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Open Access Highly Accessed Research article

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

Zahra-Katy Navabi1, Terry Huebert1, Andrew G Sharpe2, Carmel M O’Neill3, Ian Bancroft3 and Isobel AP Parkin1*

Author Affiliations

1 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada

2 DNA Technologies Laboratory, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada

3 John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

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BMC Genomics 2013, 14:250  doi:10.1186/1471-2164-14-250

Published: 15 April 2013

Abstract

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.

Keywords:
Brassiceae; Brassica nigra; Sequence analyses; Speciation; Genome organization; Collinearity; Divergence time; Inversion