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Title: Bacterial Genomes: Trees and Networks

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WCAG 2.0 AA 00000
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Best Practice 00000
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Metadata

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Publication metadata.
Name Value
dc:title Bacterial Genomes: Trees and Networks
dc:creator Aswin Sai Narain Seshasayee
dc:rights ©2025 Aswin Sai Narain Seshasaye, CC BY-NC 4.0
dc:identifier calibre:166 | uuid:cacf79e1-36bf-4f7d-af4f-c854d7fdf96a | urn:uuid:e81c2161-05be-466b-b569-c54d384ce5a4
dc:language en-US
dc:date 2025-02-25T14:48:35+00:00
dc:description Microbes form the “unseen majority” of life on Earth, with bacteria at the forefront as both the architects of life’s chemical foundations and agents of disease. But their story is far more complex. Bacteria thrive in diverse and extreme environments, driven by the dynamic evolution of their genomes. These tiny organisms wield an extraordinary ability to adapt, balancing genetic changes across generations with rapid physiological responses to environmental shifts. 
 
In Bacterial Genomes, the evolutionary and regulatory processes that shape bacterial life are brought to life. This textbook offers a conceptual exploration of how bacterial genomes are organized, how they evolve, and how their genetic information is interpreted through intricate molecular networks. Drawing on both cutting-edge research and the historical milestones that shaped microbiology, it illuminates how bacteria navigate the intersection of genetic adaptation and ecological resilience. 
 
Designed for college students, interdisciplinary researchers, and even the determined amateur, Aswin Seshasayee moves beyond technical jargon to provide a thought-provoking synthesis of bacterial evolution and adaptation. Unlike traditional genomics texts, this book blends historical insights with contemporary discoveries, offering a fresh perspective on the role of bacteria in shaping the living world.
dc:subject Bacterial Genomics;Microbial Evolution;Regulatory Networks;Microbial Adaptation;biochemical processes;Molecular Microbiology
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dcterms:modified 2025-02-26T14:47:03Z
schema:accessibilitySummary This publication conforms to WCAG 2.0 AA.
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schema:accessModeSufficient textual
schema:accessibilityFeature structuralNavigation | alternativeText | index | tableOfContents | captions | unlocked | readingOrder
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Outlines

Go to: TOC Outline | Headings Outline | HTML Outline

TOC Outline

  1. Cover
  2. Title page
  3. Copyright
  4. Contents
  5. About the author
  6. List of figures and tables
  7. Preface
  8. 1. All creatures great and small
    1. 1.1. Bacteria: numerous and diverse
    2. 1.2. Animalcules
    3. 1.3. The golden age of microbiology: chemistry, biology and ecology
    4. 1.4. Antibiotics: microbial competition and metabolic plasticity
  9. 2. The molecules of bacteria and of life
    1. 2.1. A molecular biology primer
    2. 2.2. Viruses that prey on bacteria
    3. 2.3. The genetic material I: bacteria and the “transforming principle”
    4. 2.4. The genetic material II: the life cycle of bacteriophage
    5. 2.5. The annus mirabilis for molecular genetics
    6. 2.6. The tree of life and the place of bacteria in it
  10. 3. The genome: how much DNA?
    1. 3.1. The first genome sequences
    2. 3.2. The first bacterial genomes: minimal genomes for cellular life
    3. 3.3. Minimal genomes in action
    4. 3.4. Genome size and information content
    5. 3.5. The fate of a DNA sequence
    6. 3.6. The cost of a DNA sequence
  11. 4. The ebb and flow of bacterial genomes
    1. 4.1. Losing DNA
    2. 4.2. Gaining DNA
    3. 4.3. Changing DNA
    4. 4.4. The balance among events: gains, losses and mutations
    5. 4.5. The balance among forces: selection and drift
  12. 5. Reading and organising the genome
    1. 5.1. Expressing the genome and decision making
    2. 5.2. The transcriptional regulatory network of E. coli
    3. 5.3. Driving the stress response: σS and its competition with σD
    4. 5.4. Managing the costs of horizontally acquired DNA: the ‘genome sentinel’61
    5. 5.5. Evolving regulation
    6. 5.6. Building to read and reading to build
  13. Afterword
  14. Selected bibliography
    1. Chapter 1
    2. Chapter 2
    3. Chapter 3
    4. Chapter 4
    5. Chapter 5
  15. Index
  16. About the Team
  17. This book need not end here…
  18. You may also be interested in:
  19. Back cover

