Sequencing the Genome of Aegilops tauschii.

Aegilops tauschii is one of the three diploid progenitors of common (hexaploid) wheat. The size of its genome is between 4 and 5 Gb and a large portion of the genome consists of repeated sequences. The aim of our project funded by the National Science Foundation (http://www.nsf.gov/awardsearch/showAward?AWD_ID=1238231) is to generate a reference-quality sequence of the Ae. tauschii genome to assist in the assembly of the wheat D-genome sequence and to serve as reference for study of wheat genome evolution. We constructed a physical map of the Ae. tauschii genome based on fingerprints of bacterial artificial chromosomes (BACs) and selected BAC clones making up a minimum tiling path (MTP) consisting of 42,822 BAC clones across 3,578 BAC contigs. We combined DNAs of MTP clones, as well as about 2,000 singletons, into pools of eight overlapping BAC clones, indexed each pool, and sequenced them with Illumina’s MiSeq platform. The MiSeq reads were assembled with SOAPdenovo. We also generated 13X whole-genome shotgun sequence coverage with the P6-C4 Pacific Biosciences chemistry and are aiming for 50X genome coverage. We constructed a whole-genome consensus BioNanomap of the Ae. tauschii genome, which is an optical map of genomic DNA molecules aligned and scanned on the BioNano Genomics’ Irys^TM platform. To validate the sequence assembly, sequence scaffolds were aligned against the BioNanomap, and were reordered, reoriented, and edited if discrepancies were encountered. Genes, pseudogenes, and transposable elements (TEs) were annotated. At least 78% of the Ae. tauschii genome consists of TEs; LTR-retroelements represent ~66% of the genome. We discovered many new TE families. The sequence assemblies are publicly available on the project website (http://aegilops.wheat.ucdavis.edu/ATGSP/).