This research aims to investigate the sequence structural differences between the mitochondrial genomes of Gossypium harknessii  sterile cytoplasm (CMS-D2) and  G. trilobum  sterile cytoplasm (CMS-D8), which can establish a foundation for the screening and identification of sterility-related genes. [Methods] Based on the sequencing and assembled results of the mitochondrial genome of D2A and D8A, the Synteny and Rearrangement Identifier (SyRI) software was used to identify structural variations, and recombination variation sites containing collinear and non-collinear regions were visualized with Plotsr. The annotation results of the D8A mitochondrial genome were utilized as a reference, and the amino acid sequences encoded by the open reading frame (ORF) annotated in the D2A mitochondrial genome were used for tblastn comparison to screen out the unique ORF in the D2A mitochondrial genome. Subsequently, polymerase chain reaction (PCR) verification, relative expression level analysis, and bioinformatics analysis were performed. [Results] The mitochondrial genomes of the sterile lines D2A and D8A had two partially overlapped and adjacent inverted translocation regions. Seventeen specific ORF were found in D2A mitochondrial genome, and PCR verified the presence of 6 specific ORF ( orf114e, orf121b-1, orf121b-2, orf138b-2, orf186a-2, and orf317a-2 ) in D2A. The relative expression levels of  orf121b-1  and  orf121b-2  were higher in 3-4 mm flower buds.  orf114e ,  orf186a-2 , and  orf317a-2  have typical transmembrane domains and chimeric gene structures, which are consistent with some characteristics of sterility genes. [Conclusion] Two adjacent inverted translocation regions were identified between the mitochondrial genomes of D2A and D8A. There are six specific ORF in D2A, among which  orf114e ,  orf186a-2 , and  orf317a-2  may be potentially related to sporophytic abortion of CMS-D2.

https://doi.org/10.11963/cs20230044