Headings Outline

  • Contents
  • About the author
  • List of figures and tables
  • Preface
  • 1. All creatures great and small
    • 1.1. Bacteria: numerous and diverse
    • 1.2. Animalcules
    • 1.3. The golden age of microbiology: chemistry, biology and ecology
    • 1.4. Antibiotics: microbial competition and metabolic plasticity
  • 2. The molecules of bacteria and of life
    • 2.1. A molecular biology primer
    • 2.2. Viruses that prey on bacteria
    • 2.3. The genetic material I: bacteria and the “transforming principle”
    • 2.4. The genetic material II: the life cycle of bacteriophage
    • 2.5. The annus mirabilis for molecular genetics
    • 2.6. The tree of life and the place of bacteria in it
  • 3. The genome: how much DNA?
    • 3.1. The first genome sequences
    • 3.2. The first bacterial genomes: minimal genomes for cellular life
    • 3.3. Minimal genomes in action
    • 3.4. Genome size and information content
    • 3.5. The fate of a DNA sequence
    • 3.6. The cost of a DNA sequence
  • 4. The ebb and flow of bacterial genomes
    • 4.1. Losing DNA
    • 4.2. Gaining DNA
    • 4.3. Changing DNA
    • 4.4. The balance among events: gains, losses and mutations
    • 4.5. The balance among forces: selection and drift
  • 5. Reading and organising the genome
    • 5.1. Expressing the genome and decision making
    • 5.2. The transcriptional regulatory network of E. coli
    • 5.3. Driving the stress response: σS and its competition with σD
    • 5.4. Managing the costs of horizontally acquired DNA: the ‘genome sentinel’61
    • 5.5. Evolving regulation
    • 5.6. Building to read and reading to build
  • Afterword
  • Selected bibliography
    • Chapter 1
    • Chapter 2
    • Chapter 3
    • Chapter 4
    • Chapter 5
  • Index
  • Contents
    • Landmarks

HTML Outline

    1. Untitled BODY
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
      1. Contents
    1. Untitled BODY
      1. About the author
    1. Untitled BODY
      1. List of figures and tables
    1. Untitled BODY
      1. Preface
        1. Untitled SECTION
    1. Untitled BODY
      1. 1. All creatures great and small
        1. 1.1. Bacteria: numerous and diverse
        2. 1.2. Animalcules
        3. 1.3. The golden age of microbiology: chemistry, biology and ecology
        4. 1.4. Antibiotics: microbial competition and metabolic plasticity
        5. Untitled SECTION
    1. Untitled BODY
      1. 2. The molecules of bacteria and of life
        1. 2.1. A molecular biology primer
        2. 2.2. Viruses that prey on bacteria
        3. 2.3. The genetic material I: bacteria and the “transforming principle”
        4. 2.4. The genetic material II: the life cycle of bacteriophage
        5. 2.5. The annus mirabilis for molecular genetics
        6. 2.6. The tree of life and the place of bacteria in it
        7. Untitled SECTION
    1. Untitled BODY
      1. 3. The genome: how much DNA?
        1. 3.1. The first genome sequences
        2. 3.2. The first bacterial genomes: minimal genomes for cellular life
        3. 3.3. Minimal genomes in action
        4. 3.4. Genome size and information content
    1. Untitled BODY
      1. 3.5. The fate of a DNA sequence
      2. 3.6. The cost of a DNA sequence
        1. Untitled SECTION
    1. Untitled BODY
      1. 4. The ebb and flow of bacterial genomes
        1. 4.1. Losing DNA
        2. 4.2. Gaining DNA
    1. Untitled BODY
      1. 4.3. Changing DNA
      2. 4.4. The balance among events: gains, losses and mutations
      3. 4.5. The balance among forces: selection and drift
        1. Untitled SECTION
    1. Untitled BODY
      1. 5. Reading and organising the genome
        1. 5.1. Expressing the genome and decision making
        2. 5.2. The transcriptional regulatory network of E. coli
        3. 5.3. Driving the stress response: σS and its competition with σD
        4. 5.4. Managing the costs of horizontally acquired DNA: the ‘genome sentinel’61
    1. 5.5. Evolving regulation
    2. 5.6. Building to read and reading to build
      1. Untitled SECTION
    1. Untitled BODY
      1. Afterword
        1. Untitled SECTION
    1. Untitled BODY
      1. Selected bibliography
        1. Chapter 1
        2. Chapter 2
        3. Chapter 3
        4. Chapter 4
        5. Chapter 5
    1. Untitled BODY
      1. Index
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
      1. Untitled SECTION
    1. Untitled BODY
    1. Untitled BODY
      1. Contents
      2. Landmarks

