Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 3, 2006
Briefings in Functional Genomics and Proteomics 2006 4(4):377-378; doi:10.1093/bfgp/eli008
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Book Review |
The Evolution of the Genome
Edited by T. Ryan Gregory
Elsevier Academic Press, Inc., London, UK; 2005; ISBN 0-12-301463-8; 768 pp.; £39.99; Hardback. The Evolution of the Genome is an ambitious project that aims to compress a wealth of information about all kinds of genomes, and combine this with a perspective on how genomes evolve. It is easy for volumes such as this to fall into the trap of becoming little more than an almanac of useful facts and figures and whilst this is something that the editor is amply qualified to do, the resulting tome is in fact a surprisingly interesting read, mixing evolutionary theory and conundrums, with insights into some of the mechanisms of genome change.
The book is split into five roughly symmetrical parts, each with two chapters, with a final section, consisting essentially of a discussion of evolutionary theory, a concept that is generally considered unifying, even if debate continues over the details. In all the parts, the breadth and depth of each section is well balanced, with the odd slightly eccentric choice of focus, and the authors are all well respected in their fields. The book covers both plant and animal, simple and complex and examines genome change on both the macro- and micro-evolutionary scale.
Part 1 contains two chapters, one devoted to Genome Size Evolution in Animals, the second to the same topic in plants. These chapters are by definition rather descriptive and centred on the C-value Paradox (Enigma), a phenomenon that both baffled and surprised biologists before the advent of large-scale genome sequencing, and which still holds a number of mysteries. The editor and author of the first chapter, T. Ryan Gregory, also maintains an extremely informative database of genome sizes (www.genomesize.com), which contains a large collection of C-values (genome sizes, measured in picograms) and data from this is used to demonstrate the tremendous range of genome sizes, even for animals that have essentially the same number of genes. The second chapter, by Michael Bennett and Ilia Leitch, basically runs in parallel with the first, echoing some of the topics covered by Gregory. Of interest in this section is a description of Mechanisms of Genome Size Change (which could also be titled ‘Mechanisms that give rise to Genome Variation’), which outlines both minor (as in single base) and major (e.g. chromosomal) events in the life (or death) of a genome.
The second section focuses on some of the more major contributors to genome evolution, genomic parasites. Margaret Kidwell discusses the rise of transposable elements (TEs) from a historical perspective and explains how different classes of elements are identified and characterized. A description of the utility of TEs is provided, demonstrating their extensive use as molecular tools for cloning, mutagenesis and gene targeting. Chapter 4 discusses the occurrence of a rather less well-known phenomenon, at least outside the plant world, that of B chromosomes. They originate from ‘A’ chromosomes, but are generally dispensable and consequently only appear in individuals rather than the population as a whole. They are highly heterogeneous in nature and lack regular meiotic behaviour. The B chromosomes are known to be widespread in both monocots and dicots, but are also well represented in animals, in particular insects. Whether these chromosomes are true genomic parasites is still under debate, but given their dynamic relationship with their host, they are likely to contribute, at least at the level of recombination, to genome evolution.
Section 3 describes the major effect that Gene (chapter 5) and Genome (chapter 6) duplications have had on evolution. Gene duplication can occur in a variety of different ways. Local, tandem duplications can lead to enormous arrays of duplicate genes. Duplication followed by transposition results in copies of genes in totally different locations. Segmental duplications can lead to regions containing any number of genes being duplicated. Messenger RNA copies can also be reverse transcribed back into the genome giving rise to intronless gene copies or pseudogenes. Whatever the mechanism, there may be a requirement for gene copies to define a new, or subfunction in order that they are retained as active genes. This is discussed in some detail here. In chapter 6, Yves Van de Peer and Axel Meyer move up a scale to discuss the impact of large scale Gene and Ancient Genome Duplications on the shaping of modern genomes. The authors start by explaining how large-scale duplications are tracked and identified in genomes, and then look at the evidence for these major events throughout evolution. There is now general (although not universal) agreement that at least two rounds of ‘whole’-genome duplication occurred early in the chordate lineage, but their exact timing is the subject of much debate. Furthermore, teleost fish have undergone a further, third duplication event more recently. These events give rise to a huge number of potential new genes, of which a certain percentage will be retained. Once again, the maintenance of duplicated genes is briefly discussed.
The fourth section, a logical extension of chapter 6, describes polyploidy events and states in first plants, then animals, describing how these states might arise and how they are maintained. Clearly having at least twice the amount of genomic DNA provides both advantages and disadvantages. The authors in this section describe the delicate balance between the two, and how polyploids ‘downsize’ to diploids, a somewhat neglected area of genomics.
The fifth, and last, two chapter section deals with comparative genomics, both in eukaryotes (chapter 9) and prokaryotes (chapter 10). The genome sequencing revolution has resulted in the ‘near’ complete genomes of nearly 200 organisms, many of them prokaryotes, which allows meaningful comparison between both closely related and highly divergent species. This section charts progress in this field and describes the enormous impact that large-scale sequencing has had on the kinds of analyses that are now being carried out routinely.
And so to the final section, The Genome in Evolution, which covers a broad spectrum of subjects associated with evolutionary theory and practice. Inevitably, there are discussions on how the evolution of genomes does, or does not, fit Darwinian theory as well as a hatful of sound bites covering other themes that affect, or are affected by, evolution.
The Evolution of the Genome is a useful reference guide; it covers a selected number of key areas in considerable depth, and makes us aware that there are many other factors that also play a role in genome evolution. I look forward in earnest to Volume 2, if it ever evolves.
Reader in Functional Genomics School of Biological and Chemical Sciences Queen Mary, University of London Mile End Road, London E1 4NS E-mail: g.elgar{at}qmul.ac.uk
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