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Nat Commun. 2016 Nov 11;7:13390. doi: 10.1038/ncomms13390.

The pangenome of an agronomically important crop plant Brassica oleracea.

Author information

1
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
2
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
3
School of Life Sciences, The University of Warwick, Warwick CV35 9EF, UK.
4
Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA.
5
Korea Research Institute of Bioscience &Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
6
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
7
Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, Canada S7N0X2.
8
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
9
Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA.
10
National Research Council Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N0W9.
11
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, Fuzhou, Fujian 350002, China.
12
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.

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.

PMID:
27834372
PMCID:
PMC5114598
DOI:
10.1038/ncomms13390
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

W.R.M. has participated in Illumina-sponsored meetings over the past 4 years and has received travel reimbursement and an honorarium for presenting at these events. Illumina had no role in decisions relating to the study/work to be published, data collection, analysis of data and the decision to publish. W.R.M. has participated in Pacific Biosciences-sponsored meetings over the past 3 years and received travel reimbursement for presenting at these events. W.R.M. is a founder and shared holder of Orion Genomics, which focuses on plant genomics and cancer genetics. W.R.M. is an SAB member for RainDance Technologies, Inc. The remaining authors declare no competing financial interests.

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