Images

Images in the EPUB, with their description
Image alt aria-describedby figcaption Location Role
Cover of Bacterial Genomes: Trees and Networks N/A N/A cover.xhtml#epubcfi(/4/2/2) doc-cover
Open Book Publishers logo N/A N/A title.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container004]/8/2) N/A
Creative Commons logo N/A N/A copyright.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container004]/8/2/2[CC-logo]/2) N/A
Open Access logo N/A N/A copyright.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container004]/8/4/2[CP-logo]/2) N/A
A phylogenetic tree illustrating the three domains of life: Bacteria (in purple, the largest cluster with many branches), Archaea (in green, forming a distinct cluster), and Eukarya (in red, forming another distinct cluster). The tree shows evolutionary relationships between organisms within these domains. N/A N/A ch2.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container014]/200/2[Container013]/2) N/A
Diagram showing synteny comparison between H. influenzae and M. genitalium genomes with shared genes connected by coloured lines and their functional classification represented in a bar plot (B). N/A N/A ch3a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/48/2[Container016]/2) N/A
Metabolic pathway map of Candidatus Baumannia cicadellinicola and Candidatus Sulcia muelleri with annotations for key biosynthesis and metabolic processes. N/A N/A ch3a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/80/2[Container017]/2) N/A
Scatter plot illustrating the relationship between log10 genome size and log10 number of genes across diverse taxonomic categories including animals, plants, fungi, and bacteria. N/A N/A ch3a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/120/2[Container018]/2) N/A
Multiple sequence alignment of RPOB and FNR genes with blue shading indicating conserved regions and sequence variation across organisms. N/A N/A ch3a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/134/2[Container019]/2) N/A
Scatter plot showing the correlation between haploid genome size (pg) and total repeat content (%) for various species, with species names annotated on the plot. N/A N/A ch3b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/12/2[Container020]/2) N/A
Heat map displaying the relationship between Log10 effective population size (Ne) and Log10 selection coefficient (-s), with colour scale representing Log10 probability (P). N/A N/A ch3b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container026]/56/2[Container025]/2) N/A
Circular phylogenetic trees comparing relationships between Enterobacteriaceae (panel A), Alphaproteobacteria (panel B), and other bacteria (panel C). Panels illustrate evolutionary divergences and clustering within these groups, with species names labelled at the tips. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/18/2[Container028]/2) N/A
Genomic alignment between Mycobacterium leprae and Mycobacterium tuberculosis, depicted with diagonal red lines representing conserved syntenic regions, while gaps and breaks indicate rearrangements or sequence divergence. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/36/2[Container029]/2) N/A
Phylogenetic tree of Prochlorococcus and Synechococcus lineages with gene gain and loss events annotated along branches. Highlighted is an early genome reduction in Prochlorococcus, with numbers indicating net gene gains and losses. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/52/2[Container030]/2) N/A
Phylogenetic tree of Escherichia coli showing horizontal gene transfer (HGT) events, indicated by pie charts representing IS elements, prophage elements, and genes with unknown or other functions. Nodes are annotated with gene gain and loss values, shown in red and black, respectively. Highlighted branches correspond to E. coli and closely related lineages, with strains labelled according to their phylogenetic groups. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/80/2[Container031]/2) N/A
A phylogenetic tree of Streptomyces and other Actinobacteria (panel A) showing lateral gene transfer (LGT) rates per node, with clades annotated by average number of LGT events per million years. A scatter plot (panel B) correlates LGT rates with branch lengths, showing a negative correlation with R-squared value and fitted regression line. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/90/2[Container032]/2) N/A
