Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats

Abstract

SummaryTransposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring.Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes.Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions.TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.

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

“…As fully discussed in Senerchia et al . (), quantitative comparisons of genome change levels from a large number of SSAP loci to corresponding levels in random sequences (AFLP) account for possible ambiguities inherent to fingerprint methods (e.g. Petit et al .…”

“…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.…”

Genome reorganization in F 1 hybrids uncovers the role of retrotransposons in reproductive isolation

“…PCR-based techniques generate ambiguities (discussed in e.g. [31,44]), but biases were here taken into consideration, offering reliable insights on the molecular events underlying genome reorganization in F 1 hybrids. In particular, genotyping of equimolar mixes of parental DNA mimicking F 1 hybrids quantified biased amplification, whereas quantitative comparison of LTR-RT insertions (i.e.…”

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

“…Indeed, the repeat distribution of Ae. tauschii 5D chromosome suggests that the modern wheat D genome has undergone an expansion of the specific LTR retroelements coupled with the reduction of the relative contribution of DNA transposons compared to its progenitor20.Since transposable elements are known to have family-specific and species-specific evolutionary trajectories22, which repeat families might have expanded in Tdic5B remains elusive at the time. All repeat annotations with regard to repeat families are given in Supplementary Table 1.…”