration of viral genome into the chromosomes of the host cell is mandatory
for the successful completion of the virus lytic cycle. In contrast, Herpesviruses
maintains their genomes as extrachromosomal circular episomes in the nuclei of
infected cells without the need for integration. There are also reports of chromosomal
integration of Herpesviral DNA, suggesting that Herpesviruses are also capable of
integrating into the host’s chromosomes under few circumstances. It was
hypothesized that the replication of non-integrated Herpesviral DNA occurs through
the rolling-circle mechanism, yielding long DNA concatemers that are subsequently
cleaved into single genome equivalents during nucleic acid encapsidation. In addi-
tion, Human Herpesvirus 6 (HHV-6) is found to be integrated into the germ-
lines of approximately 1% of the world’s population. But how the replication of
linear CIHHV DNA occurs still remains unknown. Chromosomal insertions of
α-Herpesvirus DNA, Herpes simplex viruses and Equine Herpesvirus have been
detected following infection with defective interfering particles or transfection of
sheared or subgenomic viral DNA fragments. The integrated viral genome consists
of mostly subgenomic fragments without any possibility for the production of
infectious viral particles to occur. Many of the cells carrying integrated viral DNA
displayed a transformed phenotype, fueling the hypotheses on the oncogenic nature
of these viruses.

1.3.2.1 Analysis of Herpes Simplex Virus Genome

The prototype member of the Herpesviridae family is Herpes Simplex Virus (HSV),
whose genome is 152 kbp, composed of double-stranded DNA. The complete
nucleotide sequence of the Herpes Simplex Virus has now been determined. This
virus contains about 80 genes, densely packed and with overlapping open reading
frames. Each gene is expressed under its own promoter. HSV-1 is perhaps the most
intensively studied complex virus genome. Before the development of nucleotide
sequencing, the HSV genome has been extensively mapped by conventional genetic
analysis and mutant analysis. The HSV-1 genome is composed of a single linear
double stranded DNA of 152,261 base pairs in length. The genome is divided into
two segments called Unique Long (UL) and Unique Short (US). Small regions of
repeated sequence occur at the genome ends between the L and S segments. As DNA
is replicated, the inversion of L and S segments takes place at a very high rate,
creating four genome isomers, occurring at equal frequencies in most of the HSV-1
wild type populations. This virus genome synthesizes 75 genes encoding for known
proteins. Among them, 69 genes are found to exist in a single copy and three genes in
two copies each. Among the 75 genes with identified functions, 43 are considered to
be the core genes common to α, β and γ Herpesviruses located in the UL segment of
10 1 Structure and Organization of Virus Genomes

the genome. These genes are involved in many vital functions including the entry of
the core DNA into the host cell and its replication, assembly into the capsid and its
dispersal. All genes located in the unique short segment are non-core and are highly
divergent. These are mainly found at the ends of the segment. Proteins encoded by
the non-core genes are involved in both lineage and species-specific functions such
as transcriptional transactivation, immune evasion, and host cell recognition.
Type 1 Herpes simplex virus is a member of the α-Herpesvirinae subfamily of the
Herpesviridae family, whose infection results in cold, ocular, genital sores and
encephalitis. Several strains of HSV-1 have been isolated varying in virulence,
which might be due to base substitutions resulting in amino acid or cis-regulatory
changes. One of the HSV-1 strains, KOS isolated from a human labial lesion and is
frequently used as a marker to investigate the HSV-1 gene function and pathogene-
sis. KOS is less virulent compared with other HSV-1 strains, such as McCrae and
17, which has raised the curiosity for the comparative genomics. KOS genomic
DNA was isolated from infected African green monkey (Vero) kidney cells and an
unpaired 42-bp Illumina library was generated and run at Genome Technology
Access Center, Washington University. Since viral DNA was isolated from Vero
cells, potential contaminating host reads that matched the Rhesus macaque and/or
human genomes were removed using Bowtie. The remaining reads of 16,494,831 bp
were assembled into contigs using the Velvet de novo assembler against the refer-
ence HSV-1 strain 17 genome (GenBank accession number NC_001806) with
SeqMan Pro (DNASTAR, Inc.). Because the HSV-1 genome includes two sets of
inverted repeat regions TRL/IRL and IRS/TRS, contigs assembling into one of the
repeat units were reverse complemented and also placed into the other repeat unit.
The final KOS genome is a linear double stranded DNA of 152,011 bp, consisting of
80 genes and has 13 gaps, exclusively at VNTR regions, totaling up to 1582 bp in
length. In the Gen Bank annotation, the sequence and length of each VNTR were
copied from strain 17. Using Bowtie for aligning the filtered reads against the de
novo assembly, the average sequence coverage per base pair for the KOS genome
was determined to be 4257 (Fig. 1.2).
To identify nucleotide variants between the genomes of strains KOS and 17, the
genomes were aligned using fast statistical alignment (FSA) and applied custom
Perl and R scripts. KOS differs from strain 17 by 1024 SNPs, 320 of them are
non-synonymous changes in 65 of 77 HSV-1 open reading frames. The two
genomes also differ by 172 indels, most of them are insertions or deletions of single
bases in non-coding regions. However, 26 indels are in frame additions or deletions
of codons. Further analyses are in progress for the comparative genomics of
KOS with other genomes of HSV-1 strains. Such studies will increase the scope
for better identification of the genetic attributes of KOS and its contributions to its
pathogenesis.

