Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

作者：Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Munoz-Amatriain, Maria; Close, Timothy J.; Wise, Roger P.; Schulman, Alan H.; Himmelbach, Axel; Mayer, Klaus F. X.; Scholz, Uwe; Poland, Jesse A.; Stein, Nils^*; Waugh, Robbie

来源：Plant Journal, 2013, 76(4): 718-727.

DOI：10.1111/tpj.12319

• next-generation sequencing
• genome assembly
• genetic mapping
• barley
• Hordeum vulgare
• population sequencing
• technical advance

Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.

• 出版日期2013-11