*sylviej.cloutier@agr.gc.ca

The Aegilops genus comprises 11 diploid, ten tetraploid and four hexaploid species. Belonging to all three gene pools of wheat, these species represent a largely untapped genetic diversity for its improvement. To create a resource for exploiting this diversity, we sequenced, assembled and annotated the genomes of diploid Aegilops species with the C, M, N, S and U genomes. Sequencing was done using PacBio HiFi and assemblies were scaffolded with Bionano optical maps and genetic maps. Annotation was performed using evidence based IsoSeq and RNASeq data as well as ab initio approaches.

The high-quality assemblies have N50 values ranging from 48 to 665 Mb with BUSCO scores ranging from 97.8 to 98.5. Comparative analyses of genomes revealed chromosome-scale rearrangements across and within species. Using strict criteria, 59-72K high-confidence (HC) genes were identified for each genome. These HC gene estimates exceed previously reported estimates for other Aegilops genome annotations, a likely consequence of the high-quality and depth of the IsoSeq and RNASeq data.

Phylogenetic analysis of the single-copy core genes of all diploid Triticum and Aegilops species assemblies released to date revealed the B-lineage of Ae. speltoides and the D-lineage of all other Aegilops species, including all remaining Sitopsis and the genomes sequenced in our study. The polyploid Aegilops species represent various combinations of the diploid genomes. To understand their evolution, we sequenced them using a combination of technologies.

While having a higher number of scaffolds than the diploid assemblies, these assemblies have N50 values of 116 Mb to 1.4 Gb and BUSCO scores of 94.5-100, which largely suffice to investigate chromosomal rearrangements and transposable element evolution. This comprehensive Aegilops genome assembly database is expected to be a useful resource for broadening the genetic diversity of wheat.