TRL IRL IRS TRS

UL US

Fig. 1.2 Organisation of the Herpes Simplex Virus-1 genome

1.4 Genomes of Single Stranded DNA Viruses and their Mosaicism 11

1.4 Genomes of Single Stranded DNA Viruses and their

Mosaicism

Viruses with single stranded DNA genomes infect hosts that belong to all three
domains of life and are considered to be economically, medically and environmen-
tally important pathogens. Recent studies have shown that these single stranded
DNA viruses exist in great numbers in highly diverse habitats, ranging from extreme
geothermal springs to the gut of humans and other animals. International Committee
on Taxonomy of Viruses currently classified single stranded DNA viruses into
10 different taxa. However, several viruses that can be classified into additional
groups have been isolated and many of their genomes were sequenced. All single
stranded DNA viruses are pathogenic on eukaryotes, possess non-enveloped, icosa-
hedral capsids, along with Microviridae family members, which infects bacteria.
Single stranded DNA viruses pathogenic on other prokaryotes have filamentous
(Inovirus), rod-shaped (Plectrovirus), coil-shaped (Spiraviridae), or pleomorphic
(proposed family“Pleolipoviridae”) virions (Table 1.2).
Single stranded DNA viruses are the group comprising of smallest viruses and
their genomes are as small as 1–2 kb, encoding two proteins; one for capsid formation
and the other for genome replication. Such irreducible simplicity of single stranded
DNA viruses epitomizes their essence of being a virus and makes them an attractive
model for investigating virus origins and evolution. Numerous metagenomic studies
have revealed a high range of genetic diversity existing in single stranded DNA
viruses in the environment, suggesting a highly dynamic interaction between these
viruses and their respective hosts. Also, single stranded DNA viruses with the
smallest genomes and simplest proteomes were found to be widespread in cellular
chromosomes, providing new important insight into the evolution of these viral.

Table 1.2 Morphological diversity of single stranded DNA viruses

Host virus Virion Genome
taxon morphology Genome topology size
Microviridae Icosahedral Circular 4.4–6.1
Inoviridae
Inovirus Filamentous 5.8–12.4
Plectrovirus Rod-shaped 4.5–8.2
Pleolipoviridae Pleomorphic Circular 7–10.6
Spiraviridae Coil-shaped Circular 24.9
Anelloviridae Icosahedral Circular 2–4
Bidnaviridae Icosahedral Linear, segmented, 6.5 per segment
Circoviridae Icosahedral Circular 1.7–2.3
Geminiviridae Icosahedral Circular, segmented 3 per segment
Nanoviridae Icosahedral Circular, segmented 0.98–1.1per segment
Parvoviridae Icosahedral Linear 4–6.3
12 1 Structure and Organization of Virus Genomes

