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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 e-ISBN 978-981-15-0702-1

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

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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
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 instrumentation 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 relationship 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 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.
K. V. Chaitanya
Visakhapatnam, Andhra Pradesh, India
Knowledge of Sequences Could Contribute Much to Our Understanding
of Living Matter
Frederick Sanger
Contents
1 Structure and Organization of Virus Genomes
1.1 Introduction
1.2 General Features of Viral Genomes and their Classification
1.2.1 Classification of Viral Genomes
1.3 Size, Structure, and Composition of Double Stranded DNA
Virus Genomes
1.3.1 Analysis of Adenovirus 2(AD2) Genome
1.3.2 Herpesviridae
1.4 Genomes of Single Stranded DNA Viruses and their
Mosaicism
1.4.1 Genomes of Bacteriophages
1.4.2 Phage Genome Sequence Diversity
1.4.3 Genome Mosaicism of Phages
1.4.4 Genomes of Enterobacteria Phage M13 and λ Phages
1.4.5 The Genome of T4 Phage
1.5 Positive and Negative Stranded RNA Viral Genomes
1.5.1 Positive Stranded RNA Viral Genomes
1.5.2 Negative Stranded RNA Viral Genomes
1.6 Segmentation in Viral Genomes
1.6.1 Influenza Virus
1.7 Multipartite Viral Genomes
1.7.1 The Genome of Gemini Virus
1.8 Evolution of Viral Genomes
1.9 Conclusions
2 Archeal Genomics
2.1 Introduction
2.2 Archaea, the Third Main Domain of Life
2.3 Unique Features of Archaea
2.3.1 Cell Envelopes and Cell Structure
2.3.2 Unusual Appendages
2.3.3 Exosome
2.3.4 Archaeal Virus Families
2.3.5 Archaea and Extra Terrestrial Life
2.4 Archaea and Eukaryotes
2.5 Archaeal Genomes
2.5.1 Structure and Organization of Archaeal Genomes
2.6 Plasmids of Archaea
2.7 Horizontal Gene Transfer (HGT)
2.8 Integrase-Mediated Insertion and Deletion of Archaeal DNA
2.9 Genome of Methanogenic ArcheonMethanococcus
Jannaschii
2.9.1 The Methodology of Genome Sequencing
2.9.2 Properties of the Genome
2.9.3 Identification of Proteins by Shotgun Proteomics
2.10 Genome ofArchaeoglobus Fulgidus
2.10.1 Genome Sequencing and Assembly
2.10.2 ORF Prediction and Gene Identification
2.10.3 Features of the Genome
2.11 Comparative Genomics ofA. Fulgidus andM. Jannaschii
2.12 Conclusions
3 Structure, Function, and Evolution of Bacterial Genomes
3.1 Introduction
3.2 Structure and Organization of Bacterial Genomes
3.2.1 Bacterial Chromosomes and Plasmids
3.2.2 Bacterial Genomes with Primary and Secondary
Chromosomes
3.2.3 Insertion Sequence (IS) Elements
3.2.4 Conjugative Transposons
3.2.5 Invertrons
3.2.6 Integrons
3.2.7 Integratable Plasmids and Phages
3.3 Genome Rearrangements in Bacteria
3.3.1 Rearrangements Due to Mobile Genetic Elements
3.3.2 Transposons
3.3.3 Genomic Islands in Bacteria
3.3.4 Inteins
3.3.5 Introns
3.3.6 Homing Endonucleases
3.3.7 Retro Elements
3.4 Evolution of Bacterial Genomes
3.4.1 Role of Mutations in Bacterial Genome Evolution
3.4.2 Role of Recombinations in Bacterial Genome Evolution
3.4.3 Evolution of Bacterial Pathogens
3.5 Genetic Diversity of Pathogenic Bacteria
3.5.1 Mechanisms of Genetic Diversity
3.5.2 Horizontal Gene Transfer
3.5.3 Pathogenicity Islands
3.5.4 Genetic Diversity and Origin of New Bacterial
Pathogens
3.5.5 Techniques Used for Studying the Genetic Diversity of
Pathogenic Bacteria
3.6 Genome ofEscherichia coli K-12 Strain
3.6.1 Genome Sequencing
3.6.2 Annotation of the Genome
3.6.3 Overview
3.6.4 Compositional Organization of the Genome
3.6.5 Open Reading Frames and Gene Function
3.6.6 Operons, Promoters and Protein Binding Sites
3.6.7 Repeated Sequences and Insertion Sequences
3.6.8 Cryptic Prophage and Phage Remnants
3.7 Genome of EnterohaemorrhagicE. coli O157: H7
3.7.1 Genome Sequencing and Annotation
3.7.2 Outline
3.7.3 Comparison BetweenE. coli O157 andE. coli K-12
Genomes
3.8 Genome ofMycoplasma genitalium
3.8.1 Genome Sequencing, Assembly and Annotation
3.8.2 Overview of the Genome
3.9 Synthetic Genome ofMycoplasma genitalium
3.9.1 Strategy for Synthesis and Assembly
3.9.2 Minimal Number of Genes
3.10 Conclusions
4 Orgenellar Genome Analysis
4.1 Introduction
4.2 Resemblances of Chloroplast and Mitochondria with
Bacteria
4.3 Architecture of Organelle Genomes
4.3.1 Genome Size and Structure
4.3.2 Nucleotide Composition
4.3.3 Chromosome Number
4.3.4 Non-coding DNA
4.3.5 Coding Regions
4.3.6 Genome Loss
4.3.7 Gene Fragmentation
4.3.8 Non-Canonical Genetic Codes and RNA Editing
4.3.9 Horizontal Gene Transfer and Acquisition of Foreign
DNA
4.4 Evolution of Organelle Genomes
4.4.1 Evolution of Traits and Characteristics in Organelle
Genomes
4.5 Chloroplast Genomes
4.5.1 Sequencing Technologies for Chloroplast Genomes
4.5.2 Chloroplast Genome Sequencing
4.5.3 Structure of Chloroplast Genome
4.5.4 Phylogeny of Chloroplast Genomes
4.5.5 Chloroplast Genome Engineering
4.5.6 Chloroplast Genome ofEuglena gracilis
4.6 Mitochondrial Genomes
4.6.1 Sequencing Technologies for Mitochondrial Genomes
4.6.2 Structure of Mitochondrial Genome
4.6.3 Mutations in the Human Mitochondrial DNA and
Diseases
4.6.4 Mitochondrial Genome of Neandertal Fossil
4.6.5 Structure and Organization of Plant Mitochondrial
Genome
4.7 Conclusions
5 Eukaryotic Genome Organization, Regulation, Evolution and
Control
5.1 Introduction
5.2 Organisation of Eukaryotic Genomes
5.2.1 Organization of Chromosomes
5.2.2 Centromeres of Eukaryotic Chromosomes
5.2.3 Telomeres
