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Background  Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the  hau  CMS line and its maintainer line in  B. juneca  ( Brassica juncea ) may help show the origin of the CMS-associated gene  orf288 .    Results  Through next-generation sequencing, the  B. juncea hau  CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene  orf288 , the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line “J163-4” are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the  hau  CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in  hau  CMS lines and its maintainer lines in  B. juncea . The number of repeats larger than 100 bp in the  hau  CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene  orf288  and four other homologous sequences in  Brassicaceae  show that  orf288  was clearly different from  orf263  in  Brassica tournefortii  despite of strong similarity.    Conclusion  The  hau  CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the mechanism of natural CMS in  B. juncea , performing comparative analysis on sequenced mitochondrial genomes in  Brassicas , and uncovering the origin of the  hau  CMS mitotype and structural and evolutionary differences between different mitotypes.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.

bmc genomics

Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288