Improving the Aegilops tauschii Genome by Comparative Genomics

Aegilops tauschii (goatgrass) is the diploid progenitor of the bread wheat D-genome, providing important evolutionary information about the origin of hexaploid wheat. Recent progress to obtain a complete reference assembly for Ae. tauschii includes a draft assembly released by BGI and an integrated genetic/physical map released by NSF/USDA funded scientists. To build an improved reference assembly with particular focus on the discovery of missing gene space, we are applying new sequence assembly data. More than 100x Illumina coverage of the genome was sequenced and assembled with ALLPATHS-LG at the PSC Blacklight supercomputer to yield a 1.98G scaffolds assembly. Guided by the integrated genetic/physical map, we anchored to seven chromosomes an additional 1322 BGI scaffolds that were previously unanchored, which increased the total number of anchored genes to 81.5%. To investigate missing gene space we analyzed orthologous relationships among annotations of Ae. tauschii, rice, maize, Brachypodium, hexaploid wheat, and sorghum, using orthology data available from Gramene release 42 (Ensembl Genomes 23). Several thousand genes were expected but not found in the BGI assembly/annotation. Many missing genes were successfully predicted using ab initio methods, while others may be absent due to gaps in the assembly. Comparison of the BGI assembly to the CSHL draft assembly indicated that more than a thousand BGI scaffolds can be extended using sequence from the CSHL assembly. Despite these improvements, challenges in generating a high-quality reference remain due to limitations of sequence read length and the highly repetitive nature of the Ae. tauschii genome. This work was funded by NSF #1032105.