1.4.1 Genomes of Bacteriophages

Bacteriophages are the smallest viruses with simple genomes. Since their discovery
in 1915 and 1917 by Fredrick Twort and Felix d’Herelle respectively,
bacteriophages have been studied in many laboratories and are being used in a
variety of practical applications. The Density of phage viruses present in the oceans
is 106–107 particles per ml. It was estimated that the total population of the
bacteriophages is 1031 particles and the ratio of environmental virus and bacteria
are 5–10:1, after the validation of 1030 bacterial cells in the biosphere. Altogether,
the prokaryotic population is highly dynamic, with an estimated number of ~1023
global infections per second. It has been hypothesized that oceanic bacteriophages
infect bacterial cells at the rate of 1029 phage infections per day, which releases over
1011 kg of carbon from the biological pool per day. Over the past three decades,
research on bacteriophages has revealed their abundance in nature, genome diver-
sity, impact on the evolution of microbial diversity, their utilization in control of
infectious diseases and their influence in regulating the microbial balance in the
ecosystem has been explored, leading to a resurgence of interest in the phage
research. Research on phages has played a pivotal role in the most significant
discoveries, that were made in biological sciences right from the identification of
DNA as the genetic material, in the elucidation of the genetic code, leading to the
development of the molecular biology. Research on phages has continuously broken
new grounds in our understanding of the basic molecular mechanisms of gene
expression and their structure. In recent times, phage genomics has revealed novel
biochemical mechanisms for replication, maintenance, and expression of the genetic
material and is providing new insights into the origins of infectious diseases,
utilization of phage gene products and even whole phage as an agent for the gene
therapy.
In addition to the killing of bacterial cells, temperate phage genomes also carry
toxins and other critical virulence factor genes that are important for many bacterial
pathogens to infect human beings. Phages also contribute to the diversity of the
bacterial community by serving as vectors for the transduction of different genetic
alleles, such as antibiotic resistance genes, between bacterial cells. Phages also
have great medical and nanotechnological potential. Strategies for using tailed
phages for detecting bacteria, curing bacterial diseases through phage therapy or
decontaminating surfaces have been implemented for almost 100 years in Russia and
Georgia. These phages are currently being used to treat agricultural diseases as well
as in the prevention of food contamination in western countries. Phage virions are
being developed as nanocontainers for specific chemical cargoes that can be deliv-
ered to specific targets.
Small size and the simplicity of isolation have made bacteriophages as the primary
choice for the complete genome sequencing. Phage φX174 is the first organism with
the complete genome sequence of 5386 bases of single stranded DNA and λ phage
genome is the first organism with double stranded DNA of 48,502 bp, followed by
phage T7 genome of 39,936 bp. dsDNA tailed mycobacteriophage L5 is the first
among non-E. coli phage genomes to be fully sequenced. Further, the sequencing of
the bacteriophage genomes are propelled exponentially with two main objectives;
Discovering Diverse Content Through
Random Scribd Documents
homes and furniture and utensils of various sorts. Close upon these
came the distilleries, which proved a mingled curse and blessing.
Whisky was used with a freedom that would appear startling at this
day, and was not essentially different in its effects then than now.
The demand for these distilleries came not from the demand for
drink, but from the demand for a market for their corn, which grew
in such fruitful abundance. D fy
 t±. 436 HISTORY OF DELAWARE COUNTY. There were, at
different times, three "stills" in operation within the limits of
Berkshire Township. A grist-mill had been built, about 1810, by
Nicholas Manville, half a mile southeast of the present village of
Sunbury, and, five years later, he added a saw-mill, and, a few years
later, added a "still." It passed into the hands of Maj. Strong about
1817, and from him to Eleazer Gaylord in 1825. In its palmiest days,
the business was carried on in- a two-story stone building, about
25x35 feet. This sufficed to use ufi a large part of the surplus corn,
or, rather, rendered it more to the taste of the pioneer. Here pure
whisky was sold at 20 cents a gallon, and the settlers felt bound to
support home institutions. Another " still " was erected just north of
the village of Galena in 1820, by Joseph and Steven Larkin. This
they soon after sold to George Vanfleet, an early settler in Galena,
and built another just below the town, near the races which connect
the Big and Little Walnut Rivers. A walnut tree and an abandoned
well just south of the railroad depot in Galena, marks the site of the
Vanfleet " still." The habit of using whisky without restraint was not
contracted in the new country. The early settlers, many of them,
brought not only the custom with them, but the means to maintain
its practice. The Oosterhaus brothers brought several barrels of
whisky with them from the East, and supplied their less fortunate
neighbors at 3 cents a drink or 16 cents a gallon. It is said that
Gideon Oosterhaus' books are still preserved, which show accounts
for whisky at the current rates against many of the names familiar to
the present citizens of Berkshire. Nor was this whisky shorn of its
intoxicating qualities. A story is related of two intoxicated fellows
who became enraged at each other, and proceeded each to " take it
out of the other's hide." Long time the battle stood in doubtful poise.
The combatants, with nothing in the way of clothing left but their
pants, were captured and separated. No sooner were they left than
they sought each other out and began their pounding. At last they
were captured and put over the fence in fields on opposite sides of
the road, and there, too drunk to get over the fence, they remained
breathing forth defiance like two enraged bulls. But the society of
Berkshire by no means tolerated such bestiality. The boys of
Sunbury, for their own amusement, and to exhibit in some sense the
feeling of the community, adopted a summary mode of punishing
such delinquents. When found drunk upon the ground, one would
seize each arm and leg, and, laying the victim on a barrel face
downward, he was rolled until his stomach yielded its con-' tents,
and he was sobered up. One or two applications of this treatment
sufficed to keep the victim off the street when in an intoxicated
state. One inveterate old case, who was familiarly known as Uncle
Tommy, seemed to defy the correctional force of the old method,
and more stringent methods had to be adopted. He was seized one
time, thrust into a hogshead, and rolled some fifty yards into the
creek. The treatment was severe, but the cure was radical for the
time. Next in order came the establishing of tanneries. The distance
of markets and the great cost of transportation made the tannery of
prime importance to the early settler. All the material that entered
into the making of shoes or harness, and for a long time a large part
of men's clothes, called for a tannery to niake it available. As early
as 1816, William Myers sunk vats, and began to manufactture
