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

Ruyi Wang; Xunhui Cai; Shengnan Hu; Ying Li; Yanjun Fan; Siqiao Tan; Qiyuan Liu; Wei Zhou

doi:10.3389/fgene.2020.00257

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

Front Genet. 2020 Mar 20:11:257. doi: 10.3389/fgene.2020.00257. eCollection 2020.

Authors

Ruyi Wang^{1

2}, Xunhui Cai³, Shengnan Hu^{1

2}, Ying Li^{1

2}, Yanjun Fan^{1

2}, Siqiao Tan^{1

4}, Qiyuan Liu⁵, Wei Zhou^{1

2}

Affiliations

¹ Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Changsha, China.
² Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China.
³ School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, China.
⁴ Hunan Engineer Research Center for Information Technology in Agriculture, Changsha, China.
⁵ Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China.

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 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.

Keywords: Nicotiana tabacum; comparative analysis; cytoplasmic male sterility; mitochondrial genome; rearrangement.