5.2.4 Spatial Organisation of Eukaryotic Genomes
5.2.5 Whole Genome Duplications and Segmental
Duplications
5.2.6 Transposable Elements
5.2.7 Satellite DNA
5.3 Complexity of the Eukaryotic Genomes
5.4 Yeast Genome
5.4.1 Genome Sequencing
5.4.2 Genome Overview
5.4.3 Chromosomal Organization
5.4.4 Organellar, Plasmid, and Viruses in Yeast Genome
5.4.5 Genome Evolution
5.4.6 Comparative Genomics of Yeast
5.4.7 Yeast Proteome
5.4.8 Future Research
5.5Caenorhabditis elegans Genome
5.5.1 Importance ofC. elegans as a Model Organism
5.5.2 Genome Sequencing
5.5.3 Overview of the Genome
5.6 The Genome ofDrosophila melanogaster
5.6.1Drosophila melanogaster as a Model Organism
5.6.2 Genetic Markers
5.6.3 Genome Sequencing
5.6.4 Gene Prediction
5.6.5 Gene Similarity with Humans
5.7 Genome ofArabidopsis thaliana
5.7.1Arabidopsis thaliana as a Model Organism
5.7.2 Genome Sequencing
5.7.3 Gene Prediction
5.7.4 Genome Organization and Duplication
5.7.5 Telomeres and Centromeres
5.7.6 Transposable Elements
5.7.7 Gene Regulation
5.7.8 Developmental Regulation
5.7.9 Photomorphogenesis and Photosynthesis
5.7.10 Metabolism
5.7.11 Comparative Genomics withB. oleracea
5.8 The Soybean Genome
5.8.1 Soybean and its Importance
5.8.2 Genome Sequencing and Assembly
5.8.3 Gene Annotation
5.8.4 Repetitive Elements
5.8.5 Structural Organization of the Genome
5.8.6 Importance of Soybean Genome
5.8.7 Database
5.9 The Rice Genome
5.9.1 Importance of Rice Crop to the World
5.9.2 International Rice Genome Sequencing Project
(IRGSP)
5.9.3 Physical Map and Sequencing of the Rice Genome
5.9.4 Genome Annotation
5.9.5 Components of Rice Genome
5.9.6 Outcomes of the Rice Genome Project
5.10 The Human Genome
5.10.1 Sources of DNA and Sequencing Methods
5.10.2 Genome Assembly Strategy and Characterization
5.10.3 Whole-Genome Assembly
5.10.4 Gene Prediction and Annotation
5.10.5 Genome Structure
5.10.6 Evolution of Human Genome
5.10.7 Sequence Variations in the Human Genome
5.10.8 Analysis of Predicted Protein-Coding Genes
5.10.9 Evolutionary Studies and Comparative Genomics
5.10.10 80% of the Human Genome has an Active Function
5.11 Conclusions
6 Genome Sequencing, Assembly, and Annotation
6.1 Introduction
6.2 Sequencing Technologies and Genome Sequencing
6.2.1 First-Generation DNA Sequencing
6.2.2 Second Generation DNA Sequencing
6.2.3 Third Generation DNA Sequencing
6.2.4 Sequencing of Fungal Genomes
6.2.5 Sequencing of Plant Genomes
6.2.6 Sequencing of Animal Genomes
6.2.7 Sequencing of Degraded and Ancient Fossil DNA
6.2.8 Structural Variations in the Drosophila Genome
6.3 Whole Genome Sequencing
6.3.1 Major Strategies for Whole Genome Sequencing
6.4 Genome Sequencing by Mass Spectrometry
6.4.1 Mass Analysis of Sanger Sequencing Reaction Products
6.4.2 DNA Ladder Sequencing
6.4.3 Gas-Phase Fragmentation
6.4.4 Mass Spectrometry and SNP Genotyping
6.5 Mapping of Genomes
6.5.1 Genetic Map
6.5.2 Physical Mapping
6.6 Genome Assembly
6.6.1 Overlap Phase
6.6.2 Layout Phase
6.6.3 Derivation of a Consensus Sequence
6.6.4 Repeats and Sequencing Errors in the Genome
Assembly
6.6.5 Assembly Algorithms and Notable Assembly Programs
6.7 Scaffolding
6.8 Finishing
6.9 Genome Annotation
6.9.1 Nucleotide Annotation
6.9.2 Protein-Level Annotation
6.9.3 Process-Level Annotation
6.10 Applications of Next Generation Sequencing Systems
6.10.1 Transcriptome Sequencing
6.10.2 The Resurrection of Ancient Genomes
6.10.3 Analysis of Epigenetic Modifications of Histones and
DNA
6.10.4 Sequencing of Cancer Genome
6.10.5 Diagnosis of Rare Diseases and Exome Sequencing
6.11 Conclusions
7 Other ‘Omics’ Integrated into Biosciences
7.1 Introduction
7.2 Transcriptomics
7.2.1 Categories of RNA
7.2.2 Transcriptome Sequencing and Analysis
7.3 Proteomics
7.3.1 Life and Death of a Protein
7.3.2 Types of Proteomics
7.3.3 Gene Expression and Codon Bias Affecting the Protein
Levels
7.3.4 Techniques that are Involved in the Proteomics Studies
7.3.5 Applications of Proteomics
7.4 Metabolomics
7.4.1 Approaches for Metabolomics
7.5 Exposomics
7.5.1 External Exposome
7.5.2 Internal Expsome
7.6 Connectomics
7.6.1 Need for the Connectome
7.6.2 Measurement of Regional Connections in the Living
Human Brain
7.7 Microbiomics
7.7.1 Human Microbiome
7.8 Conclusions
8 Applications of Genomics
8.1 Introduction
8.2 Application of Genomics in Agriculture
8.2.1 Plant Breeding
8.2.2 Genome Wide SNP Studies
8.2.3 Construction of Genetic Maps
8.2.4 Identification of QTL Related Markers
8.2.5 Association Mapping
8.2.6 Abiotic Stress Tolerance
8.3 Application of Genomics in Genetic Testing and Molecular
Diagnostics
8.3.1 Single Gene Disorders
8.3.2 Multifactorial Gene Disorders
8.4 Epigenetics and Epigenomics
8.5 Genomic Medicine
8.6 Genomics and Cancer Therapy
8.7 Cytogenomics
8.7.1 Cytogenomics of Brain Diseases
8.7.2 Cytogenomics of Plants
8.8 Microarrays
8.8.1 Genomic Microarrays
8.9 Comparative Genomics
8.9.1 Comparative Genomics of Human and Mouse
8.9.2 Evolution of Sex-Chromosomes in Humans
8.9.3 Language Adaptation in Humans
8.10 Conclusions
9 Important Databases Related to Genomes
9.1 Virus Databases
9.2 Archaeal Databases
9.3 Bacterial Databases
9.4 Cell Organelle Databases
9.5 In-Vertebrate Genome Databases
9.6 Vertebrate Genome Databases
9.7 Human Genome Databases
9.8 Plant Genome Databases
9.9 Genomes of Economically Important and Model Plants
Glossary
Bibliography
Index
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 postdoctoral 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.
© Springer Nature Singapore Pte Ltd. 2019
K. V. Chaitanya, Genome and Genomics
https://doi.org/10.1007/978-981-15-0702-1_1