leather a half a mile southeast of Sunbury Village, across the creek
from the saw and grist mill. Three years later, a Mr. Whitehead built
a similar building at Galena, and did a thriving business. The
business continued through a change of hands, and was
discontinued in 1873. The building and tools are still there, near the
mill-race, and are owned by Mr. Vanfleet. Traffic in stock was limited
by the necessities of the situation to the breeding and selling of
hogs. These easily became acclimated and found a rich support in
the nuts with which the woods abounded. Horses could not be
raised fast enough to supply the home demand, and cattle were
more difficult to keep, and for years were subject to diseases that
took them off in herds. The hogs were of a halfwild breed, and were
suffered to run at will in the woods. They were sold to dealers, and
the whole neighborhood would turn out to drive them to the place of
rendezvous. This was no easy task, but then the work was only half
completed. Each hog had to be caught, his tusks — which frequently
grew to the length of several inches — broken off, and then swung
by a band to a pair of steelyards for weighing. A hog turning 200
pounds was considered a heavy weight, and a drove averaging this
would be the pride of a dealer and the envy of his fellows. Steven
Bennett and David and Joseph Prince followed this business for
some years driving them to Baltimore. The task of driving such herds
of swine as they took to market can hardly be appreciated at this
day. The ani^ ;V
 l^ HISTOEY or DELAWARE COUNTY. 437 mals were more
than half wild, and likely to stampede at the first opportunity, and
numbers of them were lost on every trip. At an early day, Steven
Bennett brought sheep from Kentucky, and traded them for hogs,
and it took a good hog of those days to buy a sheep. This was the
first introduction of sheep into the township. There seem to have
been two Indian thoroughfares through Berkshire when the red man
roamed, unmolested over the country. One led from a place known
as Raccoon, in Licking County, northwest through Berkshire toward
Sandusky. Another led from the east through the northeast corner of
Berkshire to the salt licks in Brown Township, thence northward and
west. The earliest of the settlers used these trails to a considerable
extent when traveling on foot or on horseback, as th>) safest and
most direct route. Much of the hardware and glass used at the
Byxbe settlement was obtained at Sandusky, and these trails were
used as the most distinct and plain to follow. The necessity for a
wagon road soon caused the blazed roads to give way to more direct
and more commodious thoroughfares. The road from Galena to
Lancaster was an early one, and that from Columbus to Mount
Vernon, passing through Galena and Sunbury, was laid out soon
after 1810. The information as to particular dates in this matter is
very unsatisfactory. Roads improve so gradually from trails to "cut-
out" roads and then to graded thoroughfares, that even those who
have seen the change almost forget that they were not always
improved. As early as 1820, a line of four-horse coaches ran
between the terminal points of this road, making the half-way stop
at Sunbury. The coaches met daily near Galena, and constituted for
that point the great event of the day. This was the main artery that
connected the Berkshire settlements with the outside world, and the
appearance of the passengers, the change of mails, and the
marvelous stories of the drivers, afibrded abundant material for
gossip. The coaches were of the regulation pattern, so often seen in
old prints. They were painted a fawn color, ornamented with red.
The body was swung high above the wheels on heavy leather
springs, so that every lurch of the coach seemed to threaten sure
destruction to the passengers. Azel and David Ingham were the
noted Jehus of that day, and their exploits were the theme of many
a thrilling story told about the roaring fireplaces of the settler's
cabin. The road was cut up at times so as to be almost impassable,
and the theory of the drivers seemed to be to gain sufficient
momentum in rushing into these ruts to carry the coach out of them
at the other end. The result of this theory to the passengers can
better be imagined than described, and was endured with a patience
that has not been handed down to the modern traveler. It was the
delight of the young men to be invited by the driver to try their skill
at handling a four-horse team. Hon. 0. 1). Hough relates an
experience of this kind, where, just as he was congratulating himself
on his success, he ran against a post and stuck fast. A tale is told of
a driver who was given to drinking, and when in this mood was
inclined to give an exhibition of his skill by some foolhardy driving.
One moonlight night, having some one on the box with him whom
he desired to startle, he whipped his team into a full gallop, and,
taking to the woods beside the road, wound in and out among the
trees and then to the roadway again without a mishap, enjoying only
as such a character can the terrified expression of his companion. It
is natural that such a road would be greatly prized by the fortunate
communities through which it passed, and there was a continual
strife between them and less fortunate villages to control the route.
Below Galena there was a bad strip of road, which passed through a
swampy piece of woods. Effort was made by those living along
another and better road to divert the stage line from the old course.
This appealed at once to the dearest interests of the people of "
Yankee street," and a moonlight " bee " of all interested was made,
and the road repaired. La Fayette, when , visiting this country, took
this stage line in June, 1825, and it is remembered that his cane,
which had been lost, coming on a stage a few days afterward,
attracted as much curious attention as did the distinguished visitor.
The Delaware, Sunbury and Berkshire Pike is a much later
corporation. The Company was formed in the cotfnty in 1868, and
the road fitted up to furnish a good thoroughfare . from Sunbury and
intermediate points to Delaware. Some $40,000 were subscribed,
but little, if any, over $35,000 was paid. There are two toll-gates,
with receipts amounting to about $2,000 per annum, which just
about pays the cost of keeping up the road. No dividends have ever
been paid, and none are ever expected. There has been of late
some agitation to make it a free road, but the people along the line
of road are not disposed to vote a tax upon themselves for that
purpose. The Cleveland, Columbus & Mount Vernon Railroad came in
1873, and tapped the
 ±i trade which the pike was intended to convey to
Delaware, leaving no good reason for its existence as a toll road.
The first tavern in the township was kept at Berkshire Corners by
Adonijah Rice. He was also the first Posttnaster, and kept the oflBce
in his hotel. Maj. Brown opened his house for hotel purposes about
the same time. The prices charged in these primitive inns have a
pleasant sound in these times, Board by the week was only from |1
to $1.50, and single meals from 15 to 20 cents. Rice's "hotel" was
the great attraction for the loungers of the neighborhood, and many
a tale is told where " Care, mad to see a man sae happy, E'en
drowned himself amang the nappy." At this time, the people who
lived near Galena were obliged to come to the Corners for their mail,
and some one of the neighbors would get the mail for the whole
neighborhood. Mr. 0. D. Hough relates that one cold afternoon he
