Annotation of the 4.1 Gb Aegilops tauschii Reference Genome Sequence

Seven pseudomolecules, corresponding to the seven chromosomes of Aegilops tauschii, the D-genome donor to bread wheat, have been generated under NSF project IOS-1238231.  The pseudomolecules were produced by combining information from assemblies of MiSeq data from pools of overlapping BAC clones selected from the Ae. tauschii minimum tiling path, a NRGene assembly based on HiSeq whole genome shotgun data and whole genome BioNano optical maps. Repeat annotation included de novo and homology-based identification of long terminal repeat (LTR) retrotransposons, short interspersed nuclear elements (SINEs), miniature inverted-repeat transposable elements (MITEs), and homology-based identification of other DNA elements, Helitrons and long interspersed nuclear elements (LINEs).  Approximately 80% of the genome consists of transposable elements, the vast majority of which are LTR retrotransposons.  Most of these elements inserted in the Ae. tauschii genome in the past 4 million years. Clustering of intact elements showed that many of the low-copy-elements belonged to previously unidentified families.  A preliminary de novo and homology-based annotation of genes in the repeat-masked Ae. tauschii sequence identified 33,826 high confidence genes.  This number is very similar to the number of genes annotated in the D genome of hexaploid wheat. About 90% of the high confidence genes annotated in the wheat and Ae. tauschii D genomes overlapped, suggesting that the total number of genes in the Ae. tauschii genome might be close to 37,000.