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

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

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  • 1Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT, Gatersleben, Germany.

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.

© 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

KEYWORDS:

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

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