persuaded his father to let him get the mail. He is represented as
being a bashful, timid lad when young, and, when he got to Rice's
establishment, he found it crowded with a boisterous company of
men, drinking, shouting and scuffling. This was more than he had
counted upon, and the longer he stayed the more frightened he got.
Finally, as the fun grew fast and furious, he incontinently broke for
the door and made for home as fast as fear could impel his nimble
feet, without so much as hinting his errand to any one. When he
reached home, his pride returned with his courage, and he informed
the expectant neighbors that there was no mail at the office. Other
hotels were afterward erected at Sunbury and Galena, which are
noticed hereafter. The information in regard to the organization of
the township of Berkshire, is very meager. The name was given by
Maj. Thomas Brown from the county of which he and Col. Byxbe
were formerly residents. For some years this name included
considerably more territory than now, the community gathering at
Joseph Eaton's house, in Berlin, to vote and afterward at Dr. Louf
bourrow's. Here was the general muster-ground in the palmy days of
the early militia, the townships of Orange, Berlin, and Berkshire,
uniting to form a company. Of the first township officers, it is known
that Asa Scott, of Berlin was the first Treasurer, before the
organization of that township, and Mr. David Prince was one of the
Trustees. In 1819 Henry Hodgeson, now known as 'Squire
Hodgeson, of Galena, was Township Clerk, but who his predecessors
were is not known. Maj. Brown was the first Justice of the Peace,
followed by Solomon Jones, David Prince, and James Gregory. As to
the first birth, there seems to be a diversity of opinion, but it is.
pretty well established in the minds of those who have carefully
gone over the ground, that Albert Root, born in 1807, was the first
white child born in Berkshire Township. A son of Ralph Slack was an
early birth, and, when this boy was born, Mr. John Patterson, one of
the earliest settlers, told Slack, if he would name the boy for him, he
would give him three months' schooling, both parts of which
contract were carried out. The boy died an old man some few years
ago in Berlin Township. The first death was that of Mrs. ViniDg,wife
of Elem Vining,Sr., in 1806. The incident in regard to her burial
illustrates the straitened circumstances of the settlers in a very
forcible way. Of course, undertakers and cabinet-makers were
unknown in the woods, and, what was worse, there was nothing but
the standing timber, with an ax and a crosscut saw to supply their
absence. These were made to furnish the burial casket, and Mrs.
Vining sleeps, some forty rods south of the " Corners," as peacefully
as though above her was reared the " storied urn or animated bust."
Doctors and ministers were the only professional men that the
earlier settlers had needP of in their simple life, greater, perhaps, of
ministers than of doctors. The earliest follower of .5]lsculapius was
Dr. Lamb, who came from Worthington to the " Corners," and later
to Delaware. Dr. Skeel is another name which appears early in
Berkshire's history. The first improvement on log cabins was a brick
house built by Maj. Brown. About the first frame house was built
some five years later in 1816, by David and Joseph Prince. The work
on this house was done by Lovell Caulkins, an early settler in Berlin,
and now stands on property owned by Hon. O. D. Hough. Two years
later David Armstrong put up a frame building. An incident
connected with the digging of the well near this house illustrates the
fact that all the marvelous stories are not of a latter-day growth.
John B. Grist did the digging, and, in going down, struck a six-foot
stratum of slate stone. About midway of this layer. Grist found,
imbedded in the solid stone, a toad, to all appearances lifeless. He
tossed it out upon the ground, where it soon showed signs of
animation, and before long happed ofi^ as natural as though it had
never f
 ^j^ HISTORY OF DELAWARE COUNTY. 489 been buriedt
But such dwellings could be afforded only by the well-to-do of the
settlements. Iron latches and regularly made doors held together
with nails were luxuries to be dreamed of by the masses, and to be
indulged in only by the rich. The same state of things, in regard to
the furniture and the culinary conveniences of the cabins, existed.
The commonest iron utensils were more highly prized than those of
nilver at this time. The distance from markets and the lack of roads
made the transportation more expensive than the original price of
the goods, and afforded opportunities for traflSc which were not left
long unimproved. John B. Grist was among the first to take
advantage of this fact, and for years supplied most of the staple
articles to his neighbors. He drove to Zanesville, taking out grain and
bringing back iron goods, salt, etc. A staple article was a certain
make of skillet manufactured at Zanesville, and this article formed in
many a family their only dish with which to accomplish the various
culinary operations incident to the domestic life of the cabin. It was
the only oven ; in it the meat was cooked, the potatoes boiled, the
tea made, and in it the cow would have been milked if one had been
possessed. This state of tfiings existed but a short time, for, as the
settler prospered, the iron pot and tea-kettle were added, but, with
these additions, many a housewife labored for years under
disadvantages that would send a modern housekeeper to the insane
asylum. Salt, which is such a staple article in the domestic economy,
was in large demand and diflBicult to get. The indications of salt in
the township north never proved to be of any considerable value,
and this article was to be procured only at the expense of long,
tedious journeys. Grist bought this by the bushel at Zanesville, and
sold it in Berkshire at $1.50 for a half-bushel. Even at such prices, it
did not prove a very lucrative business. The trip to market and back,
under favorable circumstances, took four days. In the mean while he
camped out, cooking his meals in the inevitable skillet, frequently
obliged to wait for a favorable opportunity to ford streams, and
bringing home at last but a mere handful when compared with
wagon loads of to-day. Under such disadvantages, it seems almost a
marvel that the settlers were ever able to pay for their farms, even
at the low price for which land was sold. It was years before any
considerable quantity of grain could be sold, and then a market had
to be sought so far away that the transportation robbed the farmer
of half the fruits of his toil. The explanation is that every settler
supplied his necessities by the industry of himself and family. The
little patch of flax supplied the coarse fiber which the busy wheel of
the housewife prepared for the loom. Prom the loom it found its way
to the dye-trough, where, in a decoction of butternut bark, it took on
the fashionable color of that day. This cloth was made up of part
wool and part linen, called " linsey-woolsey," and furnished the
garments for both men and women. For hats, men wore fur skins
fashioned at home, while the women wore such things as they could
contrive out of the coarse materials at hand. Leather was procured
in the annual trip to Zanesville, or cf some nearer establishment
where skins were tanned on shares. Prom this the shoes of the
family were made by shoemakers who traveled from house to house,
making up the leather in shoes or harness as desired. In the same
