Abstract
BackgroundCytoplasmic 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.ResultsThrough 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.ConclusionThe 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 materialThe online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.
Highlights
Cytoplasmic male sterility (CMS) is important for exploiting heterosis in crop plants, and as a model for investigating nuclear-cytoplasmic interaction
The PCR primers used for the confirmation of contig linkage are listed in Additional file 1 and the mitochondrial DNA extracted from the etiolated seedlings in 7 days of the hau CMS line and its isonuclear maintainer line were used as templates
The B. juncea hau CMS mitochondrial genome was assembled into a single, circularmapping molecule with a size of 247,903 bp and GC content of 45.08%, both of which are close to the median values of other fully sequenced seed plant mitochondrial genomes
Summary
Cytoplasmic male sterility (CMS) is important for exploiting heterosis in crop plants, and as a model for investigating nuclear-cytoplasmic interaction. 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. Numerous studies have shown that cytoplasmic male sterility in plants is associated with aberrant recombination in the mitochondrial genome, which results in the production of chimeric ORFs that are expressed as novel polypeptides [2]. As in other higher plants, all three sequenced mitochondrial genomes had large sizes and distinctive features, including slow evolutionary rates, rapid rearrangement, frequent insertion, complex multipartite structures, specific modes of gene expression, cis- and trans-splicing, RNA editing and the use of universal genetic code [21]. Comparative analysis of the CMS line and its isonuclear maintainer line may help us verify the CMSassociated gene in hau CMS line, and contribute to a better understanding of the plant mitochondrial genome in Brassicas
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