1. Structure and Organization of Virus

Genomes
K. V. Chaitanya1

(1) Department of Biotechnology, GITAM University, Visakhapatnam,

Andhra Pradesh, India

K. V. Chaitanya

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 different 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, genetically 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 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
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 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 Polyomavirus 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 control 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 splicing. 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
mechanism, 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 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, particularly
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.

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

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 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 pneumonia, requiring hospitalization in ~25% of diagnosed cases. It
also causes other localized diseases, such as colitis, hemorrhagic
cystitis, hepatitis, nephritis, encephalitis, 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 adenoviral 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 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
transcription 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.
Fig. 1.1 Organisation of the Adenovirus genome (Courtesy Russel WC, School of
Biology, University of St Andrews, UK)
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
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 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 existence 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 addition, Human
Herpesvirus 6 (HHV-6) is found to be integrated into the germlines 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 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
pathogenesis. 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 reference 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).

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

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.

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 environmentally 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, icosahedral 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).
Table 1.2 Morphological diversity of single stranded DNA viruses

Host virus Virion Genome topology Genome

taxon morphology size
Microviridae Icosahedral Circular 4.4–6.1
Host virus Virion Genome topology Genome
taxon morphology size
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
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.

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
diversity, 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
delivered 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;
1. To understand the relationship between the phage genomes the
evolutionary mechanisms that shaped these bacteriophage
populations.

2. For increased utilization of bacteriophages in the development of

tools, utilities, and techniques related to genetics and
biotechnology.