spirit of economy the house was fitted up and furnished. Doors were
put together with wooden pegs, tables were constructed of
puncheons laid upon pegs driven into the logs, and beds only
differed from t^em in proportions and height from the floor. In the
latter article of furniture a corner leg was found necfessary, and is
remembered now as the one-legged bedstead. But, even . with such
rigid economy as this,' it was often almost impossible to meet the
payments upon the little farm. It is related of one of the earlier
settlers of Berkshire Corners, that he had failed to meet his
payments to Col. Byxbe for his land, After considerable delay, the
property was put in the hands of the Sheriff and advertised for sale.
The distressed man sought everywhere to borrow money, writing' to
friends in the East in vain. Coming home disheartened and in despair
the night before the sale was to take place, he learned that in the
township north was a man who had a little money to lend. He did
not wait for his supper, but started out, taking with him a friend to
sign with him as security for the payment of the loan. He needed
$240, which he succeeded in getting, and paid to the Sheriff the
next morning. The note given for this money was not so easily paid.
For ten years, this debt, growing gradually smaller, hung over him,
and was finally extinguished by turning over to his creditor five
sheep, the whole of his flock, and his cow. The Indian is often met
with in the traditions of the earliest settlements of Berkshire. Their
trails took them through this section, and, attracted •^
 tiu 440 HISTORY OF DELAWARE COUNTY. by curiosity and
the results of begging, became frequent visitors at the settlements
previous to the war. They seem to have accepted the logic of events
with the unquestioning stoicism of their race, and were disposed to
be on good terms with the whites without raising the question of
proprietary rights in land or game. A marked characteristic of the
Indian was his entire lack of anything like modesty in his demands. A
story is told of one which sounds more like an exploit of a modern
tramp than of the poetic red man of the forest. A pioneer, overtaken
by night, had rolled himself in a blanket and lost himself in sleep,
when he felt some one crawling under his blanket and making
himself as comfortable as the situation would permit. There was
nothing to do but to await quietly further developments. The Indian
soon went to sleep and remained till morning, when he arose,
expressed his thanks as best he could, and left the discomfited
pioneer to regain his composure at his leisure. He considered it no
breach of courtesy to enter a cabin unannounced, and it was no
unusual thing for the settler to look up from his breakfast or supper
and find in another room one or more Indians watching the family
repast with greedy eyes. They expected to be fed, and the pioneers
soon learned the wisest course to adopt. They supplied these
aboriginal tramps with a generous portion of the meal in their hands,
which they devoured with sundry grunts expressive of their
satisfaction. This done, they departed with the same nonchalance ■
with which they approached. Occasionally one was found who felt
that some recompense was due for such favors and who seemed
willing to make such remuneration as he was able. Such a one made
the acquaintance of Mr. George Fisher in the usual Indian fashion.
While busy at his clearing, he became aware of the presence of an
Indian who was busily gathering brush and placing it in piles DO be
burned. He seemed to pay no attention to Mr. Fisher, nor to care
whether he was observed or not. Finally, after doing as much as, he
thought would pay for a meal, he went up to the proprietor of the
patch and made known his desire for something to eat. Mr. Fisher,
probably desiring to encourage such industrious habits in his
newfound assistant, promptly produced the wished-for meal. This
maneuver was frequently repeated with fair satisfaction to both
parties. Mr. Fisher had an occasion subsequently to reap the benefit
of his wisdom in this-oase. This Indian absented himself after a little
while, and had been entirely forgotten. Subsequently, when Mr.
Fisher was returning from Sandusky with goods, his wagonaxle
broke near the Indian camp, on their reservation. The delay was
vexatious, but the diflSculty was greatly increased by the long
distance from any workmen or tools to repair the damage. He
learned, however, of an Indian who had a set of tools, but could not
prevail on him to lend them. He was about giving up in despair,
when he was approached by a native, who made signs expressive of
the utmost good will. He turned out to be the Indian of the clearing,
and, learning the difficulty, at once secured the tools and assisted
him to get his wagon righted up again. There was an Indian camp
about two miles north of the Corners, and this furnished almost all
the loafers that the earlier settlements had. They were ever ready
for sport, challenging the settlers to wrestle, shoot, jump or run.
Occasionally, when a pioneer accepted the challenge and threw, his
antagonist, the vanquished brave jumped up with a laugh as hearty
and good natured as that of his successful opponent. ' They watched
the traps of the settlers, and were the first to bring information of
the game caught. Those set for wolves were of especial interest to
them as providing them with capital sport. These traps were of
various plans ; but a very common design was to build a log pen, six
feet square and about three feet high, with a roof sloping up to a
point some two feet higher in the center. The roof was supported so
as to leave a hole in the center just large enough to admit the body
of a wolf. The bait was fastened to the ground below the aperture.
When once in, the animal found it impos sible to jump up straight
enough to effect his escape, and thus found himself entrapped. One
of the settlers by the name of Helt had such a trap, and the Indians
informed him of the capture of a wolf, at the same time asking the
privilege of taking the animal out alive for their own sport. This was
readily granted, and the braves proceeded to " beard the lion in his
den." Cutting forked sticks, two Indians thrust them between~the
logs and pinned the animal by the neck and body to the opposite
side of the trap. A third leaped lightly into the trap and skillfully
muzzled the animal with strips of bark. The wolf's legs were then
trammeled so that he could run, but threw himself when trotting or
walking. He was then turned loose, and the Indians, like overgrown
schoolboys, chased and sported with the terrified animal, until,
completely exhausted, it refused to furnish further sport, when it
was dispatched. The
 l^ HISTOEY OF DELAWARE COUNTY. 443 intercourse of the
whites with the natives were of a perfectly peaceful nature
throughout, until the war of 1812 removed them from this vicinity.
They were counted by the pioneers as generally well disposed and
faithful to their friends, taking especial pains to manifest their loyalty
on every occasion. Of the villages in this township, Berkshire
Corners, though not the most important, came first in point of time,
and for a while promised to play an important part in the affairs of
the county. Its history was the history of Berkshire Township, and
has therefore been rehearsed somewhat fully in the foregoing pages.
Its first settlement was the first settlement of the township, but in its
most brilliant days it never approached the dignity of a village. It
was dubbed the " Corners," and is that now and nothing more, a
