Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat (Triticum aestivum, BBAADD) is an allohexaploid species originating from two polyploidization events. The progenitors of A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research speculated that Aegilops speltoides was the closest but not the direct ancestor of B subgenome. However, it is unclear whether Ae. speltoides has genomic contributed to the wheat B subgenome, and which chromosome regions are conserved between Ae. speltoides genome and B subgenome. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species [Ae. bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, Ae. speltoides, Ae. mutica (syn. Amblyopyrum muticum), and Triticum dicoccoides], and uncovered their genomic contribution wheat B subgenome. Our results discovered the centromeric regions were especially conserved among Aegilops and Triticum, and identified 0.17 Gb conserved blocks between Ae. speltoides and B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, and revealed the biological characteristics with differentiation patterns of gene expression and collinear relationships between Ae. speltoides and wheat B subgenome. We also discovered expanded genes in Ae. speltoides during its evolution and revealed 789 Ae. speltoides specific genes. These genes could serve as the genetic resources for the improvement of adaptabilities to biotic and abiotic stresses. The newly constructed reference genome and large-scale resequencing data of Sitopsis will provide a valuable genomic resource for wheat genetic improvement and genomic studies.