Abstract
<title>Abstract</title> <p> Rambutan ( <italic>Nephelium lappaceum</italic> L.) is an economically important tropical fruit tree in the Sapindaceae, phylogenetically allied with lychee and longan. Although its postharvest physiology — particularly mitochondrial activity implicated in pericarp browning — has been extensively investigated at the biochemical level, no complete mitochondrial genome has been reported to date, leaving a conspicuous reference gap that constrains comparative mitogenomic analyses across this clade. Here, we assembled the first complete mitochondrial genome of rambutan from publicly available hybrid sequencing data (Illumina short reads and PacBio long reads) retrieved from the NCBI SRA, using GetOrganelle for organelle-read enrichment followed by Unicycler-based hybrid assembly. The rambutan mitogenome spans 460,603 bp with a GC content of 45.77%, and harbours 39 protein-coding genes (PCGs), 18 tRNA genes and 3 rRNA genes. RNA editing prediction identified 434 sites within PCGs, the majority of which were nonsynonymous. Selection pressure analysis indicated that most PCGs evolve under purifying selection, whereas atp8, rpl5, rpl2 and atp4 exhibited elevated nonsynonymous substitution signals requiring codon model validation. Repeat profiling recovered 243 dispersed repeats, 62 SSRs and 34 tandem repeats, alongside 20.2 kb of chloroplast-to-mitochondrion sequence transfers. Comparative analysis with three representative Sapindaceae species ( <italic>Sapindus mukorossi</italic> , <italic>Xanthoceras sorbifolium</italic> and <italic>Acer yangbiense</italic> ) revealed conserved gene content but pronounced divergence in genome size, repeat architecture and structural organisation. Phylogenetic reconstruction based on conserved mitochondrial PCGs robustly supported a rambutan–lychee sister relationship and refined evolutionary placement within Sapindales, while synteny analysis disclosed extensive gene rearrangements and limited collinearity, consistent with rapid structural evolution against a backdrop of sequence-level conservation. Collectively, this work delivers the first reference-quality mitochondrial genome for rambutan and provides a comparative framework for understanding mitogenome structural evolution in Sapindaceae. The resource lays a foundation for germplasm identification, molecular marker development and downstream functional and evolutionary investigations in tropical fruit trees of this family. </p>