place where two roads cross. But influence is not measured by
geographical boundaries, and in this respect the " Corners " in its
time occupied a place not less desirable than the other villages.
From this point went out at an early date the dominating spirit of the
township, and to it is largely due the eminent characteristics which
marked its early history. After the removal of Col. Byxbe, and with
him the hope of its future greatness, the place languished, and its
business was diverted to other places. It was never platted, and the
suspicion is entertained that Byxbe never intended it sliould interfere
with his further projects. The first store or, rather, the first goods
offered for sale, was kept by Maj . Brown. His stock consisted of
lead, powder, tea and coffee, with a few pieces of calico and cotton
cloth. A quantity of brown earthenware was added, but cost almost
as much as the ordinary stone china of to-day. These goods were
brought by wagon from Philadelphia to Pittsburgh, thence by boats
down the Ohio to the Scioto River, and thence on pack animals or in
wagons to the consumer. The prices charged for these goods are
astounding when the prices received for grain and meat, the
farmer's only resource, are remembered. Tea sold at $2 per pound ;
coffee at 50 to 75 cents per pound ; salt, at 10 cents per pound, and
calico as high as $1 per yard. Maj. Brown died in 1816, and was
succeeded in trade by Flavins Fuller. The laying-out of Sunbury about
this time began to attract trade and enterprise in that direction, and
Fuller's business was but short-lived. S. S. Bennett was an active
business man, and did much for the business growth of the "
Corners." In company with a Mr. Comstock, of Worthington, he
bought hogs all through that section of the country, driving them to
Cleveland, Pittsburgh and Baltimore. The hogs were taken in and
weighed at the " Corners," and on such days made the little would-
be village as lively as a bee hive. The hogs were paid for in goods,
and thus added largely to the business attractions of the place. The
former prestige has long since passed away, and a store, a
blacksmithshop, two wagon-shops and two churches, with a quiet
cluster of homes, now serve to mark where the early metropolis of
Berkshire flourished. Sunbury, located southeast of the " Corners,"
and east of the central part of the township, is the legitimate
successor of the " Corners " to metropolitan distinction. It was laid
out by William and Lawrence Meyers on land formerly owned by a
Mr. Alden, the original plat bearing the date of November 9, 1816.
The site seems to have been admirably chosen for the future
prospects of the village. It was situated near the conjunction of
three counties — Knox, Licking and Delaware, and on the Columbus
and Mount Vernon road, which was for years the only thoroughfare
by which to reach the outside world. It was reasonable to suppose,
that, with such natural advantages to attract enterprising men, the
newly formed village might grow to considerable size and attract to
itself the business of that part of the three counties' which was so
remote from any town of considerable size. It is quite probable that
the changes wrought by the substitution of railroads for coach lines
has somewhat modified the sanguine expectations of its citizens, but
there is still enough truth in the theory of its location to make it now
a very active village. Sunbury, at this writing, is not incorporated.
Several efforts have been made to secure its incorporation, but the
majority of those to be affected, overawed by fears of the burden of
taxation, have opposfed the measure. But the village has not on that
account stood still. It has pushed improvements in schools,
sidewalks, roads and public buildings, by private subscription, to an
extent which reflects the highest credit upon the enterprise of its
citizens. . About a year before the town was regularly laid out, the
first store in Sunbury was opened by a Mr. Whitmore, from
Worthington. He occupied a small brick house which stood on the
spot where now stands the residence of Mr. Joseph Letts. He sold
goods for a short time only, when he engaged in another enterprise,
and was succeeded by Benjamin Webb, who opened up the first
 i^ 444 HISTORY OF DELAWARE COUNTY. regular business
in the place. He occupied a small room on the corner of Columbus
and Granville streets, and built a house near it. The two buildings
have since been united by inclosing the space between them and
tearing down partitions, and it is now used as a hotel. A third store
was built by Steven R. Bennett, which was situated diagonally across
from Webb's, establishment on the corner of what is now the public
square, and occupied the site of the old log schoolhouse — the first
one in Sunbury. He afterward built another, putting the first store in
the rear for a warehouse, which may still be found, occupied by
James Stockwell, where, it was moved in 1837. Following close upon
the building of the first stoife was the first tavern. This was a hewed-
log building, and was placed on the lot adjoining Webb's, on the
south. A Mr. Rogers kept hotel and accommodated the traveling
public of 1816 with the best that the season afforded. There are
those now living in Sunbury who remember the fare set forth in the
old hotel, and who do not seem to think that hotelkeeping has
improved any on the days of the old log house. In 1820, the stage
line bringing more hotel trade to the town, naturally built up
competition, and Lawrence Meyers put up the hotel which now faces
the west side of the square. This was a frame building, and entirely
eclipsed the Rogers house. Here the stage stopped, and it finally
absorbed so much of the business that its humble competitor,
accepting the logic of events, gave up entertaining strangers, and
"kept boarders " at $1.25 a week. About this time, B. H. Taylor and
B. Chase built a fulling-mill, provided with apparatus for carding and
pressing. The motor power was a tread-wheel worked by oxen, and
is described as follows : the wheel was laid flat upon its hub, the
axle being inclined a little from perpendicular so as to afford an
inclined surface on the wheel. In place of spokes, the upper surface
of the wheel formed an inclined platform provided with cleats, upon
which the oxen traveled. The upper end of the axle was provided
with a spurwheel, which, acting upon gearing on horizontal shafting,
communicated the motion to the machinery of the mill. The old mill
is now the property of Mr. Joseph Letts, and is used as a stable. The
curious will find there the pit in which the treadwheel revolved, and
the great timbers which once supported the heavy machinery of the
mill. The establishment of this mill was a piece of enterprise which
did much to stimulate the growth of the village. The people then
made all their own flannel, but it needed fulling, carding and
pressing, before it was merchantable. This was the only mill of the
kind for miles about, and naturally attracted a good deal of business
to the town. It afterward passed into the hands of Bennett, and
finally passed away with the demand that called it into existence.
Another old landmark is the old hewed-log schoolhouse, which stood
on the southwest corner of the square. This was the first institution
of the kind built in Sunbury, and served the public until 18.31, when
it was removed, and its successor built on the east side of the
square. The new schoolhouse was about 20x30 feet, built of brick
made by Rufus Atherton, on the place now known as the Widow
