Comparative Genomic Analysis of Mitochondrial Genomes from Two Lychee Cultivars

Background: Lychee fruits are sweet and juicy, yet mitochondrial genomic data for this species remains scarce, limiting in-depth studies of its genetic and evolutionary characteristics. To address this gap, in this study, the abortive-seeded cultivar ‘Xianjinfeng’ (XJF) and the large-seeded cultivar ‘Xinqiumili’ (XQML) were selected for analysis. Using third-generation sequencing technology, we sequenced, assembled, and annotated their mitochondrial genomes, and compared their structural characteristics and evolutionary relationships. Results: Assembly revealed mitochondrial genome sizes of 579,270 bp for XJF and 579,261 bp for XQML, both with 45.41% GC content. The mitogenomes contain 396 repetitive sequences, including 47 tandem repeats and 165 dispersed repeats, with SSR loci primarily 10–14 bp in length. Each genome encoded 62 genes, comprising 22 tRNAs, 3 rRNAs, and 35 protein-coding genes. Further analysis revealed 15 homologous sequences originating from chloroplasts in both mitochondrial genomes, totaling 12,194 bp (2.11% of the mitochondrial genome). These included 9 tRNA genes, 4 rRNA genes, and partial protein-coding sequences. Additionally, 184 simple sequence repeats (SSRs) were identified in both cultivars, whereas 564 and 563 potential RNA editing sites were predicted by computational tools in XJF and XQML, respectively, indicating subtle genetic differences between the cultivars. This study also analyzed codon usage preferences, nucleotide diversity, and chloroplast-to-mitochondria gene transfer events. Collinearity and comparative genomics results indicate that lychee is closely related to Nephelium lappaceum L. and Xanthoceras sorbifolium Bunge within the Sapindaceae family. Conclusions: In this study, two high-quality lychee mitochondrial genomes were successfully assembled and annotated, enriching the mitochondrial genome resources of Sapindaceae plants and laying a foundation for future lychee phylogenetic and evolutionary studies of closely related species.