Chloroplast-genome-based insights into the systematic relationship of Eriobotrya (Rhaphiolepis)

The taxonomy of <i>Eriobotrya</i> and <i>Rhaphiolepis</i> has long been contentious due to unclear interspecific relationships, morphological ambiguities, low barcode resolution, and lack of molecular phylogenetic support. Using shallow genome sequencing, this study analyzed 29 newly assembled chloroplast genomes (159,101-159,718 bp; GC 36.6%-36.7%) comprising 113 unique genes (78 protein-coding, 31 tRNA, and 4 rRNA). Structural variation was observed in the <i>rpl2-trnH</i> spacer along with six small inversions. Comparative analyses revealed 13 highly variable regions in <i>Eriobotrya</i>, 2 in <i>Rhaphiolepis</i>, and 12 shared regions. Phylogenomic analysis of 42 plastomes resolved five well-supported clades, confirming the monophyly of each genus. Nuclear-plastid conflict in species such as <i>Eriobotrya japonica</i> suggests ancient hybridization and chloroplast capture, likely linked to overlapping flowering times and distributions. These findings clarify phylogenetic relationships and provide theoretical and practical support for taxonomy, germplasm utilization, and genetic research of <i>Eriobotrya</i> and <i>Rhaphiolepis</i>.