Abstract
BackgroundCytoplasmic 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.ResultsThe 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.ConclusionAlthough 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.
Highlights
As of September 2019, a total of 10,249 mitochondrial genomes, including 9,034, 616, 163, 290 and 146 mitochondrial genomes of animals, fungi, protists, plants, and others, respectively, were collected in the NCBI
Conclusion: the majority of the sequences, genes and gene clusters were shared by the mitochondrial genomes of the maintainer and the Cytoplasmic male sterility (CMS) lines in Mitochondrial Genomes of Nicotiana tabacum 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
This could explain the evolution and expansion of the plant mitochondrial genomes. mtDNA expansion occurred in the maintainer line (ZY100, GenBank: KR780036) and its CMS line of zhongyan100 from NCBI
Summary
As of September 2019, a total of 10,249 mitochondrial genomes, including 9,034, 616, 163, 290 and 146 mitochondrial genomes of animals, fungi, protists, plants, and others, respectively, were collected in the NCBI. The mitochondrial genome data of Solanaceae are mostly generation sequencing data, but third generation sequencing data is lacking. The structure of plant mitochondrial genome is very complex and requires third generation sequencing technology, and third generation sequencing technology is widely used in methylation research, mutation identification and detection of DNA modifications (Xiao et al, 2017, 2018; Liu et al, 2019). The majority of plant mitochondrial genomes are non-coding sequences composed of repeated sequences, gene spacing sequences and introns. 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. 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
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