Academic journal article Genetics

Dynamics and Differential Proliferation of Transposable Elements during the Evolution of the B and A Genomes of Wheat

Academic journal article Genetics

Dynamics and Differential Proliferation of Transposable Elements during the Evolution of the B and A Genomes of Wheat

Article excerpt

ABSTRACT

Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.

GENOMES of higher eukaryotes, and particularly those of plants, vary extensively in size (Bennett and Smith 1976, 1991; Bennett and Leitch 1997, 2005). This is observed not only among distantly related organisms, but also between species belonging to the same family or genus (Chooi 1971; Jones and Brown 1976). More than 90% of genes are conserved in sequenced plant genomes (Bennetzen 2000a; Sasaki et al. 2005; Jaillon et al. 2007) and thus differences in gene content explain only a small fraction of the genome size variation. It is widely accepted that whole-genome duplication by polyploidization (Blanc et al. 2000; Paterson et al. 2004; Adams and Wendel 2005) and differential proliferation of transposable elements (TEs) are the main driving forces of genome size variation. The differential proliferation of TEs results from their transposition (SanMiguel et al. 1996; Bennetzen 2000b, 2002a,b; Kidwell 2002; Bennetzen et al. 2005; Hawkins et al. 2006; Piegu et al. 2006; Zuccolo et al. 2007) as well as the differential efficiency of their removal (Petrov et al. 2000; Petrov 2002a,b; Wendel et al. 2002). Polyploidization and differential proliferation of TEs are particularly obvious in the case of wheat species belonging to the closely related Triticum and Aegilops genera. Rice (Oryza sativa), Brachypodium, and diploid Triticum or Aegilops species underwent the same wholegenome duplications (Adams and Wendel 2005; Salse et al. 2008), but Triticum or Aegilops genomes are >10 times larger (Bennett and Smith 1991), mainly due to proliferation of repetitiveDNA, which represents>80% of the genome size (Smith and Flavell 1975; Vedel and Delseny 1987). Diploid wheat species can differ in their genome sizes by hundreds or even thousands of megabases (Bennett and Smith 1976, 1991; http:// data.kew.org/cvalues/homepage.html). For example, the genome size of Triticum monococcum (6. …

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