Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of and its allies in the Old World.

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for , , sensu lato, and . In addition, we present a comprehensive taxonomic synopsis of and its morphological allies in the Old World, recognizing 27 species and ten varieties within , three species and two varieties within , and two species and three varieties within . Furthermore, we also lectotypified 12 names and made two new combinations, (J.E.Vidal) B.B.Liu and (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.