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

Martin Mascher, Gary J. Muehlbauer, Daniel S. Rokhsar, Jarrod Chapman, Jeremy Schmutz, Kerrie Barry, María Muñoz-Amatriaín, Timothy J. Close, Roger P. Wise, Alan H. Schulman, Axel Himmelbach, Klaus F.X. Mayer, Uwe Scholz, Jesse A. Poland, Nils Stein, Robbie Waugh

Research output: Contribution to journalArticlepeer-review

176 Scopus citations

Abstract

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 5.1 Gb 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.

Original languageEnglish (US)
Pages (from-to)718-727
Number of pages10
JournalPlant Journal
Volume76
Issue number4
DOIs
StatePublished - Nov 2013

Keywords

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

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