Superscaffolding of Bread Wheat Survey Sequence Assemblies

The current bread wheat survey sequence assemblies contain over 10 million scaffolds. The large number of scaffolds limits the use of the reference sequence and hinders some of the important marker discovery methods such as bulk segregant analysis. In order to improve the quality of the reference sequence, 17 Illumina-Nextera mate-pair libraries with insert size ranges from 1.4Kb to 40Kb were prepared from a ChineseSpring+7EL line. The libraries were sequenced using Illumina Miseq and Hiseq platforms providing approximately 11-fold sequence coverage (193 Gbp) after processing. The mate-pair data were used to scaffold the survey assembly sequences using SSPACE. The resulting L50 of the assemblies increased by an average of 23-fold (52.5kb). We validated our scaffolding approach by comparing the scaffolded 3B survey assembly against the public 3B pseudo-molecule sequence. The results will be presented. This increase in the continuity should greatly increase the utility of the survey sequence. Additionally, the mate pairs generated here may be used to assist with assembly and/or validation of the current Chinese Spring reference assemblies.