Boxplot comparing horizontal gene transfer (HGT) rates of antibiotic resistance genes between and within individuals, across taxonomic levels. Rates are highest between species and genera, gradually decreasing at higher taxonomic levels, with statistical significance indicated by asterisks (*, **, ***). N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/108/2[Container033]/2) N/A
Graph showing GC content variability along a genomic region, with annotated genes of interest, including ctxA and ctxB. Below, the genome's structural features and conserved regions are depicted, highlighting variability and alignment with other genomic sequences. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/118/2[Container034]/2) N/A
Phylogenetic tree depicting cyanobacteria, with marine Synechococcus, Prochlorococcus, and their associated phages. Branch lengths correspond to substitutions per position, and bootstrap support values are indicated for major nodes. Distinct groups, including high-light (HL) and low-light (LL) Prochlorococcus, are highlighted. N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/132/2[Container035]/2) N/A
Bar chart showing the percentage of horizontal gene transfer (HGT) across various bacterial clades. Clades like Bradyrhizobiaceae and Pseudomonas exhibit the highest rates (~100%), while Neisseria shows the lowest (~88%). N/A N/A ch4a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/150/2[Container036]/2) N/A
A 3D graph showing mutual information (MI) in bits on the y-axis for different antibiotics on the x-axis and pan-genome alleles on the z-axis. Peaks correspond to significant mutations associated with resistance genes for antibiotics such as Isoniazid, Rifampicin, Ethambutol, and others. N/A N/A ch4b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/24/2[Container037]/2) N/A
A scatterplot showing the relationship between ethanol (EtOH) tolerance and mutation rates relative to wild type. Red markers represent higher mutation rates and tolerance, while blue markers represent lower rates and tolerance. An inset displays Spearman correlation (r = 0.8787, p = 0.0003). N/A N/A ch4b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/36/2[Container038]/2) N/A
A radial phylogenetic tree with concentric circles indicating gene family dynamics: reduction, expansion, loss, and gain. Taxonomic groups such as Actinobacteria, Firmicutes, and Proteobacteria are annotated, with circles representing events and their sizes indicating frequency. N/A N/A ch4b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/66/2[Container039]/2) N/A
Two scatterplots: (A) shows the number of genes (log scale) vs. dN/dS ratio with individual points and error bars, and (B) shows the number of genes vs. effective population size (Ne) with a red regression line indicating a positive correlation. N/A N/A ch4b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/92/2[Container040]/2) N/A
A schematic of restriction-modification systems in bacteria. (B) shows a scatterplot of sequence identity (%) for methyltransferase (MT) vs. restriction enzyme (RE) with a Spearman correlation (? = 0.88). (C) Density plots indicate the degree of conservation across systems. N/A N/A ch4b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container042]/112/2[Container041]/2) N/A
RNA polymerase holoenzyme formation: schematic showing core enzyme, sigma factor, and promoter interaction during transcription initiation.","A two-part diagram showing RNA polymerase holoenzyme assembly. The core enzyme combines with a sigma factor, targeting a promoter site with specific sequences, initiating transcription by interacting with -35 and -10 elements. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/16/2[Container044]/2) N/A
A line graph showing AT content percentages across different genomic positions. Three curves represent relaxation-induced, relaxation-repressed, and non-SSG states, with noticeable AT-content variations around the centre position. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/28/2[Container045]/2) N/A
Repressor mechanisms: illustrations of steric hindrance and DNA looping blocking RNA polymerase, and activators aiding transcription via structural changes.","Illustrations detailing transcriptional repression and activation. Repressors block RNA polymerase via steric hindrance or DNA looping, while activators aid transcription by modifying DNA conformation or directly interacting with polymerase. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/42/2[Container046]/2) N/A
