Duplications and Turnover in Plant Genomes
Cytologists have long documented differences in chromosome number and organization among plants, but the truly dynamic nature of plant genome evolution is only becoming apparent with fully sequenced and assembled genomes. A major result of these new data
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Michael S. Barker, Gregory J. Baute, and Shao-Lun Liu
Contents
11.1
11.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
11.2
Frequency and Sources of Duplications in Plant Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 Small-Scale Duplications: Segmental Duplication . . . . . . 157 Large-Scale Duplications: Polyploidy . . . . . . . . . . . . . . . . . . . 158
11.2.1 11.2.2 11.3 11.3.1 11.3.2 11.3.3 11.3.4 11.3.5 11.4 11.4.1
Differential Fates of Duplicated Genes in Plant Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Introduction and Nonfunctionalization . . . . . . . . . . . . . . . . . . Neofunctionalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Subfunctionalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Frequency of Subfunctionalization and Neofunctionalization on a Genome-Wide Scale . . . . Gene Dosage Balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
158 158 159 160 161 163
Duplication, Turnover, and Re-organization of Plant Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 Re-organization of Polyploid Plant Genomes . . . . . . . . . . . 166
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Cytologists have long documented differences in chromosome number and organization among plants, but the truly dynamic nature of plant genome evolution is only becoming apparent with fully sequenced and assembled genomes. A major result of these new data is that duplication—of single genes, chromosomes, and whole genomes—is a major force in the evolution of plant genome structure and content. For example, genomic comparisons among divergent animals are able to recover significant signatures of synteny (Hiller et al. 2004), but less divergent flowering plant genomes often demonstrate relatively lower large-scale collinearity because of cycles of polyploidy and diploidization (Tang et al. 2008; Salse et al. 2009). Among individuals and closely related species, copy number variation and changes in gene family size are now recognized as critical sources of genetic variation (Lynch 2007). Duplication and subsequent resolution have yielded a continually changing genome whose elements are constantly turning-over. Although gene and genome duplication has long garnered attention as a potentially important source of evolutionary novelty (Haldane 1933; Stebbins 1950; Ohno 1970), the perspective of a dynamic plant genome fueled by duplication and loss stands in contrast to classical concepts of a largely stable genome. In this chapter we provide an overview of how duplicationdriven genomic turn-over has influenced the evolution and diversity of plant genomes.
11.2
M.S. Barker (*) Department of
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