Assembly of whole genome shotgun sequence of Aegilops tauschii, the progenitor of the wheat D genome, with the DeNovoMAGIC software

The aim of this NSF-funded project (IOS-1238231) is to generate a reference sequence for the genome of Aegilops tauschii, the diploid progenitor of the D genome of hexaploid wheat. The genome is over 4Gb in size and contains 80% recently evolved transposable elements, making sequencing exceedingly challenging. A past attempt to sequence the Ae. tauschii genome using a whole genome shotgun (WGS) sequencing approach generated scaffolds with a N50 of 57kb. To generate longer scaffolds, we used the ordered-clone sequencing (OCS) approach as the primary strategy in sequencing the Ae. tauschii genome. Inevitable byproducts of the OCS strategy are gaps between BAC contigs, which can potentially be closed by merging OCS scaffolds with WGS scaffolds. To generate the WGS scaffolds, a shotgun library and mate-paired 2-4kb, 5-7 kb, and 8-10kb libraries were prepared and sequenced with the Illumina HiSeq 2500 next generation sequencing platform at the Roy J. Carver Biotechnology Center / W.M. Keck Center of the University of Illinois, Urbana-Champaign. Reads were assembled by NRGene with their proprietary DeNovoMAGIC^TM software. An assembly with a scaffold N50 of 11.4Mb was produced. Scaffolds were aligned on the Ae. tauschii physical map and BioNano Genome (BNG) map contigs to validate them. A vast majority of WGS scaffolds aligned correctly and only 1.1% were chimeric, indicating that their structure faithfully reflected the Ae. tauschii genome sequence. The merge of the OCS and WGS scaffolds and BNG map contigs generated superscaffolds with a N50 of 32Mb.