title: 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.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.forename: Shuangping
authors.initials: S
authors.lastname: Heng
authors.forename: Chao
authors.initials: C
authors.lastname: Wei
authors.forename: Bing
authors.initials: B
authors.lastname: Jing
authors.forename: Zhengjie
authors.initials: Z
authors.lastname: Wan
authors.forename: Jing
authors.initials: J
authors.lastname: Wen
authors.forename: Bin
authors.initials: B
authors.lastname: Yi
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Ma
authors.forename: Jinxing
authors.initials: J
authors.lastname: Tu
authors.forename: Tingdong
authors.initials: T
authors.lastname: Fu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P,R, China. jxshen@mail.hzau.edu.cn.
authors.forename: Jinxiong
authors.initials: J
authors.lastname: Shen
mesh_terms: D003593:Cytoplasm / Q000378:metabolism; D017343:Genes, Plant; D054629:Genome, Mitochondrial; D008969:Molecular Sequence Data; D009149:Mustard Plant / Q000235:genetics* / Q000502:physiology; D016366:Open Reading Frames; D010802:Phylogeny