Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.

BackgroundTransposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.ResultsThe overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.ConclusionsEven though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1479-0) contains supplementary material, which is available to authorized users.

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

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...

† These authors contributed equally to this work. 15 One Sentence Summary:A phylogeographical study reveals the complex history of wheat genetic diversity through time and space.