Comparative organellar genomics of two East Asian simple-leaved Sorbus species reveals insights into organelle evolution and phylogeny of Sorbus sensu lato

Abstract

The genus Sorbus sensu lato (Maleae, Rosaceae) represents one of the most taxonomically complex groups in Rosaceae due to extensive hybridization, polyploidization, and morphological convergence. Although East Asia represents a major center of diversity for Sorbus s.l., the organellar genomes of East Asian simple-leaved taxa remain poorly characterized. Here, we assembled and comparatively analyzed the complete chloroplast and mitochondrial genomes of two East Asian simple-leaved species, Sorbus medogensis and S. thibetica , together with representative taxa of Sorbus s.l. and related Maleae. The chloroplast genomes were highly conserved in structure and gene content, whereas sequence divergence was concentrated in 16 hypervariable regions (e.g., trnH-psbA , atpF , accD ), which may serve as potential molecular markers for future phylogenetic and population-level studies. In contrast, mitochondrial genomes exhibited substantial variation in genome size and extensive structural rearrangements, including large inversions (up to 322 kb) and translocations. Further comparative analyses of the mitochondrial genomes revealed interspecific variation in the abundance and size distribution of simple sequence repeats (SSRs) and long sequence repeats (LSRs) . Mitochondrial protein-coding genes were generally under strong purifying selection, and abundant predicted C-to-U RNA-editing sites were detected. We also detected 114 inter-organellar gene transfer events (including three fully transferred tRNA genes), mainly representing chloroplast-derived sequences in mitochondrial genomes. Chloroplast phylogenomic analyses recovered four major lineages within Sorbus s.l., whereas the more limited mitochondrial dataset recovered a broadly similar division of major lineages but differed in the placement of several European and East Asian simple-leaved taxa. Both S. medogensis and S. thibetica were nested within the East Asian simple-leaved lineage. Our comparative analyses reveal contrasting evolutionary patterns between the chloroplast and mitochondrial genomes of Sorbus s.l. and clarify the phylogenetic placement of S. medogensis and S. thibetica within the East Asian simple-leaved lineage. These findings provide new insights into organellar genome evolution and phylogenetic relationships within Sorbus s.l., while highlighting the need for broader mitochondrial and nuclear genomic sampling to further resolve its complex evolutionary history.