Grrist farm. This building served the community as schoolhouse and
church for sixteen years. Under its sheltering roof the citizen of
Sunbury became a cosmopolite in religious matters. Here the
Methodist, the Universalist, the Baptist, the Presbyterian, the
Episcopalian, the New Light and the Mormon worshiped in his own
way, " with none to molest or make him afraid." In 1847, it was
replaced by a wooden structure, 24x60 feet, which still remains. The
saw and grist mill and distillery, built by Manville, and the tannery
which was erected across the stream from them, are noticed in
another place. Later, another saw-mill was erected by Samuel Peck
and T. P. Meyers, a half-mile due east of Sunbury. In 1848, six years
later, it was sold to Bailey, who added a grist-mill. From his hand it
passed through the possession of two other parties into that of Mr.
Burr, who moved the mill, in 1875, to the village, and it is now an
institution to which the citizen points with pride, Berkshire's early
settlement was peculiarly favored in the number of its skilled
tradesmen, and the result appears in the substantial progress of the
early community. Brick residences and schoolhouses succeeded the
primitive log structures, and frame buildings appear to be only ad
evidence of the degeneracy of a later day, and, reasoning from
analogy, it is but fair to suppose that the pioneers wore better-fitting
clothes than did their cotemporaries. At any rate, it was not for the
lack of tailors if they did not. As early as 1816, the CoUum Brothers
set up their business of tailoring at Berkshire Corners. They
furnished the first tailor in Sunbury from their list of apprentices.
Haultz Evans first let the " goose hang high" in this village about
1828, but left for Granville about two years later. He was sue 
 ihL^ HISTORY OP DELAWARE COUNTY. 445 ceeded by
James Smith in 1831, who has remained in the village, though
having laid by the goose and press-board. About 1865, a company
was formed to manufacture a general line of furniture. Machinery
was procured, and the business got well a-going, but the project
was marked more by the enterprise of the members of the company
than by good management, and it failed in the crash of 1873,
leaving a considerable loss to be shared by the stockholders. An
attempt was made to manufacture extension tables exclusively. This
promised well for a time, but eventually succumbed to the pressure
of the panic. In 1868, the large building which occupies the center of
the public square was erected, at a cost of $6,500, by public
subscription. Fifteen 'hundred dollars of this amount was contributed
by the lodge of Masons in the village, to build the third story, which
they own and occupy. The building is about 35x55 feet, three stories
high, and built of brick. Col. G. A. Prambes, who was teaching a
select school in the village, origin ited the movement, and was ably
seconded by Mr. George Armstrong and others, and the building
was. soon furnished for school purposes, and known as the Sunbury
Institute. Since the erection of the special school district, in 1868,
the second story has been used as a public hall, and the lower story
for church purposes. It is now called the Sunbury Town Hall. In
October, 1872, the Farmers' Bank of Sunbury, with a capital of
$50,000, was organized. This is a joint-stock concern, and had for its
stockholders some of the most substantial men of Berkshire. The
original stockholders were E. Kimball, John Hall, Alanson Knox,
George Armstrong, George Grist, E. R. Thompson, 0. D. Hough and
B. Moore. The first officers were: Elias Kimball, President; W. A.
Thompson, Cashier ; Elias Kimball, E. R. Thompson, Elanson Knox,
0. D. Hough and B. Moore, Directors. On the death of Mr. Kimball,
which occurred very soon after the formation of the bank, Mr. Moore
succeeded h,im as President, and still holds that position. In January,
1875, Mr. 0. H. Kimball succeeded as cashier, and still serves in that
capacity with acceptance. Business was begun in a building on the
east side of the square, built by Mr. Marble, but was afterward
transferred to a building erected for the purpose by Mr. Moore, three
years later, on the south side of the square. In 1873, a number of
the prominent citizens of Sunbury formed a stock company and
furnished means to establish a weekly paper in the village ; it was
very appropriately named the Sunbury Enterprise, and was managed
for some nine months by D. M. Pyle. It was expected that he would
take the paper and pay for it as he could earn it out of the office.
The people supported the project, but there was an evident lack of
the right man in the right place, and it was sold to Mr. Wayman
Perfect, who changed the name to the Spectator. In this gentleman's
hands, the paper made rapid progress. It grew in popularity, and
gainedv a paying subscription list of some six hundred, with an
advertising patronage which affi)rded an ample support. In 1876, it
was sold to J. S. Watson. He seemed to meet with the same
success, but a better business arrangement' being offered at another
place, he suspended the publication of the paper in the spring of
1879, and moved the office and material out of the county.* The
agitation in regard to the numerous grave robberies, resulted in
Sunbury, as in many other places, in the formation of a Cemetery
Association in the summer of 1879. This association bought about
two acres of finely situated land, joining the old cemetery, and are
just finishing a fine stone vault at a cost of $750. Located here is
Sparrow Lodge, No. 400, of Free and Accepted Masons. The Lodge
first worked under a dispensation from the Grand Lodge of 1867,
and was chartered by that of 1868. There were eleven charter
members, but the membership has increased to about eighty-five in
the last ten years. The meetings were held twice a month during the
first year, in the old " hotel building," but since then in their new
rooms, in the third story of the town hall. There are three general
stores, two jewelry stores, one hardware store, two shoe-shops, a
machine-shop, two carriage-shops, two harness-shops, two tailor-
shops, two blacksmith-shops, two millinery stores, three saloons, to
one of which is attached a bakery, a bank of discount, flouringmill,
warehouse, tin-shop, picture-gallery, barbershop, drug store, gun-
shop, three churches, Methodist, Baptist and Presbyterian ; two
hotels, and a handle factory. This factory is a recently established
enterprise, but has been quite successful, shipping goods to
California and Europe. Machinery for turning spokes is to be put in,
and * Since the above was written, a weekly paper called the
Sunbury Monitor has been established by J. 6. Sharpe. "a) ^y
Welcome to our website – the ideal destination for book lovers and
knowledge seekers. With a mission to inspire endlessly, we offer a
vast collection of books, ranging from classic literary works to
specialized publications, self-development books, and children's
literature. Each book is a new journey of discovery, expanding
knowledge and enriching the soul of the reade

Our website is not just a platform for buying books, but a bridge
connecting readers to the timeless values of culture and wisdom. With
an elegant, user-friendly interface and an intelligent search system,
we are committed to providing a quick and convenient shopping
experience. Additionally, our special promotions and home delivery
services ensure that you save time and fully enjoy the joy of reading.

Let us accompany you on the journey of exploring knowledge and

personal growth!

textbookfull.com