The pangenome of an agronomically important crop plant Brassica oleracea.

Agnieszka A Golicz,Graham R Teakle,Patrick P Edger,Guy C Barker,Paula A Martinez,Haibao Tang,Hyeran Kim,Isobel A P Parkin,David Edwards,Andrew H Paterson,Christopher D Town,Chon Kit Kenneth Chan,J Chris Pires,Philipp E Bayer,Andrew G Sharpe,Anita Severn-Ellis,W Richard Mccombie,Jacqueline Batley

doi:10.1038/ncomms13390

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.

Highlights

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
While two reference genomes of B. oleracea are available[1,2], a reference sequence cannot capture the entire gene content of a species owing to structural variants, namely the presence/absence variants (PAVs) and copy number variants[3,4,5,6]
Several of the variable genes are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis, suggesting that PAVs may be important for the breeding of improved Brassica crops

Summary

Introduction

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. 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. While two reference genomes of B. oleracea are available[1,2], a reference sequence cannot capture the entire gene content of a species owing to structural variants, namely the presence/absence variants (PAVs) and copy number variants[3,4,5,6]. Several of the variable genes are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis, suggesting that PAVs may be important for the breeding of improved Brassica crops

Methods

Results

Conclusion