Comparative Chloroplast and Mitochondrial Genomics of Sorbus L. Sensu Lato: Genome Diversity, Structural Variation, and Phylogeny

Sorbus L. sensu lato represents a taxonomically complex group within Rosaceae, but organelle genome variation remains insufficiently characterized, particularly at the intraspecific level. Here, we assembled the complete mitochondrial genome of S. discolor and 214 complete chloroplast genomes, comprising 71 S. discolor and 143 S. pohuashanensis accessions, and performed comparative and phylogenetic analyses alongside published genomes. The S. discolor mitogenome spanned 372,987 bp and contained 56 genes, representing the smallest genome yet exhibiting the highest number of annotated genes among the six mitogenomes examined; it also possessed the fewest simple and long sequence repeats. A GAA-to-TAA substitution introduced a premature stop codon in mitochondrial sdh3, resulting in pseudogenization. Across six species, sdh3 was either intact, pseudogenized, or absent, whereas putative nuclear sdh3 homologs were identified in S. discolor and S. pohuashanensis. Comparative analysis of 263 chloroplast genomes revealed that highly variable regions differed between interspecific and intraspecific datasets, whereas trnH-GUG–psbA consistently exhibited relatively high nucleotide diversity. The chloroplast phylogeny placed all sampled compound-leaved species within Sorbus s. s., whereas the sampled simple-leaved taxa were positioned closer to the base, with a similar pattern observed in the mitochondrial phylogeny based on six species. These findings reveal contrasting patterns of organelle genome variation and provide resources for genetic diversity assessment, marker development, and future studies of Sorbus genetic resources.