Complete mitochondrial genome sequence of Koelreuteria paniculata (Sapindaceae) and comparative analysis within the family Sapindaceae

Koelreuteria paniculata (Sapindaceae) is an economically and culturally important species with ornamental traits, durable wood, and medicinal use. Plant mitochondrial (MT) genomes exhibit complex structures and variations in size. Thus, they provide valuable insights into species identification and evolution. However, the K. paniculat MT genome remains largely understudied. Herein, we report the first complete MT genomic sequence of K. paniculata. The complete circular genome contains 58 unique genes: 32 protein-coding, four ribosomal RNA, and 22 transfer RNA genes. The transfer of a 2,047-bp chloroplast-derived fragment containing rrn16 and trnV-GAC into the MT genome was verified. Additionally, we identified 197 simple sequence repeats and 352 dispersed repeats; the longest repeats spanned 2,084 bp. Codon usage favored A/U-ending codons, a conserved feature in terrestrial plants. Moreover, 468 C-to-U RNA-editing sites were predicted across protein-coding genes (PCGs); nad4 was the most affected. For 25 shared PCGs among Sapindaceae species, the mean Ka/Ks ratio (0.64) indicated purifying selection. Meanwhile, atp8, matR, and nad2 showed positive selection, implying adaptive evolution. Phylogenetic analysis of 28 conserved PCGs placed K. paniculata within Sapindaceae. Dynamic MT rearrangements were observed within this family, elucidating the genome architecture and evolutionary dynamics of K. paniculata. These results provide a basis for future comparative and evolutionary studies.