Robust phylogeny from 481 nuclear genes and plastomes refines infrageneric classification and species delimitation in Chinese hawthorns (Crataegus, Rosaceae)

Crataegus L. (hawthorns) is a taxonomically challenging genus within the Rosaceae family, exhibiting extensive morphological variation, frequent hybridization, and polyploidy. In China, approximately 17–18 species are recognized, but their subgeneric classification and species boundaries remain unresolved. To clarify these relationships, we analyzed 481 nuclear genes, 73 plastid coding sequences, and comprehensive plastome dataset for 17 Chinese Crataegus species to date. Phylogenomic analyses of both nuclear and plastid data produced well-supported trees that refine the taxonomy and elucidate evolutionary relationships within the genus. All Chinese species are resolved within two subgenera, C. subg. Crataegus and C. subg. Sanguineae, although most currently recognized species are not monophyletic, reflecting complex reticulate evolution involving hybridization and polyploidy. Integrating phylogenomic and morphological evidence, we provide an updated taxonomic synopsis of Chinese Crataegus, describe one new species, five new combinations, and designate 31 lectotypes. This study establishes a robust framework for future systematic, conservation, and horticultural research on this ecologically and economically important lineage.