Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China

Sapindus mukorossi is a species of great value in the oil, cosmetic and pharmaceutical industries. However, there have been little progress in industrialization development of S. mukorossi for a long time due to lacking genomics resources and fuzzy genetic relationships. In this study, the S. mukorossi mitochondrial genome was sequenced and compared with other Sapindales for the first time. The genome organization, gene number, type, repeat sequences were compared, and a phylogenetic tree was also constructed. The S. mukorossi mitogenome is circular and 602,121 bp in length with 36 protein-coding genes (PCGs), 18 tRNA genes, 3 rRNA genes, and 13 protein-coding genes (PCGs) contain introns. In the entire mitogenome, AT content (54.16%) was slightly higher than GC content (45.84%). RNA-editing sites analysis identified 487 RNA editing sites in the PCG region, and all sites were nonsynonymous. Gene selection pressure analysis showed that most PCGs were purifying selection genes, and only three PCGs (nad6, ccmB, and ccmFN) were positive selection genes. Among six Sapindales species examined, S. mukorossi mitogenome host the highest proportion of repetitive regions, in which transposable elements (TEs) comprised the largest (7.50%). Mitogenomic synteny analysis revealed several gene rearrangements and seldom shared DNA among Sapindales mitogenomes. Further comparative analysis indicated large variation and frequent gene transfer in plants. This study shows great variation among Sapindales mitogenomes and is of great importance to the improved variety breeding, variety identification and development of genetic resources of S. mukorossi.