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

Abstract

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 CMSspecific 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

Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites

“…Thus, the divided subgenome might be more common in plants [ 60 ]. In our study, we confirmed the existence of alternative conformations, and previously, this low-frequency recombination has been reported to have certain effects on plant growth, such as the induction of cytoplasmic male sterility (CMS) [ 61 , 62 ].…”

Fragariamitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions

“…In many seed plants, rearrangement endpoints in organellar genomes are often associated with repeats ranging in size from tens to hundreds of nucleotides (Marechal & Brisson, 2010; Cole et al ., 2018; Mower & Vickrey, 2018; Wu et al ., 2021). Moreover, operons are more tightly maintained in the plastome (Cui et al ., 2006; Wicke et al ., 2011) than in the mitogenome (Liu et al ., 2020; Wang et al ., 2020). Finally, we speculate that, in plant mitogenomes, the rearrangements themselves may be an adaptive phenomenon, potentially serving as a mechanism to prevent runaway size expansion.…”

“…Similarly, repeats of hundreds to thousands of base pairs are abundant in plant mitogenomes (Wynn & Christensen, 2019), whereas in the plastome, repeats > 100 bp are generally absent except for the single large inverted repeat (Mower & Vickrey, 2018). In many seed plants, rearrangement endpoints in organellar genomes are often associated with repeats ranging in size from tens to hundreds of nucleotides (Marechal & Brisson, 2010;Cole et al, 2018;Mower & Vickrey, 2018;Wu et al, 2021) New Phytologist the plastome (Cui et al, 2006;Wicke et al, 2011) than in the mitogenome (Liu et al, 2020;Wang et al, 2020). Finally, we speculate that, in plant mitogenomes, the rearrangements themselves may be an adaptive phenomenon, potentially serving as a mechanism to prevent runaway size expansion.…”

Characterization of the CMS genetic regulation through comparative complete mitochondrial genome sequencing in Nicotiana tabacum

“…sequences, and introns, the third-generation sequencing technology with PacBio library (8-10 kb) was used to sequence both CMS lines and maintainer lines of two Nicotiana cultivars (YY85, sYY85, ZY90, and sZY90), 16 CMS specific ORFs with three (orf91, orf115b, and orf100) ever reported were screened (Wang et al, 2020;Zheng et al, 2018).…”