Producing a Physical Map and Genome Sequence for Wheat Chromosome Arm 7DS

Specific features of the bread wheat genome, such as its size (17 Gbp), polyploid nature and prevalence of repetitive sequences make whole-genome-sequencing a challenge. NGS technologies, despite rapid progress, are not yet advanced enough to generate a high quality wheat reference sequence using the shotgun approach. Because of this, a BAC-by-BAC sequencing strategy has been adopted by the International Wheat Genome Sequencing Consortium.

As a part of this international effort, we constructed a 7DS-specific BAC library, fingerprinted the clones and assembled BAC contigs using FPC. Integration of the 7DS physical map with whole-genome map of Aegilops tauschii (D genome progenitor) provided a clue for further merging contigs and positioning them on 7DS. Present physical map consists of 931 BAC contigs, covering 95% of the arm and comprising a minimal tiling path (MTP) of 4,608 BAC clones. Around 51% of the contig assembly was anchored to genetic maps using 619 markers. The BAC sequencing strategy involves sequencing 96 pools, each of 4 BACs using the Illumina HiSeq. The resulting pair-end reads are assembled using a custom assembler Sassy. This approach results in 1-7 contigs per clone. Deconvoluting the pools, scaffolding the contigs and assembly validation is performed using whole-genome mate-pair data, 7DS PacBio sequence data and BAC-end sequences of the MTP clones. Assembled BAC sequences will support in silico anchoring the physical map to existing genetic and radiation hybrid maps and a GenomeZipper. The work has been supported by Czech Science Foundation (P501/12/2554), the Australian Research Council (LP110100200) and Australia Awards.