Phage genomes display a considerable amount of variation in their

size, varying from Leuconostoc phage L5 (2435 bp) to Pseudomonas
phage 201 (316,674 b). Tailed phages with double stranded DNA
genomes vary in their size from >10 kbp to <15 kbp, consistent with
their overall virion structure and gene assembly, which encompass up
to 15 kbp of the genome space. Siphoviruses of the genome size 1.5–
6 kbp are characterized by a long flexible non-contractile tail with a
tape measure protein gene, whose length corresponds to the phage tail
length Many phages with the morphologies similar to Siphoviruses have
genomes longer than 20 kbp. Contrastingly, Myoviruses with contractile
tails are the phages with larger genomes of >125 kbp and the Bacillus
phage SPBc2, is the largest Siphoviral genome of the length 134,416 bp.
The main reason for the absence of large Siphoviruses is still unknown.

1.4.2 Phage Genome Sequence Diversity

Bacteriophages are estimated to be the most widely distributed
biological entity of the biosphere. They are found in all habitats of the
world, where bacteria proliferate. Most of the viral population is
dominated by bacteriophages, with double stranded DNA tailed phages,
or Caudovirales, accounting for 95% of all the phages, possibly making
up the majority of phages on the planet. However, phages belonging to
other groups also occur abundantly in the biosphere, such as phages
with different virions , genomes, and lifestyles. Two key approaches
were made for studying the viral diversity are metagenomics of total
concentrated phage samples collected from the environment and a
genome-by-genome strategy of individually isolated phages. These two
approaches are compatible, having distinct outcomes. Metagenomics
generates a large amount of sequence data, which provides a good
insight into their diversity. Sequencing and analysis of individually
isolated phages generate small data sets, which are structured into
whole genomes. As phage genomes are architecturally mosaic, the
availability of complete genomes contextualizes the complexities of
their relationships. The nucleotide sequences of phage genomes with
non-overlapping hosts rarely share sequence similarity, as noticed in
the published genomes of four Streptomyces phages and available
collection of 50 mycobacteriophage genomes. Phages infecting a
common bacterial host are in genetic contact with each other, and they
share common nucleotide sequences. Genomes of over 30 phages with
common host have been isolated and sequenced from Pseudomonas,
Staphylococcus, and Mycobacterium containing related sequences, with
a few exceptions. Most of these phages share a very low or no sequence
similarity, as illustrated by the nucleotide sequence comparisons of
mycobacteriophages and Pseudomonas phages .

1.4.3 Genome Mosaicism of Phages

Phages were evolved not only by the accumulation of mutations but
also through the recombination events, during which they exchanged
genetic material with other phages. These events have been suggested
to explain the mosaic structure of the phages, arisen by comparison of
two or more phage genomes. During the comparison of the genomes,
nearly identical sequences alternate with merely similar sequences or
completely divergent sequences. Such type of exchanges in
bacteriophages was obtained by heteroduplex mapping in the early
1990s. Since then, numerous mosaics have been identified by sequence
comparison, and the mosaic structure of bacteriophages is now a well-
documented phenomenon. This mosaicism is also found to be
ubiquitous among bacteria, where the genes are acquired through
horizontal genetic exchange mostly through transduction,
transformation, and conjugation. But, the extent of mosaicism is highly
remarkable in phage genomes as evidenced by the increasing number
of genomes available for comparative genomics analysis.
The mechanism of genome mosaicism in bacteriophages can be
understood at two levels; 1. by comparing nucleotide sequence through
DNA heteroduplex mapping, 2. by comparing their DNA sequences.
There are two models which explain the recombination mechanisms
that are responsible for these patterns. Model 1 describes the role of
short conserved boundary sequences that are located at gene junctions
in targeting various exchange events that are catalyzed by homologous
recombinations , by using the recombinases synthesized by either host-
or phages. Model 2 attempts to explain that the homologous
recombination events are not specifically targeted and occur randomly
with the preference of a few short sequences so that most of the events
results in non-functional genomic trash. Comparison of the predicted
amino acid sequences encoding phage gene products is an alternative
manifestation of mosaicism. This is an informative approach, since
many phages including those that infect common hosts may not share
any nucleotide sequence information. In that case, protein sequence
data reveals genes that share much older ancestry.

1.4.4 Genomes of Enterobacteria Phage M13 and λ

Phages
M13 Enterobacteria phage infects E. coli. The genome of M13 phage
consists of 6.4 kb single-stranded, (+) sense, circular DNA, which
encodes for 10 genes. Unlike most icosahedral virions , the capsid of
M13 phage is filamentous, which can be expanded by the addition of
further protein subunits. Hence, the genome size can also be increased
by the addition of extra sequences in the nonessential intergenic region
without becoming incapable of being packaged into the capsid (Fig.
1.3).

Fig. 1.3 Genome map of M13 phage

In λ phage, the packaging constraints are much more rigid with DNA
of ∼46–54 kbp of the normal genome size can be packaged into the
virus capsid and the substrate packaged into the phage heads during
assembly consists of long concatemers of phage DNA that are produced
during the later stages of vegetative replication. The DNA is apparently
reeled into the phage head and after the incorporation of the complete
genome, DNA is cleaved at a specific sequence by a phage-coded
endonuclease, leaving a 12-bp 5¢ overhang on the end of each of the
cleaved strands, known as the cos site. Hydrogen bond formation
between these ‘sticky ends’ can result in the formation of a circular
molecule (Fig. 1.4).
Fig. 1.4 Genetic map of λ phage
In a newly infected cell, the gaps on either side of the cos site are
closed by DNA ligase, and resulting circular DNA undergoes vegetative
replication and integration into the bacterial chromosome .

