The pangenome of an agronomically important crop plant Brassica oleracea.
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.
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
Agnieszka A
AA
Golicz
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
Philipp E
0000-0001-8530-3067
PE
Bayer
School of Life Sciences, The University of Warwick, Warwick CV35 9EF, UK.
Guy C
GC
Barker
Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA.
Patrick P
PP
Edger
Korea Research Institute of Bioscience &Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
HyeRan
H
Kim
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
Paula A
PA
Martinez
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
Chon Kit Kenneth
0000-0003-0413-6397
CK
Chan
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
Anita
A
Severn-Ellis
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
W Richard
WR
McCombie
Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, Canada S7N0X2.
Isobel A P
IA
Parkin
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
Andrew H
AH
Paterson
Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA.
J Chris
JC
Pires
National Research Council Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N0W9.
Andrew G
AG
Sharpe
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.
Haibao
0000-0002-3460-8570
H
Tang
School of Life Sciences, The University of Warwick, Warwick CV35 9EF, UK.
Graham R
GR
Teakle
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.
Christopher D
CD
Town
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
Jacqueline
J
Batley
School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
David
0000-0001-7599-6760
D
Edwards
D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018556:Crops, Agricultural / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
D010940:Plant Proteins