The Evolution of the Genome

T. Ryan Gregory

• Publisher: Academic Press
• Year: 2011
• ISBN:
  9780080470528
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

The Evolution of the Genome provides a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. This includes the evolution of genome size, genomic parasites, gene and ancient genome duplications, polypoidy, comparative genomics, and the implications of these genome-level phenomena for evolutionary theory. In addition to reviewing the current state of knowledge of these fields in an accessible way, the various chapters also provide historical and conceptual background information, highlight the ways in which the critical questions are actually being studied, indicate some important areas for future research, and build bridges across traditional professional and taxonomic boundaries.

The Evolution of the Genome will serve as a critical resource for graduate students, postdoctoral fellows, and established scientists alike who are interested in the issue of genome evolution in the broadest sense.

• Provides detailed, clearly written chapters authored by leading researchers in their respective fields
• Presents a much-needed overview of the historical and theoretical context of the various areas of genomic study
• Creates important links between topics in order to promote integration across subdisciplines, including descriptions of how each subject is actually studied
• Provides information specifically designed to be accessible to established researchers, postdoctoral fellows, and graduate students alike

Part I

The C-value Enigma

Outline

Chapter 1: Genome Size Evolution in Animals

Chapter 2: Genome Size Evolution in Plants

CHAPTER 1

Genome Size Evolution in Animals

T. RYAN GREGORY

Publisher Summary

This chapter focuses on genomic size evolution in animals. There are many ways of studying the evolution of genome. The chapter looks on the examination of genome level phenomena from a variety of different structural and temporal perspectives. The term “genom(e)” was coined by Hans Winkler in 1920 as a portmanteau of gene and chromosome. This canonical etymology has been challenged by Lederberg and McCray, who suggested that Winkler probably merged gene with the generalized suffix-ome (referring to “the entire collectivity of units”), and not -some (“body”) from chromosome. The chapter also emphasizes the view that variation in genome size, which can be generated by a variety of mechanisms, casually influences cell size via effects on nucleus size and cell division rate. These cell-level relationships appear to be ubiquitous, and apply to several different cell types in animals, as well as within plants and protists. Animal genome sizes vary with existing estimates ranging more than 3300-fold, from 0.04 pg in the placozoan Trichoplax adhaerens to 133 pg in the marbled African lungfish Protopterus aethiopicus. As with plants the members of most animal groups have relatively small genomes, with only a few taxa exhibiting large and highly variable DNA contents. The evolution of complete metamorphosis in insects has had a profound impact on the global fauna, and may have involved similar genome size-related requirements.

According to the Oxford English Dictionary, the term “genom(e)” was coined by Hans Winkler in 1920 as a portmanteau of gene and chromosome. This canonical etymology has been challenged by Lederberg and McCray (2001), who suggested that Winkler probably merged gene with the generalized suffix -ome (referring to “the entire collectivity of units”), and not -some (“body”) from chromosome. In either case, Winkler’s intent was to “propose the expression Genom for the haploid chromosome set, which, together with the pertinent protoplasm, specifies the material foundations of the species” (translation as in Lederberg and McCray, 2001). Based on this initial formulation, “genome” can accurately be taken to mean either the complete gene complement (in the sense of “genotype”), or the total DNA amount per haploid chromosome set—but not both simultaneously, as will be seen.

As the diversity of topics covered in this volume shows, there are many ways of studying the evolution of the genome. This relates only partially to the multiple meanings of the term, and instead is based primarily on the examination of genome-level phenomena from a variety of different structural and temporal perspectives. The chapters in this book deal with scales ranging from the level of individual sequences through to entire chromosome sets, and from individual replication events to patterns in deep time. The first two chapters begin at the more holistic end of this spectrum, and describe the bulk properties of genomes as reflected by variation in their sizes. On the surface, this may appear to be a relatively simple issue, but in fact it lies at the heart of one of the longest-running puzzles in genome biology.

WHY SHOULD ANYONE CARE ABOUT GENOME SIZE?

Mass is perhaps the most fundamental property of any physical entity, and is usually much more straightforward to characterize than features like composition, structure, or organization. In this sense, even a basic understanding of the nature of a given genome requires information regarding the amount of DNA contained within it. Genome size, which in eukaryotes has traditionally been given as the mass (in picograms, pg¹) of DNA per haploid nucleus, also sets the context in which analyses of component sequences and organizational characteristics can be interpreted. On these grounds alone, genome size should be considered a crucial aspect of any truly comprehensive program of comparative genomic analysis.

There are also some important practical reasons to be concerned with variation in genome size among eukaryotes. Most obviously, size is a major consideration when choosing targets for complete genome sequencing projects, because DNA amount can be expected to be directly proportional to both the financial and labor costs involved. This applies to all stages of the process, from mapping, to the construction of genomic libraries, to reading the sequence of nucleotides, to reassembling the individual sequenced fragments (see Chapter 9). Indeed, Evans and Gundersen-Rindal (2003) list genome size first among relevant criteria for selecting the next wave of insect species for genome sequencing, along with such parameters as existing gene sequence information, overall biodiversity, and impact on human health and/or agriculture. Targeted genome size measurements of disease vectors and pests are becoming more common as well (e.g., Gregory, 2003a; Panzera et al., 2004).

It is also becoming apparent that smaller-scale genetic studies are influenced by the amount of nuclear DNA. For example, Garner (2002) recently demonstrated a strong negative effect of genome size on the polymerase chain reaction (PCR) amplification potential of microsatellites used in DNA fingerprinting and population genetics studies. Even though the number of microsatellites generally increases with genome size (see later section), this difficulty may arise because more DNA decreases the ratio of target to nontarget DNA and/or dilutes the pool of available primers by nonspecific binding (Garner, 2002). Likewise, the applicability of fingerprinting by amplified fragment length polymorphisms (AFLPs), which is also commonly used in population genetics studies and is based on PCR amplification, can be strongly influenced by genome size (Fay et al., 2005).

However, from the perspective of this chapter, the most important reasons to study genome size are not so pragmatic in nature, but rather have to do with the major biological and evolutionary significance of this topic (see also Chapters 2 and 11).

GENOME SIZE IN ANIMALS: A HISTORICAL PERSPECTIVE

THE DISCOVERY OF DNA

In the mid- to late 1800s (and to an extent, well into the 20th century), proteins were considered the most significant components of cells. Their very name reflects this fact, being derived from the Greek proteios, meaning “of the first importance.” In 1869, while developing techniques to isolate nuclei from white blood cells (which he obtained from pus-filled bandages, a plentiful source of cellular material in the days before antiseptic surgical techniques), 25-year-old Swiss biologist Friedrich Miescher stumbled across a phosphorous-rich substance which, he stated, “cannot belong among any of the protein substances known hitherto” (quoted in Portugal and Cohen, 1977). To this substance he gave the name nucl...

Table of contents

• Cover image
• Title page
• Table of Contents
• LIST OF CONTRIBUTORS
• PREFACE: THE EVOLUTION OF THE EVOLUTION OF THE GENOME
• ABOUT THE EDITOR
• Part I: The C-value Enigma
• Part II: The Evolution of Genomic Parasites
• Part III: Duplications, Duplications…
• Part IV: …And More Duplications
• Part V: Sequence and Structure
• Part VI: The Genome in Evolution
• INDEX