Never Eat Shredded Wheat – Navigating through Reference and Survey Wheat Assemblies Using Diverse Mate-Pair Libraries

David J. F. Konkin¹, Yifang Tan¹, Ron MacLachlan², Kevin Koh¹, Carling Clarke¹, Janet Condie¹, Jennifer Ens², Krysta Wiebe², Curtis Pozniak² and Andrew G. Sharpe¹

¹National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada, S7N 0W9

²University of Saskatchewan, College of Agriculture, Department of Plant Science, 51 Campus Drive, Saskatoon, Saskatchewan, Canada, S7N 5A8

Long range sequence information is needed during genome assembly to span repetitive sequences and areas with limited sequencing depth. To improve existing wheat survey assemblies, an assembly of chromosome 7EL from Thinopyrum elongatumand to facilitate the assembly of reference sequences, we created 17 long range paired end libraries from a Chinese Spring + 7EL addition line using Illumina Nextera and Lucigen NxSeq approaches.  We modified the Nextera protocol to create in parallel a large number of diverse libraries with tight size distributions that collectively span a large range (1 to 20 kb). We preferentially sequenced the most diverse libraries to greater depth using an Illumina Hiseq 2500 operating in rapid mode (2x150 bp). In total 584 Gbp of raw sequence data was acquired yielding 185 Gbp of useful processed sequence. Here I report the how we have used these sequences to improve to the IWGSC Chinese spring survey sequence, the whole genome shotgun assembly of synthetic hexaploid wheat W7984 and in the reference assembly of chromosome 1A.