Brassica Genome

This site hosts Brassica genome databases.

Links to available Brassica genome viewer and search are below:

Brassica napus GBrowse Viewers and Search

1. B. napus pangenome GBrowse: including snps and functional annotation of genes.
2. B. napus pangenome GBrowse Fast Keyword Search: Fast search on functional annotation of genes.
3. B. napus cultivar Tapidor genome browser: including snps and functional annotation of genes.
4. B. napus cultivar Darmor genome browser: including snps and functional annotation of genes.

Brassica oleracea GBrowse Viewers and Search

1. B. oleracea pan genome GBrowse: including snps and functional annotation of genes.
2. B. oleracea pan genome GBrowse Fast Keyword Search: Fast search on functional annotation of genes.

Brassica rapa GBrowse Viewers and Search

1. This database is currently being updated

Brassica oleracea/rapa/napus pangenome JBrowse Viewers and Search

1. JBrowse genome browser including presence/absence variation across the three species.
2. KnetMiner instance allowing to compare predicted genes with the Arabidopsis thaliana KnetMiner instance.

Batch Download

1. B. oleracea/rapa/napus pangenome of Bayer et al.:
   • Assembly and annotation
2. B. napus pangenome of Hurgobin et al.:
   • Pangenome - before placing de novo contigs into pseudomolecules
     • Novel pangenome contigs (53MB, md5: c921407e30fc3be3ff95e3b2ce5ed6e5),
     • Novel pangenome annotation, Novel pangenome annotation CDS sequences, Novel pangenome annotation peptide sequences,
     • Whole pangenome (Damor-bzh v8.1 and 52 additional accessions) SNPs download (760MB, md5: 1410b96101b4f5071d6f582c93f7364b)
     • Placement of pangenome contigs along the Darmor-bzh v8.1 chromosomes, Whole pangenome presence/absence table,
     • The Darmor-bzh v8.1 reference genome assembly and annotation is available here
   • Pangenome - after placing de novo contigs into pseudomolecules (the placement may not be 100% accurate), used for GBrowse
     • GBrowse Pangenome Reference
     • GBrowse Pangenome Annotations, GBrowse Pangenome SNPs
     • GBrowse Pangenome PAV
3. B. oleracea pangenome of Golicz et al.:
   • Pangenome - before placing de novo contigs into pseudomolecules
     • Pangenome contigs,
     • Pangenome annotation, Pangenome annotation CDS sequences, Pangenome annotation peptide sequences,
     • Placement of pangenome contigs along the TO1000 chromosomes, PAVs in vcf format,
     • SNPs, SNPs in vcf format,
     • List of TE related genes
   • Pangenome - after placing de novo contigs into pseudomolecules (the placement may not be 100% accurate), used for GBrowse
     • GBrowse Pangenome Reference
     • GBrowse Pangenome Annotations, GBrowse Pangenome SNPs
     • GBrowse Pangenome PAV

Analysis Tools

BlastGbrowse: A sequence similarity search portal for blasting a query sequence to the Brassica genomes and conveniently viewing hits in the corresponding Genome Browsers.

Illumina paired read sequence data for several Brassica species, wild relatives and pathogens is available at TAGdb [2].

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

Please cite

• Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Hurgobin, B., Golicz, A.A., Bayer, P.E., Chan, C.K.K., Tirnaz, S., Dolatabadian, A., Schiessl, S.V., Samans, B., Montenegro, J.D. and Parkin, I.A. Plant biotechnology journal 2018, 16, 1265-1274.
• The pangenome of an agronomically important crop plant Brassica oleracea. Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al. Nature Communications 2016, 7:13390
• The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035-1040
• Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19

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