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Harvesting wheat genomes: Triticum aestivum sequenced by computational force.

Common bread wheat, Triticum aestivum, is the most widely grown of all crops, and the cereal with the highest monetary yield, but unlike other staples has not had a good quality reference genome available to help researchers improve its breeding and yield. This is due to it having one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall haploid size of more than 15 billion bases. Multiple past attempts to assemble the genome have produced assemblies that were well short of the estimated genome size.

Just published in GigaScience, the Zimin & Salzberg labs at Johns Hopkins University report the first near-complete assembly of T. aestivum, utilizing a brute force approach producing deep sequencing coverage from a combination of 7 billion short Illumina reads and 55 million very long Pacific Biosciences reads. The final assembly was 15,344,693,583bp in length and had an N50 contig size of 232,659 bp. The key factor in producing a draft assembly for this exceptionally repetitive genome was the use of very long reads, averaging just under 10,000 bp each, which were required to span the long, ubiquitous repeats. All together, the various assembly steps took 880,000 CPU hours, or just over 100 CPU years. This heavy computational cost was not simply a function of the genome size, but was more critically a function of its repetitiveness. The presence of large numbers of unusually long exact and near-exact repeats means that all of these sequences overlaped each other, leading to a quadratic increase in the number of sequence alignments that an assembler must consider. By using large multi-core computers to run these steps in parallel, these steps took 1.5 months of elapsed (wall clock) time and the peak memory 100(RAM) usage was 1.2 terabytes.

This research will provide an effective resource for the wheat breeding community and has been made publically available without restriction in the NCBI database (accession: PRJNA392179) and in the GigaScience database, GigaDB, in a citable format http://dx.doi.org/10.5524/100356. As one of the winners of the inaugural GigaScience competition and prize track to promote new, cutting edge, research this work was presented in a special session at BGI’s ICG12 conference in Shenzhen.

Read the paper: The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Article source: GigaScience

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