Genome sequences ofAegilopsspecies of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

AbstractAegilopsis a close relative of wheat (Triticumspp.), andAegilopsspecies in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies ofAe. longissimaandAe. speltoides. Whole-genome comparative analysis, along with the recently sequencedAe. sharonensisgenome, showed that theAe. longissimaandAe. sharonensisgenomes are highly similar and most closely related to the wheat D subgenome. By contrast, theAe. speltoidesgenome is more closely related to the B subgenome. Haplotype block analysis supported the idea thatAe. speltoidesis the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the threeAegilopsspecies and wheat. Genome-wide analysis of nucleotide-binding site leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential ofAegilopsgenomes for wheat improvement.TeaserGenome sequences of Aegilops species provides a key for efficient exploitation of this rich genetic resource in wheat improvement.