Characterization of the complete mitochondrial genome of Rhododendron simsii var. putuoense and its comparative evolutionary analysis

Abstract

Rhododendron simsii var. putuoense is a coastal-endemic plant with significant ecological and genetic resource value. Although its chloroplast genome (cpDNA) was recently characterized, its mitochondrial genome (mtDNA) remains unexplored. Here, we report the first complete assembly and annotation of the R. simsii var. putuoense mtDNA using PacBio HiFi long-read sequencing. The genome sequence is 658,161 bp in length, organized as two subgenomic linear molecules (a major one of 633,105 bp and a minor one of 25,056 bp), and encodes 33 protein-coding genes (PCGs), 26 tRNAs, three rRNAs and 323 ORFs. Repeat analysis revealed a predominance of dispersed repeats (72%), alongside 128 SSRs and 20 tandem repeats. The mtDNA exhibits a strong A/U-ending codon usage bias, with 463 RNA editing sites predicted. Six homologous segments (0.91% of the mtDNA) provide evidence of interorganellar gene transfer (IGT). Notably, pairwise K a / K s analysis revealed an elevated ratio in the matR gene, suggesting at lineage-specific evolutionary dynamics that warrant further site-specific codon model testing. Phylogenetic and synteny analyses further confirmed a close relationship with R. simsii , while revealing structural divergence consistent with ecological specialization. Overall, these findings deepen our understanding of mitochondrial genomic diversity within Rhododendron and establish a genetic framework for conserving lineage-specific resources in this ecologically significant variety.