Impact of transposable elements on genome structure and evolution in bread wheat

Abstract

Background: Transposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid 2 bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genomewide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.Results: TEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetraor the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes. Conclusions:The chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.The genome of bread wheat (Triticum aestivum L.), one of the most important crop species, has also undergone massive TE amplification with over 85% of it being derived from such repeat elements. It is an allohexaploid comprised of three subgenomes (termed A, B, and D) that have diverged from a common ancestor around 2-3 million years ago (according to molecular dating of chloroplast DNA [16]) and hybridized within the last half million years. This led to the formation of a complex, redundant, and allohexaploid genome. These characteristics make the wheat genome by far the largest and most complex genome that has been sequenced and assembled into near complete chromosomes so far. They, however, also make wheat a unique system to study the impact of TE activity on genome structure, function and organization.Previously only one reference sequence quality wheat chromosome was available which we annotated using our automated TE annotation pipeline (CLARITE) [17,18]. However, it was unknown whether the TE content of chromosome 3B was typical of all wheat chromosomes and how TE content varied between the A, B, and D subgenomes. Therefore, in this study, we address the contribution of TEs to wheat genome evolution at a chromosome-wide scale. We report on the comparison of the three A-B-D subgenomes in terms of TE content and proliferation dynamics. We show that, although TEs have been completely reshuffled since A-B-D diverged, their proportions are quite conserved between subgenomes. In addition, the TE landscape in the direct vicinity of genes is very similar between the three subgenomes. Our results strongly suggest that TEs play a role at the structural level, and that the overall chromatin structure is likely under selection pressure. We also identified TE fa...

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

“…The remaining retrieved Fatima insertions were found in the A sub-genome (36 insertions in wild emmer and 33 insertions in bread wheat), or were unmapped (10 insertions in wild emmer and 8 insertions in bread wheat). The B sub-genome specificity of specific Fatima variants in polyploid and diploid wheat species was also reported in previous studies (Salina et al 2011;Yaakov et al 2013;Wicker et al 2018).…”

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

“…As in barley and wheat, rye LTR-RT show clear niche specialisation across genomic compartments 27,28 (fig. M-TRACKSc—f; Note S-REP): RLC_Sabrina , RLG_WHAM , and RLC_Angela are depleted in centromeres and pericentromeres, with the depleted region normally corresponding closely to the LCMs (fig.…”

“…Transposable elements, especially long terminal repeat retrotransposons (LTR-RTs), exert a primary influence on Triticeae genome structure and composition 27-29 . Full-length LTR-RTs represent the same proportion of the total assembly size as exhibited by other major Triticeae reference assemblies (fig.…”

“…Conversely, the size changes that separate rye from wheat and barley are pronounced near telomeres, indicating that genome expansion mechanisms alter over million year timescales and likely contribute to both speciation and ancient hybridisation events 32 . In rye, barley and in each individual wheat subgenome, the TE superfamilies Gypsy (RLG) and Copia (RLC) expanded in the same order 27,28 , but not at the same time: The Gypsy-to-Copia progression was probably set in motion by the LTR-RT composition of a shared ancestral genome, but the rates of expansion and suppression of each superfamily would have depended upon functional and selective peculiarities of each genome or sub-genome (arguments expanded in note S-TEEXP).…”

The impact of transposable elements on the structure, evolution and function of the rice genome

“…This has been confirmed by the many plant genome sequencing projects completed so far (see Chen et al, 2018 for review). For instance, while < 10% of the small genome of the model species Arabidopsis is composed of TEs (AGI, 2000), TEs make up > 90% of the large genome of hexaploid wheat (Wicker et al, 2018). The dynamics of the process through which TEs actually shape plant chromosomes are not so well understood.…”