Aegilops species are a reservoir of genetic diversity for agronomic and end-use quality traits as well as resistance to biotic and abiotic stresses for wheat improvement. One of the challenges associated with deploying genes from wild relatives in breeding is the scarcity of high-quality genomic resources for these species. A reference genome of Ae. tauschii (D genome) has been published (Luo et al., 2017), and assemblies of the five Sitopsis genomes have been released (Li et al., 2021). In Canada, the “4D Wheat Project” is developing annotated reference genome assemblies of the remaining diploid Aegilops species.

To date, we have assembled the genomes of four Aegilops sp. viz. Ae. comosa (M), Ae. markgrafii (C), Ae. speltoides (S) and Ae. umbellulata (U), with Ae. uniaristata (N) and Ae. mutica (T) remaining. Here, we describe the workflow for transcriptome analysis and de novo gene annotation. For transcriptome analysis, we utilized the full-length transcriptome data generated using the PacBio single-molecule real-time (SMART) long-read isoform sequencing (Iso-Seq) platform, which allowed for comprehensive analysis of complete splice isoforms, unigenes, and other post-transcriptional events. Further, our in-house genome annotation pipelines are being used to annotate the assembled genomes using both ab initio and evidence-based approaches and tissue-specific RNA-Seq data to provide tissue-specificity for more accurate assessment of the Ageilops transcriptomes.

A better understanding of the gene content and composition will be applied to decipher the origin, phylogeny and genome evolution of Triticum-Aegilops species and to broaden the genetic base of wheat. Additionally, these genomic resources will serve as an initial framework to expand the characterization of tetraploid and hexaploid Aegilops species.