Evolutionary Dynamics of Retrotransposons Assessed by High-Throughput Sequencing in Wild Relatives of Wheat

Abstract

Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.

Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum

“…Though several studies report recent LTR-retrotransposon bursts in related grasses (Piegu et al 2006;Bennetzen et al 2012;Senerchia et al 2013), we did not detect a large amount of recent activity in the Sorghum reference genome. Indeed, very few intact LTR-retrotransposons share 100 % sequence similarity between 5′ to 3′ LTRs (Fig.…”

Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats

“…Comparison of genetic variation around LTR‐RT loci (SSAP) and random sequences (AFLP) exhibited clear patterns of introgression across hybrid zones, but showed discrepant patterns of variation that are matching predictions based on the dynamics of LTR‐RTs in progenitors (Senerchia et al . , ). Quiescent LTR‐RTs such as Egug revealed nonsignificant specific admixture, indicating introgression similar to AFLP sequences (Fig.…”

“…oGenomes of wild wheats contain 80% of interspersed repeats and have been greatly affected by the differential dynamics of specific LTR‐RTs (Senerchia et al . , ). A few LTR‐RTs such as Egug have been reported as quiescent in both A. geniculata and A. triuncialis , and can thus be expected to segregate beyond species boundaries as random sequences.…”

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents

“…tauschii (D). Senerchia et al (2013) suggested that the sequencing of 2.5 % of Aegilops genomes was sufficient to survey genome-wide copies of several abundant TEs, including characteristic families from pericentromeric regions. Our SLAF method surveyed with short reads can thus be applied to abundant TEs of any genome sequencing for identifying and quantifying the TE families within genomes.…”