Comparative mitogenomics of Roscoea alpina and R. purpurea from contrasting elevations reveals mitochondrial genomic differentiation

Abstract

Plant mitochondrial genomes are structurally dynamic and contribute to energy metabolism and stress responses. Comparative mitogenomic analyses of closely related species occupying contrasting elevations can provide insights into mitochondrial genomic differentiation across elevational environments. Using PacBio HiFi reads, we assembled and compared the mitochondrial genomes of the higher-altitude species R. alpina and the lower-altitude species R. purpurea . Both mitochondrial genome assemblies yielded graph-like structures, with R. alpina exhibiting a more complex assembly-graph topology, more dispersed repeats, and extensive evidence of dispersed-repeat-mediated recombination. Despite these structural differences, the two species retained broadly similar core gene complements, codon-usage patterns, and predicted RNA-editing profiles. Among genes represented by multiple annotated copies in both species, 12 had higher annotated copy numbers in R. alpina . Most shared protein-coding genes were highly conserved, whereas nad4 and rps3 each contained two nonsynonymous substitutions between the two species. Genes with higher annotated copy numbers and those showing limited sequence divergence were both annotated into respiratory complex I and mitochondrial translation. These results reveal pronounced differentiation in mitochondrial genome architecture alongside strong conservation of coding characteristics. Both the differences in gene representation and the limited sequence divergence converge on the same functional processes, suggesting a potential link between mitochondrial genomic changes and adaptation to high-altitude environments. We hypothesize that these genomic features may be relevant to the physiological performance of R. alpina in a high-altitude environment.