A network graph highlighting interactions among transcription factors and genes. Key nodes, CRP and H-NS, are prominently labelled, illustrating their roles as hubs in a densely interconnected network of regulatory interactions. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/58/2[Container047]/2) N/A
A circular diagram depicting sigma factor regulons and their overlaps. Each regulon is represented by a circle, with connections illustrating interactions or shared gene targets among different sigma factors. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/94/2[Container048]/2) N/A
A schematic diagram (panel A) explaining the interactions between sigma factors, RNA polymerase, and regulatory elements. Panels B and C show bar graphs comparing transcription rates across different experimental conditions for Es70 and Es38. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/112/2[Container049]/2) N/A
Two line graphs showing gene enrichment levels across genome coordinates. Panel A highlights SPI-1-related enrichment, while panel B focuses on SPI-2 regions, with key genes annotated below the enrichment curves. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/126/2[Container050]/2) N/A
A series of timeline-like visualisations (panel A) tracking mutation dynamics across ?hns lineages over 30 days. Panel B shows genome coverage data on a log2 scale, highlighting variations in genome regions affected by mutations. N/A N/A ch5a.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/146/2[Container051]/2) N/A
A 3D structural model (panel A) of RNA polymerase subunits RpoB and RpoC, with mutation sites marked. Bar graphs (panels B and C) show the percentage of mutated positions at varying distances from the enzyme's active site for RpoB and RpoC. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/10/2[Container052]/2) N/A
Two line graphs comparing microarray similarity (Pearson r) for predicted operon pairs, true regulons, and random pairs in Escherichia coli K12 (A) and Bacillus subtilis (B). Trends show distinct distribution patterns of regulatory gene relationships. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/42/2[Container053]/2) N/A
A conceptual diagram illustrating the evolution of transcriptional regulatory networks (TRNs) in bacterial populations under varying environmental pressures. The scheme highlights the interplay between conservation, diversity, and mutations in regulatory elements. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/52/2[Container054]/2) N/A
A collection of pie charts illustrating types of transcriptional regulators, their evolutionary histories, duplication events, and types of horizontal gene transfer (HGT). Key insights include the predominance of putative regulators and the role of HGT in shaping regulatory networks. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/66/2[Container055]/2) N/A
A schematic representation of transcriptional activity. The RNA polymerase core enzyme unwinds upstream DNA, creating negatively-supercoiled regions, and overwinds downstream DNA into positively-supercoiled regions, with barriers preventing diffusion of these supercoils. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/94/2[Container056]/2) N/A
Multiple boxplots alongside a circular bacterial genomic map. Analysis shows the enrichment of genes and correlations for functional categories, origin and terminus bins, and horizontally acquired genes, with p-value distributions and residual correlations. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/112/2[Container057]/2) N/A
A graph displaying density curves for inter-replicon distances on bacterial chromosomes, overlaid with a circular genomic map. The bar chart indicates a significantly higher proportion of close inter-replicon genes compared to random expectation. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/122/2[Container058]/2) N/A
Comparative scatterplot highlighting inverted repeat pairs within and between replicons. A boxplot illustrates the symmetry scores, showing that observed inter-replicon repeats have higher symmetry compared to randomised data. N/A N/A ch5b.xhtml#epubcfi(/4[Seshasayee-0446]/2[Container060]/144/2[Container059]/2) N/A
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Back cover of Bacterial Genomes: Trees and Networks N/A N/A back-cover.xhtml#epubcfi(/4/2/2) N/A