Improving the Physical Map and Sequence of the 7DS with a BioNano Map

IWGSC strategy towards obtaining a reference genome sequence is based on chromosome-by-chromosome approach and BAC-by-BAC sequencing clones ordered in physical maps. As a part of this international effort, we focus on mapping and sequencing of the 7DS chromosome arm.

The 7DS physical map, assembled from HICF-fingerprinted clones by FPC and verified by LTC, consists of 912 contigs covering 95% of the arm. Hitherto, 64% of the contig assembly has been landed on the chromosome through 851 markers. The BAC sequencing strategy involved sequencing pools of four non-overlapping MTP clones using the Illumina HiSeq. The resulting pair-end reads were assembled using a custom assembler Sassy. Deconvolution of the pools, scaffolding of the contigs and assembly validation is performed using BAC-end and mate-pair sequences of the MTP clones.

With the aim to support sequence completion and validation, we constructed de novo genome map of the 7DS arm using BioNano IRYS platform. The obtained high-resolution map of a short sequence motif (GCTCTTC) consists of 371 fragments with N50 of 1.3 Mb and covers 92% of the estimated arm length. Anchoring sequence assemblies of MTP BAC clones to the BioNano map helped revealing discrepancies in the sequence assemblies and provided clues for assembly improvement. Moreover, it aided verification of the 7DS physical map, anchoring and scaffolding BAC contigs and sizing gaps. The obtained results suggest that BioNano maps derived from individual wheat chromosomes/arms will become an affordable tool to support sequence assembly and lead to the production of improved pseudomolecules.