Brassica Genome

This site hosts Brassica genome databases. Viewers, browsers and downloads are listed below.

Panache graph pangenome viewers

• B. napus Panache viewer: graph pangenome of 10 diverse B. napus whole-genome assemblies.
• B. napus, B. rapa and B. oleracea Panache viewer: graph pangenome of 15 B. rapa, 5 B. oleracea and 9 B. napus publicly available long-read assemblies.

B. oleracea / B. rapa / B. napus pangenome JBrowse

• JBrowse genome browser, including presence/absence variation across the three species.

GBrowse genome browsers

• B. napus: pangenome, cultivar Tapidor, cultivar Darmor-bzh (all including SNPs and functional annotation of genes)
• B. oleracea: pangenome (including SNPs and functional annotation of genes)
• B. rapa: genome browser (including comprehensive annotation of the repeat fraction of the genome)

Downloads

B. napus pangenome

Pangenome before placing de novo contigs into pseudomolecules:

• Novel pangenome contigs (53 MB, md5: c921407e30fc3be3ff95e3b2ce5ed6e5)
• Novel pangenome annotation: GFF3, CDS, peptides
• Whole-pangenome SNPs (Darmor-bzh v8.1 and 52 additional accessions): VCF (760 MB, md5: 1410b96101b4f5071d6f582c93f7364b)
• Placement of pangenome contigs along the Darmor-bzh v8.1 chromosomes
• Whole-pangenome presence/absence table (CSV; 1 = gene present, 0 = gene absent)

Pangenome after placing de novo contigs into pseudomolecules, as used for GBrowse (placement may not be 100% accurate):

• Reference, gene annotation, SNPs, PAV

B. oleracea pangenome

• Pangenome contigs (before placement into pseudomolecules)
• Pangenome after placing contigs into pseudomolecules, as used for GBrowse (placement may not be 100% accurate): reference, annotations, SNPs, PAV

All raw and assembled sequence data is freely available on request.

Analysis tools

• BlastGbrowse: BLAST a query sequence against the Brassica genomes and view hits in the corresponding genome browsers.

Please cite

• Hurgobin B, Golicz AA, Bayer PE, Chan CKK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP et al. (2018) Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnology Journal 16: 1265–1274
• Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al. (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications 7: 13390
• The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035–1039

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The site is supported by funds from the University of Western Australia and the Australian Research Council.