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Background  Cytoplasmic male sterility (CMS) is a complex phenomenon of plant sterility that can produce non-functional pollen. It is caused by mutation, rearrangement or recombination in the mitochondrial genome. So far, the systematic structural characteristics of the changes in the mitochondrial genome from the maintainer lines to the CMS lines have not been reported in tobacco.    Results  The mitochondrial genomes of the flower buds from both CMS lines and maintainer lines of two  Nicotiana tabacum  cultivars (YY85, sYY85, ZY90, and sZY90) were sequenced using the PacBio and Illumina Hiseq technology, and several findings were produced by comparative analysis based on the  de novo  sequencing. (1) The genomes of the CMS lines were larger, and the different areas were mostly non-coding regions. (2) A large number of rearrangement regions were detected in the CMS lines, with many translocation regions. (3) Thirteen gene clusters were shared by the four mitochondrial genomes, among which two of the gene clusters,  nad2-sdh3  and  nad6-rps4 , were far from each other in the CMS lines. (4) Thirty-three protein-coding genes were conserved in four mitochondrial genomes. However,  nad3  was detected one additional copy in the maintainer lines, and sequence differences were revealed in the four candidate genes ( atp6 ,  cox2 ,  nad2 , and  sdh3 ). Importantly, the evolutionary tree based on the four genes could be used to distinguish the CMS lines and the maintainer lines well for the sequenced mitochondrial genomes of the tobacco. (5) Sixteen CMS-specific open reading frames (ORFs) were found, three of which ( orf91 ,  orf115b , and  orf100 ) were previously reported. (6) The differences in intensity of the protein–protein (PPI) interaction in ATP6 were further verified using the yeast two-hybrid analysis.    Conclusion  Although the majority of the sequences, genes and gene clusters were shared by the mitochondrial genomes of the maintainer and the CMS lines in tobacco, extensive structural variations identified with comprehensive analysis based on the mitochondrial genomes, including rearrangement, gene order, the mitochondrial genome expansion and shrinkage events, might be related to CMS. Additionally, the candidate protein-coding genes and CMS-specific ORFs were closely associated with the CMS mechanism. Verification experiments of one of the candidate genes were performed, and the validity of our research results was supported.

frontiers in genetics

Comparative Analysis of the Mitochondrial Genomes of Nicotiana tabacum: Hints Toward the Key Factors Closely Related to the Cytoplasmic Male Sterility Mechanism