Completing Reference Sequence of the Wheat Chromosome Arm 7DS

Bread wheat genome is characterized by high complexity (~17 Gb), polyploidy (AABBDD) and high content of repetitive sequences (>85%), which hampers genome mapping and sequencing. To overcome these obstacles, BAC-by-BAC sequencing strategy based on chromosome-derived physical maps has been adopted by the International Wheat Genome Sequencing Consortium (IWGSC) as the key strategy towards obtaining a reference genome sequence.

In the framework of this effort, we focus on mapping and sequencing of the 7DS chromosome arm. Clones from a 7DS-specific BAC library were fingerprinted and assembled into contigs using FPC and the map assembly was validated by LTC. Integration of the 7DS physical map with that of Aegilops tauschii (D genome progenitor) provided a clue for further merging and landing the contigs on the chromosome. Hitherto, 74% of the physical map length has been anchored to genetic and radiation hybrid maps through 1577 markers.  Our BAC sequencing strategy involved sequencing pools of four non-overlapping clones using the Illumina HiSeq. Pair-end reads thus obtained were assembled using a custom assembler Sassy. Assembling and pool deconvolution were supported by BAC-end sequences and mate-pair data generated for pools of 384 clones. In the resulting assembly, we reached 1.9 scaffolds per BAC clone on average and scaffold N50 of 114 kb. The sequences were automatically annotated by the TriAnnot pipeline and application of wheat 7DS RNAseq data. Moreover, a BioNano genome map has been constructed for the 7DS and used to validate the physical map, anchor and orient BAC contigs, size gaps, deconvolute pools and support sequence scaffolding.