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Background  The  Brassica  B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of  Brassica nigra  was developed and screened with 17 genes from a 222 kb region of  A. thaliana  that had been well characterised in both the  Brassica  A and C genomes.    Results  Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in  B. nigra . The target region is duplicated in  A. thaliana  and six homologous contigs were found in  B. nigra  resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the  Brassica  species divide.    Conclusions  Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid  Brassica  genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage.

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea