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Genomes 5 cover

Biology

Biology

Genomes 5

Terry A. Brown

An advanced textbook that treats genetics at the level of whole genomes. It explains how genomes are sequenced, assembled and annotated, how they are organized in prokaryotes, eukaryotes and viruses, how genome expression is controlled, and how genomes are replicated, repaired, rearranged and shaped by evolution.

Prerequisites: An introductory genetics course and basic molecular biology covering DNA structure, transcription and translation.

Difficulty Level
Advanced
Academic Level
Undergraduate
genomicsmolecular geneticsgenome expressiondna replicationgenome evolutionTextbook

01 / Reading Guide

Reading Guide

Citation

Brown, T. A. (2023). Genomes 5 (5th ed.). CRC Press.

Chapter Summary

The book has eighteen chapters in four parts and about 548 pages. The publisher states that, as in earlier editions, techniques come first, then genome anatomies, then genome function, and finally genome evolution, and that every chapter ends with short-answer questions and in-depth problems.

Part 1, How Genomes Are Studied (Chapters 1–6): Genomes, Transcriptomes and Proteomes; Studying DNA; Mapping Genomes; Sequencing Genomes; Genome Annotation; Identifying Gene Functions

The opening part introduces the genome, transcriptome and proteome, then turns to methods: working with DNA, mapping, sequencing, annotating genomes and determining gene function. The description says that sequencing and assembly now include long-read sequencing, that annotation emphasizes genome-wide RNA mapping, and that CRISPR-Cas9 and GWAS appear among the methods for determining gene function.

Part 2, Genome Anatomies (Chapters 7–9): Eukaryotic Nuclear Genomes; Genomes of Prokaryotes and Eukaryotic Organelles; Virus Genomes and Mobile Genetic Elements

Three chapters describe the main types of genome: eukaryotic nuclear genomes, prokaryotic genomes together with those of eukaryotic organelles, and viral genomes with mobile genetic elements. The publisher says these chapters rest on the knowledge produced by the techniques of Part 1.

Part 3, How Genomes Are Expressed (Chapters 10–14): Accessing the Genome; The Role of DNA-Protein Interactions in Genome Expression; Transcriptomes; Proteomes; Genome Expression in the Context of Cell and Organism

Expression is treated at the level of the whole genome. According to the description, the emphasis is on genome-wide effects of DNA packaging, epigenome modifications, DNA-binding proteins, non-coding RNAs, regulatory sequences and protein-protein interactions, followed by chapters on the transcriptome and the proteome and on expression in the cell and the organism. The description also mentions examples from metabolomics and systems biology.

Part 4, How Genomes Are Replicated and Evolve (Chapters 15–18): Genome Replication; Recombination and Transposition; Mutations and DNA Repair; How Genomes Evolve

The final part covers replication, recombination and transposition, mutation and repair, and closes with genome evolution. The publisher lists the evolution of the epigenome, the use of genomics in the study of human evolution and the use of population genomics in plant breeding among the topics of the last chapter.

Key Concepts

Part 1: methods (Chapters 1–6)

  • Genome, transcriptome and proteome: the three levels of biological information introduced in Chapter 1.
  • Mapping and sequencing: separate chapters (3 and 4) cover mapping and sequencing, the second with long-read DNA sequencing.
  • Genome annotation and gene function: Chapters 5 and 6, including RNA mapping, CRISPR-Cas9 and GWAS.

Parts 2 and 3: anatomy and expression (Chapters 7–14)

  • Genome anatomies: eukaryotic nuclear, prokaryotic, organelle and viral genomes, with mobile genetic elements.
  • Epigenome and DNA-protein interactions: named in the titles of Chapters 10–11 and in the publisher's description of genome-wide expression control.
  • Transcriptomes and proteomes: treated as separate objects of study in Chapters 12 and 13.

Part 4: replication and evolution (Chapters 15–18)

  • Recombination and transposition: Chapter 16.
  • Mutation and DNA repair: Chapter 17.
  • Genome evolution: Chapter 18.

Critical Analysis

Strengths

  • Clear four-part structure. The publisher highlights a book organized into four parts to aid navigation, and the contents bear this out: methods, then anatomy, then expression, then replication and evolution.
  • Methods before results. Placing mapping, sequencing, annotation and functional methods first lets a reader interpret the later chapters on genome anatomy and expression in terms of how the data were obtained.
  • Whole-organism range. The description states that viruses, bacteria, fungi, plants and animals, including humans and other hominids, are covered, and the contents give organelle and viral genomes their own chapters.
  • Practice built in. Each chapter ends with short-answer questions and in-depth problems, and the publisher counts 546 colour illustrations in about 548 pages. Reviewers quoted on the publisher page call it a great resource for understanding genomes (Ian Gonzales, Yale School of Medicine) and say it describes the expanding field of genomics well (Tony Reynolds, The Biologist).

Limitations

  • Genomics, not classical genetics. The contents have no chapters on Mendelian crosses or population genetics; readers who need those will want a general genetics text first or alongside.
  • Prerequisites are assumed. The site lists an introductory genetics course and basic molecular biology as preparation, and the publisher recommends the book for upper-level courses on genomes and genomics.
  • A fast-moving subject. The publisher stresses references to research from the 2020s, which also means that methods chapters, such as those on sequencing and annotation, will date more quickly than the chapters on replication and repair.

Where It Fits in the Course

Genomes 5 is the genomics-focused text in the genetics list. Genes: A Very Short Introduction and Introducing Genetics: From Mendel to Molecules are first-contact books, the second beginning with Mendel's experiments and chromosomes. Introduction to Genetic Analysis and Principles of Genetics are fuller textbooks that connect classical inheritance with molecular and genomic analysis, and are the usual place to learn crosses, mapping and gene action before reading Brown. Principles of Population Genetics is a separate, theory-oriented text on how allele frequencies change; it complements Chapter 18 on genome evolution but does not substitute for it.

Read Brown after one of the general genetics textbooks, as the second or third genetics course, or alongside a molecular biology text if the course is organized around the genome.

How to Use This Book

It suits students with an introductory genetics course and the basics of DNA structure, transcription and translation, in a course on genomes and genomics.

  • Core: Parts 1 and 2 (Chapters 1–9) in order. They set out the methods and the genome types that the rest of the book assumes.
  • Expression and replication: Part 3 (Chapters 10–14) is best read after a molecular biology course; Chapter 14 pulls the genome-wide view back to the cell and organism. Part 4 (Chapters 15–18) can be taken in order or selectively, with Chapter 18 as a capstone.
  • Selective reading: a course on genome analysis can concentrate on Chapters 2–6 and 18; one on gene regulation can concentrate on Chapters 10–14.
  • Practice: answer the short-answer questions after each chapter first, then attempt the in-depth problems.