1.4.5 The Genome of T4 Phage

Bacteriophages T2 and T4 are the model organisms playing an
instrumental role in the development of modern genetics and
molecular biology since the 1940s. They were involved in the
development of many salient concepts related to biological sciences,
including the recognition of nucleic acids as genetic material,
identification of a gene through structural, mutational,
recombinational, and functional analyses, in the demonstration triplet
genetic code, in the identification of mRNA and establishing the
importance of recombination in the replication of DNA, in the light-
dependent and light-independent DNA repair mechanisms, restriction
and modification of DNA, self-splicing introns in prokaryotes, etc. The
main advantage of using T4 phage as a model system is its capability of
totally inhibiting its host’s gene expression, permitting the investigators
to identify the differences between host specific and phage specific
macromolecular syntheses. Analysis of the T4 capsid assembly and
functioning of its nucleotide-synthesizing complex, replisome, and
recombination complexes has led to important insights into
macromolecular interactions, substrate channeling, and co-operation
between phage and host proteins within such complexes.
The genome of T4 phage is considered as the best avenue for
understanding and evaluating the complete genome of a well organized
biological system. On the basis of all available information, T4 phage
genome comprises of ~300 probable genes, packed into a 168,903 bp
genome. This genome comprises 289 expressing genes, 8 tRNA genes,
and a minimum of 2 genes that encodes small, stable RNAs with
unknown function. Genes 16, 17, and 49 contains multiple coding
regions that encode more than one protein. T4 phage genome is four
times higher than that of Herpesviruses and yeast, two times higher
than E. coli. A very small number of genes contains non-coding regions
of ~9 kb, accounting for 5.3% of the genome. Regulatory regions in this
phage genome are compact, occasionally with overlapping coding
regions. Another significant feature of this genome is the overlap of one
gene’s termination codon with the start codon of the next one. T4
phage has several groups of nested genes. It was found that only 62
genes in this organism are absolutely essential under standard
laboratory conditions (rich medium, aeration, 30 to 37 °C). Mutants
generated by altering a few other genes produced very small plaques
under similar standard laboratory conditions. Many of the 62 essential
genes are larger than an average T4 gene, occupying half of the genome.
Essential genes encode proteins of the replisome and nucleotide
precursor complex, transcriptional regulatory factors, and proteins
involved in the structure and assembly of the phage particle. The
genome of T4 phage illustrates another rare molecular feature of
certain linear viral genomes, terminal redundancy. Replication this
phage genome produces long concatemers of DNA, which are cleaved
by a specific endonuclease, gets incorporated into the particle with the
length exceeding its complete genome due to the repetition of some
genes at each end of the genome. Resulting T4 phage genome
containing reiterated information is packed into the phage head.
Three T4 phage genes that encode for thymidylate synthase (td),
subunit of the aerobic ribonucleotide reductase (nrdB) and the
anaerobic ribonucleotide reductase (nrdD) are found to contain introns
that are later spliced out of these transcripts. A possibility of an unusual
relationship between the nucleic acid sequence and protein sequence
occurring through translational bypassing is demonstrated in gene 60
of the T4 phage genome. A 50 bp mRNA segment in the coding region of
this gene is not translated by the regular mechanism. This mRNA
segment is the only known and unique high-efficiency translational
bypass site in the entire T4 phage genome.
DNA in the genome of this phage contains only 34.5% GC, compared
with its host genome of E. coli consisting of 50% GC. In the genome, 18
of the known or predicted genes containing less than 60% AT and 4
predicted genes have less than 58%. Capsid proteins, which are the
most widely conserved among the T4-related phages have the lowest
AT contents. Gene 23, which encodes for the major head protein, has
the lowest AT content of 55%. A substantial decrease in the pairing of G
against C in the coding strands of translated regions has been
identified. 4 genes having more than 20% C in the coding strand, while
more than 130 genes have more than 20% G and 37 genes have more
than 22% G. A and T are equally divided between the coding strands.
However, some AT bias has been identified in the T4 phage genome,
which is stronger in the third position of codons, as expected in
genomes with a high amount of AT-rich regions.
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atmosphere. It is of course very well known that an ordinary
amphibian is not a lung breather throughout its whole life. The
metamorphosis of a gill-breathing tadpole into a lung-breathing frog,
illustrated in Fig. 85, is a phenomenon with which everyone is
familiar. And this condition, in which a change in the mode of life is
made by each individual in the course of its development, is the
typical one. But the modern amphibians include types ranging from
completely water to perfect land forms. Some, like the Austrian Olm
(Fig. 86), are gill breathers throughout their whole life. One which is
normally of this type, the Axolotyl, illustrated in Fig. 87, can be made
to acquire lungs and assume a land mode of life. Others, which
normally make the metamorphosis, can be prevented from doing so
by being confined to the water, and complete their life-histories in
the condition of gill breathers. In still other forms (e.g. the
Cœcilians, Fig. 89) the change is made before the young creature
leaves the egg, and the independent life is commenced in the
condition of a land animal.
Correlated with the development of the lungs is a change in the
structure of the nostrils, from the condition of blind sacs, as they
occur in the fishes, to that of air passages, communicating with the
upper part of the alimentary canal, and thence with the lungs.
Fig. 86.—The Olm—Proteus anguincus.
Fig. 87.—Axolotyl. The ordinary gill-breathing form, and the artificially developed
land form.
Fig. 88.—Amphibians—The Fire Salamander.
The living forms of the Amphibia differ considerably from the types
which constituted the group in those long-distant ages when it was
in the heyday of its prosperity. The latter forms were characterised
especially by a system of armour-plating over the head, which
frequently extended under the breast and even covered the greater
part of the lower surface, and which appears to have formed a
protection against the multitude of sharks which populated the
waters in which the amphibians partly lived. The armour-plated type
has long ago become extinct, but it is in it, rather than in the
modern forms of Amphibia, that we must look for the direct ancestor
of man. A fossil of this earlier group is shown on Fig. 90.

