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

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

doi:10.1111/tpj.12319

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.

Highlights

Next-generation sequencing provides the opportunity to rapidly establish gene space assemblies for virtually any species at relatively low cost
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

Summary

Introduction

Next-generation sequencing provides the opportunity to rapidly establish gene space assemblies for virtually any species at relatively low cost. The International Barley Genome Sequencing Consortium reported the development and use of a BAC-based physical map, BAC end sequences, survey sequences of flow-sorted chromosome arms, fully sequenced BAC clones and conserved synteny to fully contextualize only 410 Mb of genomic sequence from the 5.1 Gb barley genome (International Barley Genome Sequencing Consortium, 2012). These genomic resources provide an established path towards a reference sequence by sequencing a minimum tiling path of overlapping BAC clones hierarchically (Feuillet et al, 2012). The reference sequence of a single 1 Gb chromosome of hexaploid wheat (Triticum aestivum) has not been completed 5 years after publication of a physical map (Paux et al, 2008)

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Discussion

Conclusion