The pangenome of an agronomically important crop plant Brassica oleracea

Agnieszka A. Golicz, Philipp E. Bayer, Guy C. Barker, Patrick P. Edger, HyeRan Kim, Paula A. Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W. Richard McCombie, Isobel A. P. Parkin, Andrew H. Paterson, J. Chris Pires, Andrew G. Sharpe, Haibao Tang, Graham R. Teakle, Christopher D. Town, Jacqueline Batley and David Edwards ()
Additional contact information
Agnieszka A. Golicz: School of Agriculture and Food Sciences, The University of Queensland
Philipp E. Bayer: School of Plant Biology, The University of Western Australia
Guy C. Barker: School of Life Sciences, The University of Warwick
Patrick P. Edger: Michigan State University
HyeRan Kim: Korea Research Institute of Bioscience & Biotechnology
Paula A. Martinez: School of Agriculture and Food Sciences, The University of Queensland
Chon Kit Kenneth Chan: School of Plant Biology, The University of Western Australia
Anita Severn-Ellis: School of Plant Biology, The University of Western Australia
W. Richard McCombie: Cold Spring Harbor Laboratory
Isobel A. P. Parkin: Agriculture and Agri-Food Canada
Andrew H. Paterson: Plant Genome Mapping Laboratory, University of Georgia
J. Chris Pires: Bond Life Sciences Center, University of Missouri
Andrew G. Sharpe: National Research Council Canada
Haibao Tang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University
Graham R. Teakle: School of Life Sciences, The University of Warwick
Christopher D. Town: J. Craig Venter Institute
Jacqueline Batley: School of Plant Biology, The University of Western Australia
David Edwards: School of Plant Biology, The University of Western Australia

Nature Communications, 2016, vol. 7, issue 1, 1-8

Abstract: Abstract There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

Date: 2016
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DOI: 10.1038/ncomms13390

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