Fig. 89.—The Ceylon Cœcilian, Ichthyophis glutinosa, with eggs.

Fig. 90.—Fossil amphibian, Brachiosaurus, from the Permian.
Our next group in the order of Evolution is that of the reptiles, the
main differences between which and the Amphibia are of the nature
of more complete adaptions to a life on land. The reptiles have in
fact completed the conquest of the land which was undertaken by
the previous group, and many of them, living as they do in dry and
hot deserts, are as independent of the water as any form of animal
life. Thus whereas the amphibian has a thin skin, which is kept moist
by the secretions of numerous skin glands, the reptile has a body-
covering of scales, which form an effective protection against a too
rapid loss of moisture. Evidently with the same object, the reptile
egg is enclosed in a hard and resistant shell. Correlated with the
change in the skin is a much more perfect development of the lungs,
for while the amphibian breathes to a considerable extent through
its thin moist skin, this method of assisting respiration is not
available to the reptile.
Again connected with the improvement of the respiratory process,
there is a partial development of a septum dividing the ventricle or
pumping chamber of the heart. The value of this division of course
lies in the fact that the purified and oxygenated blood from the lungs
is prevented from mixing with the venous blood from the body. The
course of the blood is from the body to the right auricle, thence to
the right ventricle, and thence to the lungs. The pure blood from the
lungs returns to the left auricle, passes thence to the ventricle on
the same side to be pumped to the general circulation. The
disadvantage of a single ventricle, such as occurs in the Amphibia,
and the advantage of the regular double circulation, such as that in
man, are sufficiently obvious. The division of the ventricle into two
chambers is less complete in the lizards and snakes, very nearly
perfect in the crocodiles.
The reptiles, like the Amphibia, are 'cold blooded,' by which is
meant, not that their blood is necessarily cold, but that its
temperature varies with that of the surroundings, while that of the
blood of the mammals and birds is practically constant.
A very important feature of the reptiles, which they possess in
common with the mammals and the birds, is that the embryo
produces two membranous outgrowths called respectively the
amnion and the allantois, which completely envelop it, and which
have important functions in connection with nutrition, respiration,
and excretion during the period when the young creature is enclosed
in the egg. It is, of course, not until we reach the higher mammals
that these membranes assume their greatest importance.

Fig. 91.—Imaginative European landscape in the Cretaceous period, with

reconstructions of typical reptiles.
Plesiosaurus (swimming, up to 50 ft. long).
Three Ichthyosaurians.
Pterodactyls (flying).
Iguanodon.
Megalosaurus (40 ft. long).
Rhamphorhynchus.
For a considerable time in the world's history the reptiles were the
dominant vertebrate class, and in the chalk period especially they
were represented by a great variety of forms, and by a number of
species of colossal stature, one at least of which was over a hundred
feet long. In those times the reptiles were by no means all
condemned to crawl on their bellies, for they included a large
number of marine forms, comparable to the porpoises and whales
among the mammals, and flying forms whose aspect must have
resembled, and been equally terrifying with, that of our mythical
dragons. A few reconstructions of these are shown in Fig. 91.

Photo: Berridge.
Fig. 92.—Reptiles—A Chameleon.

Photo: Berridge.
Fig. 93.—Reptiles—Indian Python.
Fig. 94.—Reptiles—Turtle and Tortoises.
Fig. 95.—Reptiles—Alligator.
All living reptiles, with a single exception, belong to the four
comparatively modern types of the lizards, snakes, tortoises, and
crocodiles, of which examples are illustrated in Figs. 92 to 95. None
of these are closely related to the mammals or birds. For the
common ancestor of all these types we must go back to some
primitive reptile form. Fortunately such a type is represented at the
present day in a single peculiar species found in New Zealand, which
bears the Maori name of the Tuatara. It was formerly found
commonly on the mainland, but is now confined to a few small
islands in the Bay of Plenty, North Island, where it enjoys
Government protection. It is, as the illustration in Fig. 96 shows, a
lizard-like creature, and reaches a length of about two feet. It lives
in burrows near the shore, and feeds on small animals that are left
behind by the tide. The Sphenodon, as zoologists have named it, has
apparently been preserved owing to the absence of competition by
the mammals, and by adopting the rather curious mode of life just
described. In all its features, but especially in the primitive condition
of its vertebræ, it is very much lower than any other living reptile,
and it connects the higher groups with the Amphibia. Many closely
related fossil species are known, one of which is shown in Fig. 97.

Fig. 96.—The Tuatara, Sphenodon punctatus.

Fig. 97.—Homeosaurus pulchellus. A fossil early reptile from the Jurassic.

