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

Plant J. 2013 Nov;76(4):718-27. doi: 10.1111/tpj.12319. Epub 2013 Oct 10.

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.

Keywords: Hordeum vulgare; barley; genetic mapping; genome assembly; next-generation sequencing; population sequencing; technical advance.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Validation Study

MeSH terms

  • Contig Mapping / methods*
  • Genetics, Population
  • Genome, Plant*
  • Genomics / methods*
  • Hordeum / genetics*
  • Sequence Analysis, DNA*