The evolution of plant genomes — scaling up from a population perspective

Plant genomes exhibit tremendous diversity in both their size and structure, with genome sizes across land plants ranging over two to three orders of magnitude and significant variation in structural organization was observed across species (EA Kellogg, JL Bennetzen, The evolution of nuclear genome structure in seed plants, Am J Bot 2004, 91:1709–1725). Five plant genomes are now either completely sequenced or in the draft stage; the grape (O Jaillon et al., The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature 2007, 449:463–467) and papaya (R Ming et al., The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus), Nature 2008, 452:991–997) whole genome sequences were reported most recently. Moreover, sequencing of 41 additional genomes is in progress. There is now an emerging consensus that understanding genome evolution requires consideration of the population genetics of genome diversification, and that description of evolutionary forces at the level of populations and within species can help identify the features that led to plant genome diversity (M Lynch, JS Conery, The origins of genome complexity, Science 2003, 302:1401–1404). In this review we focus on advances in our understanding of the mechanisms that drive the diversification of genomes. In particular, we look at the extent to which demographic features such as effective population size changes within species can drive genome evolution, discuss population genetic models of genome diversification associated with transposable element (TE) mobilization, and describe recent studies on the evolution of gene families.