A Compact Multipartite Mitogenome of Clausena lansium ‘Ji Xin’ Highlights Structural Diversity Within Rutaceae

Plant mitochondrial genomes are important for respiration, organelle evolution, and phylogenetic inference, yet remain poorly characterized in Clausena lansium, an economically important Rutaceae fruit tree. Here, we generated the complete mitogenome of C. lansium cultivar ‘Ji Xin’ by integrating Oxford Nanopore and Illumina sequencing data, followed by comparative analyses of repeats, plastid-derived mitochondrial sequences, collinearity, RNA editing, and phylogenetic placement. The mitogenome consisted of two circular molecules totaling 499,621 bp, and encoded 56 genes, including 33 protein-coding genes, 20 tRNA genes, and three rRNA genes. Repeat analysis identified 206 SSRs, 21 tandem repeats, and 35 dispersed repeats, with dispersed repeats strongly enriched on mtChr1. We detected 21 plastid-derived mitochondrial fragments totaling approximately 9.23 kb, indicating limited but detectable plastid-to-mitochondrion DNA transfer. Comparative analyses revealed fragmented synteny between C. lansium and related Sapindales mitogenomes, suggesting lineage-specific structural rearrangement. Based on leaf rRNA-depleted lncRNA sequencing data, 402 candidate C-to-U RNA editing sites were detected in 31 mitochondrial PCGs, most of which were nonsynonymous. Phylogenetic reconstruction placed C. lansium within Rutaceae, close to Limonia and Citrus. These results provide a mitochondrial genomic resource for C. lansium and contribute to understanding mitogenome evolution in Rutaceae.