Phylogenetic Insights Into the Pace and Pattern of Plant Genome Size Evolution

Abstract

It has long been known that organismal complexity is poorly correlated with genome size and that tremendous variation in DNA content exists within many groups of organisms. This diversity has generated considerable interest in: (1) the identity and relative impact of sequences responsible for genome size variation, and (2) the suite of internal mechanisms and external evolutionary forces that collectively are responsible for the observed diversity. Genome size in any given taxon reflects the net effects of multiple mechanisms of DNA expansion and contraction, which by virtue of their complexity and temporal juxtaposition, may be challenging to tease apart into their constituent contributions. Here we review our current understanding of genome size variation in plants and the spectrum of mechanisms thought to be responsible for this variation. We present a synopsis of the insights into the mechanisms and pace of genome size change that are uniquely facilitated by a phylogenetic perspective, particularly among closely related species. We also highlight recent studies in diverse angiosperm groups where comparative genomic approaches have yielded general insights into the myriad mechanisms responsible for much of the observed genome size variation, most prominently the contribution of transposable elements (TEs). Finally, we draw attention to the possibility of divergence in the relative importance of different mechanisms of genome size evolution during cladogenesis.

Testing for the Footprint of Sexually Antagonistic Polymorphisms in the Pseudoautosomal Region of a Plant Sex Chromosome Pair

“…For example, X chromosomes in mammals and plants have a lower recombination frequency than the autosomes, because X chromosomes recombine only in females, and, in mammals and papaya, this chromosome has a detectably higher repetitive content than the genome-wide average (reviewed in Bergero et al 2008). Transposable element heterozygosity is known to reduce recombination in maize (Dooner and Martinez-Férez 1997;Fu et al 2002;Dooner and He 2008), and transposable elements are abundant in S. latifolia (Cermak et al 2008;Macas et al 2008), whose haploid genome size is similar to that of maize (Grover et al 2008). File S1…”

Recent Insights into Mechanisms of Genome Size Change in Plants

“…Repetitive elements, it was learned, and primarily LTR-retrotransposons in the case of plant genomes, could achieve surprisingly high copy numbers, by themselves accounting for half or more of the genome for species having "large" genomes [4]. Many subsequent studies have demonstrated that the fraction and composition of the genome occupied by these sequences reflects, mechanistically, the antagonistic effects of insertion, due primarily to transposable element (TE) proliferation, and deletion, primarily mediated by unequal intrastrand homologous recombination (i.e., recombination between directly repeated sequences, such as the LTRs of single or adjacent retrotransposons) and illegitimate recombination (i.e., RecA independent recombination capable of deleting sequence intervening regions of microhomology) [5][6][7]. To generate the extraordinary range in extant angiosperm genome sizes, it has been reasoned, the magnitude of these mechanisms must also vary among species.…”

“…Our understanding of the mechanisms responsible for genome size evolution has vastly improved over the past decade, with a number of reviews devoted to the patterns exhibited by these mechanisms among a variety of species [5,6,76,77]. Less discussed and only more recently addressed are the multiple factors that influence insertional and deletional processes as well as their context-dependent interactions.…”

The history and disposition of transposable elements in polyploidGossypium

“…The LTR retrotransposon subfamily, which includes Ty1-copia and Ty3-gypsy elements, represents the most widespread and abundant type of TEs in plants. The differential success of these elements among plant species has been recognized as a major influence in plant genome size variation, together with genomewide duplications through polyploidy (Grover et al 2008;Hawkins et al 2006Hawkins et al , 2008Hawkins et al , 2009Piegu et al 2006). The non-LTR retrotransposon subfamily, which includes long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), is less represented in plants (Hawkins et al 2006;Noma et al 1999;Le et al 2000;Turcotte et al 2001), in contrast to its prominence in mammalian genomes (Lander et al 2001;Venter et al 2001).…”