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Background  The genus  Brassica  mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of  B. napus  and certain detailed interspecific relationships within  Brassica  genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions.    Results  The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of  Brassica  materials, which contain 72 accessions and maximally integrated the known  Brassica  species. The  Brassica  genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around  Brassica  genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from  B. juncea  and  B. carinata , the natural  B. napus  contains three major cytoplasmic haplotypes: the  cam -type which directly inherited from  B. rapa ,  polima -type which is close to  cam -type as a sister, and the mysterious but predominant  nap -type. Certain sparse C-genome wild species might have primarily contributed the  nap -type cytoplasm and the corresponding C subgenome to  B. napus , implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the  B. napus  cytoplasmic male sterile lines (e.g.,  mori  and  nsa ). The genera  Raphanus , Sinapis,  Eruca ,  Moricandia  show a strong parallel evolutional relationships with  Brassica .    Conclusions  The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of  Brassica , which can substantially facilitate the development of novel  Brassica  germplasms.

bmc genomics

Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica