First complete mitochondrial genome of star fruit (Averrhoa carambola L.): assembly, comparative analysis, and phylogenetic placement

Abstract Background Averrhoa carambola L. belonging to the family Oxalidaceae of the order Oxalidales, is a commercially valuable fruit tree extensively grown in tropical and subtropical regions. However, its mitochondrial genome remains uncharacterized. Results In this study, we report the first complete assembly and comprehensive characterization of the A. carambola mitochondrial genome, providing an essential genomic resource for evolutionary and functional studies. The assembled mitochondrial genome is a circular, double-stranded DNA molecule of 421,040 bp with a GC content of 44.56%. It contains 39 protein-coding genes and exhibits a pronounced A/T bias in codon usage. We identified 163 simple sequence repeats (SSRs), 448 long repetitive sequences (≥ 30 bp), and 32 chloroplast-derived DNA fragments. C-to-U RNA editing was the predominant type, with 567 predicted editing sites, mainly concentrated in the nad4 gene. Comparative collinearity analysis revealed extensive structural rearrangements relative to related species, and phylogenomic analysis robustly placed A. carambola within the order Oxalidales. Conclusions These findings significantly expand the available mitochondrial genomic resources for Oxalidales and provide a foundational framework for phylogenetic inference, germplasm authentication, and molecular breeding of A. carambola .