Complete plastome and mitogenome assembly of endangered tree reveals phylogenetic architecture for sensu lato (Rosaceae).

INTRODUCTION

The genus sensu lato ( s.l.) comprises over 260 species widely distributed across temperate regions of Asia, Europe, and North America. However, hybridization and polyploidization have posed significant challenges to phylogenetic and taxonomic studies within this genus.

METHODS

Here, we assemble the first complete chloroplast and mitochondrial genomes of to characterize organellar genomic features and establish a maternally inherited phylogenetic framework for s.l.

RESULTS AND DISCUSSION

The mitochondrial genome of is circular (386,757 bp), encoding 55 genes, including 34 protein-coding genes, 18 rRNAs, and 3 tRNAs. Its chloroplast genome has a typical quadripartite structure (160,322 bp), containing 75 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and one pseudogene (). Homologous gene transfer analysis of s.l. species revealed inter-organellar gene transfer ranging from 3,021 to 3,846 bp. RNA editing analysis revealed 274-352 editing sites in s.l., with containing the greatest number of editing sites across all protein-coding genes except those in . Simple sequence repeat (SSR) analysis detected 48-52 SSRs per species, predominantly mononucleotide repeats. Phylogenetic reconstruction on the basis of organellar genomes revealed that is a sister to . Plastome-based phylogeny revealed the non-monophyletic status of s.s., attributed to the nested placement of the hybrid-origin genera and within the genus. Additionally, and should be transferred to the nothogenus . Mitochondrial genome collinearity analysis revealed extensive genomic structural rearrangements. Our findings not only delineate the structural characteristics of mitochondrial genomes across s.l. taxa but also establish a high-resolution maternal phylogenetic framework for this genus.