Reassessing the Evolutionary Relationships of Eriobotrya and Rhaphiolepis (Rosaceae): Evidence from Micromorphology, Complete Nuclear Ribosomal DNA and Mitochondrial Genomic Data

<i>Eriobotrya</i> and <i>Rhaphiolepis</i> are two closely related genera within the Maleae tribe of Rosaceae, and delineation of the boundary between these genera requires clarification. This study aims to reassess the phylogeny of two genera by integrating data from nuclear ribosomal DNA (nrDNA), mitochondrial DNA (mtDNA), and the micromorphological features of leaves, petioles, fruits, and fruit apical sepals from 53 accessions, including 16 nrDNA and one mtDNA sequences acquired from NCBI, representing 25 <i>Eriobotrya</i>, and 14 <i>Rhaphiolepis</i> species. Prior taxonomic investigations have often relied on either morphological or molecular methods; however, resolving the complex evolutionary background of these genera benefits from the application of molecular data with in-depth micromorphological analysis. Our findings indicate that molecular phylogeny derived from nrDNA sequences and leaf micromorphology elucidates the relationship between <i>Eriobotrya</i> and <i>Rhaphiolepis</i>, supporting the monophyly of <i>Rhaphiolepis</i> (with high support) and <i>Eriobotrya</i> (with moderate to low support). Supplementary micromorphological features (petioles, fruits, fruit apical sepals) support their classification as separate genera and aid in identification. Nevertheless, the mtDNA gene tree derived from 52 protein-coding genes offered restricted evolutionary insights due to low sequence variability, and displayed incongruence with the robust nuclear and morphological topologies. Furthermore, the mtDNA gene tree exhibited incongruent placements for four <i>Eriobotrya</i> species (<i>E. hookeriana</i>, <i>E. laoshanica</i>, <i>E. deflexa</i>, and <i>E. fragrans</i>) which clustered within the <i>Rhaphiolepis</i> clade, with support values ranging from low to high confidence. The observed topological incongruences, mito-nuclear discordance, and the congruent patterns of micromorphological and nrDNA sequences indicate a reticulate history. Further research employing whole genome sequencing may shed further light on the complex evolutionary history of this key clade.