To the lay mind the distinctions between the Amphibia and the
reptiles are not very obvious, and indeed in the older classifications
the former group was not separated from the latter. The differences
between a reptile and a bird, on the other hand, are very striking. It
might therefore be regarded as a matter for surprise that zoologists
now make the greater distinction between the Amphibia and the
reptiles, grouping the former in one great class with the fishes, the
latter in a second great section with the birds. But in fact there are
many fundamental points of agreement between reptiles and birds,
and it is impossible to doubt that the latter have sprung from a
reptilian stock. Indeed, a most interesting connecting link is known,
in the fossil Archiopteryx shown in Fig. 98, of which only two
specimens have been found, and which is the only creature of its
type of which we have any record. In all its skeletal features, the
Archiopteryx is reptilian, and it would undoubtedly have been
classed as a new type of reptile but for the obvious and
unmistakable traces of feathers. From what particular class of
reptiles the birds have sprung is not known.
The birds have assumed the position of almost unquestioned
masters of the air, but like other great groups they show possibilities
of evolution in other directions wherever opportunity offers, and
types like the kiwi and the penguin shown in Figs. 100 and 101 have
forsaken their native element—the one for the land, the other for the
water.
The birds agree with the mammals in the development of a four-
chambered heart, in their warm blood, in their external covering for
the skin, and in the development of arrangements and instincts for
the parental care of the young. Their line of Evolution has thus been
to some extent parallel to that of the mammals. On the other hand,
they differ obviously in the structure and function of their fore limbs,
in the absence of a diaphragm, and in their special methods for the
care of the young, and there can be no doubt that the two groups
have had quite different origins in the reptile class.
Fig. 98.—Archiopteryx, a fossil lizard-like bird.
Photo: Underwood.
Fig. 99.—Eagle, with prey.
Fig. 100.—The Kiwi, Apteryx. A practically wingless running bird.
Photo: W. P. Dando.
Fig. 101.—The King Penguin. A highly specialised diving bird.
Photo: W. P. Dando.
CHAPTER VI
THE MAMMALS AND MAN
The subject of our discussion is now narrowed down to the group of
the mammals. The mammals are characterised by two very obvious
features: a body-covering of hair, and a set of special glands in the
female which secrete milk for the nourishment of the young. These
are constant characters, and neither is ever found in any other
group. As to how the hair originated, nothing definite is known; but
(while there are certain difficulties in regard to the theory) it is on
the whole reasonable to suppose that the mammalian hair arose, as
the bird's feather undoubtedly did, as a modification of the reptile's
scale. The mammary gland appears to represent a modification of
other skin glands, either of sweat glands or more probably of the oil
glands which exist in connection with the hairs.
Another important character, already mentioned at the end of the
last chapter, is the diaphragm, a muscular partition separating the
body cavity into a thoracic and an abdominal portion. The diaphragm
has important functions in connection with the mechanism of
breathing. By means of it the thoracic cavity can be increased or
diminished in size, and air thus drawn into or expelled from the
lungs. It is interesting to observe that a similar partition, with the
same function, occurs in the Crocodiles, but this has different
relations to the abdominal organs, and has evidently evolved quite
independently.
Very characteristic of the mammals are, further, their teeth, for
whereas the teeth of the reptiles are indefinite in number, and
generally very numerous, those of the mammal are relatively few,
and each species has a definite normal number. Moreover, the teeth
of the reptile are all of a kind, and they may be replaced almost any
number of times during the animal's life, whereas those of the
mammal show differentiation according to their respective functions,
and are only once changed, that is, when the milk teeth are replaced
by the permanent set. The teeth of the mammal are of four kinds:
incisors, or chisel-like cutting teeth, canines, which are especially
well developed in carnivorous species, and which are used in the
tearing up of flesh, etc., and two groups of grinders—premolars,
which are replaced during the animal's life, and molars, which occur
only as permanent teeth.

Fig. 102.—Pareiosaurus Baini. Fossil skeleton from the Permian of South Africa.
Fig. 103.—Skull of Galesaurus, from the Permian of South Africa.
A, From side; B, from below; C, from above; D, back tooth.
Fig. 104.—Skull of Tritylodon from below.
The mammals in all probability arose from a particular group of
reptiles which flourished in the Permian and Triassic periods, and
which disappeared very shortly afterwards. These pass under the
name of the Theromorpha, and a typical specimen, Pareiosaurus, is
illustrated in Fig. 102. The skull of another, illustrated in Fig. 103,
shows distinct indications of a mammal-like differentiation of the
teeth. The Tritylodon, whose skull is shown in Fig. 104, is an
intermediate type between this group and the mammals, some
zoologists regarding it, as it were, as the last reptile, others as the
first of the mammals.
As to how the special mammalian features arose, or what special
conditions called them into existence, we are of course without
definite knowledge, for neither hair nor mammary glands are
recognisable in fossils. But it seems likely that the warm blood and
the hairy covering evolved in correlation with one another, and as
adaptions to meet a gradual cooling of the climate. It is certain at all
events that the present-day mammals (and also the birds) are far
better adapted for a cold environment than the reptiles, which very
easily get frozen to death; and it is also known that ice periods
occurred in South Africa, where many fossil Theromorpha and the
Tritylodon are found, at the time when these creatures existed; both
of which facts support the theory indicated.
At the present time the mammals are the highest and on the whole
the most successful of the vertebrate groups. They include the
largest and strongest, the swiftest-footed and the most intelligent of
the animal kind. They show refinements of the senses of sight,
hearing, and smell such as are met with nowhere else. They range
from the Equator to the coldest regions of the earth in which any
food is to be found; they people alike the forest and the plain, and
have their representatives both in the air and in the sea.
Fig. 105.—The Australian Duck-mole or Duck-billed Platypus.
The most lowly of the mammals are the Monotremes, which include
the well-known Australian duck-mole or duck-billed platypus, and
two species of spiny ant-eaters, one of which is found in Australia,
the other in New Guinea. The two types are shown in Figs. 105 to
107. The best-known and most striking fact concerning these is that,
like the birds and reptiles, and unlike all other mammals, they lay
eggs. Beyond this feature they show many affinities with the
reptiles, in their skeleton for example, and particularly in their
reproductive organs. Another interesting fact is that the blood
temperature, of the ant-eater at least, is low, and varies
considerably. It has been found to range between 80 and 93 degrees
Fahrenheit, whereas all other mammals, so far as is known, have a
blood temperature between 97 and 105, and moreover one that is
remarkably constant for each species during normal health. The
brain development and the intelligence are also much lower than in
other mammals, though distinctly superior to those met with among
the reptiles. The method of rearing the young in the case of the ant-
eater (that of the duck-mole not being yet fully known) is that the
single egg is placed, as soon as it is laid, in the pouch under the
belly of the female. Here it hatches in a very short time, and here
the young animal remains for the first two or three months of its life,
being nourished by milk produced by the mammary glands, which
open into the pouch. It is certainly owing to the absence of the
competition of the higher mammals in the regions where they are
found, that these two creatures, so interesting from the standpoint
of Evolution, have been preserved to us.

Fig. 106.—New Guinea Spiny Ant-eater.

Fig. 107.—Australian Spiny Ant-eater.
The next group, the Marsupials, is the lowest in which we get the
true mammalian characteristic of the bearing of living young. For
while occasional members of other groups, of the reptiles especially,
produce live young, the actual state of affairs is fundamentally
different. In these latter the egg is merely retained in the genital
duct until the young creature emerges. It is merely hatched inside
the body of the mother instead of outside. But in the Marsupials the
developing young receive nourishment from the mother, during
prenatal life, other than what is contained in the yolk. This
nourishment is obtained in the form of a secretion from the wall of
the uterus, there being as yet (with a single partial exception) no
real connection between mother and young.
The peculiar method of nourishing and protecting the young
Marsupial after birth is of course well known. The young are born in
a very immature and helpless condition, and are placed by the
mother in her pouch. The mouth becomes permanently attached to
the nipple of the dam, and the young creature remains thus for a
considerable time, the milk being pumped into it by the mammary
gland rather than sucked in by the efforts of the creature itself.
The Marsupials are further characterised by the possession of an
extra pair of bones in the pelvis, which function as supports for the
pouch; by the peculiar and primitive arrangement of the
reproductive organs; by their still poorly developed brain; and by
their generally large number of teeth, which reach a total of fifty or
fifty-two in some species, whereas forty-four is the ordinary
maximum number in the main mammal group. This last is to be
regarded as a character derived from the reptiles.
Fig. 108.—Kangaroo, with young.
Fig. 109.—Newborn young of Kangaroo.
It is very interesting to observe how, in Australia, where the
Marsupials have been free from the competition of other mammals,
they have evolved along many of the same general lines as the
higher group. We have indeed no marsupial whales, bats, or seals,
but there is a mole, very similar in its appearance and habits to our

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Genome and Genomics From Archaea To Eukaryotes K V Chaitanya PDF Download

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Diagnostics and Gene Therapy for Human Genetic

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ISBN 978-981-15-0701-4 e-ISBN 978-981-15-0702-1

© Springer Nature Singapore Pte Ltd. 2019

This work is subject to copyright. All rights are reserved by the

The use of general descriptive names, registered names, trademarks,

This Springer imprint is published by the registered company Springer

1. Structure and Organization of Virus

(1) Department of Biotechnology, GITAM University, Visakhapatnam,

1.2 General Features of Viral Genomes and their

1.2.1 Classification of Viral Genomes

Table 1.1 General features of viral genomes sequenced

S. No. Class Sequenced genomes Size (Nt) Proteins

1.3 Size, Structure, and Composition of Double

1.3.1 Analysis of Adenovirus 2(AD2) Genome

1.3.2.1 Analysis of Herpes Simplex Virus Genome

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

1.4 Genomes of Single Stranded DNA Viruses and

Host virus Virion Genome topology Genome

1.4.1 Genomes of Bacteriophages

2. For increased utilization of bacteriophages in the development of

Phage genomes display a considerable amount of variation in their

1.4.2 Phage Genome Sequence Diversity

1.4.3 Genome Mosaicism of Phages

1.4.4 Genomes of Enterobacteria Phage M13 and λ

Fig. 1.3 Genome map of M13 phage

1.4.5 The Genome of T4 Phage

Fig. 89.—The Ceylon Cœcilian, Ichthyophis glutinosa, with eggs.

Fig. 91.—Imaginative European landscape in the Cretaceous period, with

Fig. 96.—The Tuatara, Sphenodon punctatus.

Fig. 97.—Homeosaurus pulchellus. A fossil early reptile from the Jurassic.

Fig. 106.—New Guinea Spiny Ant-eater.

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