Insights into Phylogeny, Taxonomy, Origins and Evolution of Crataegus and Mespilus, Based on Comparative Chloroplast Genome Analysis

Hawthorns (<i>Crataegus</i> L.) are widely distributed and well known for their medicinal properties and health benefits. Nevertheless, the phylogenetic relationships among <i>Crataegus</i> native to China remain unclear. Additionally, no consensus exists on the origin and evolution of <i>Crataegus</i>, and the relationship between <i>Crataegus</i> and <i>Mespilus</i> is is unclear. Here, we sequenced 20 chloroplast (cp) genomes (19 from <i>Crataegus</i> and 1 from <i>Mespilus</i>) and combined them with 2 existing cp genomes to investigate the phylogenetic relationships, divergence times and biogeographic history of <i>Crataegus</i>. Four hypervariable loci emerged from the newly sequenced genomes. The phylogenetic results indicated that the 14 Chinese <i>Crataegus</i> species analyzed clustered into two clades. One clade and the North American <i>Crataegus</i> species grouped together, while the other clade grouped with the European <i>Crataegus</i> species. Our results favor recognizing <i>Mespilus</i> and <i>Crataegus</i> as one genus. Molecular dating and biogeographic analyses showed that <i>Crataegus</i> originated in Southwest China during the early Oligocene, approximately 30.23 Ma ago. Transoceanic migration of East Asian <i>Crataegus</i> species across the Bering land bridge led to the development of North American species, whereas westward migration of the ancestors of <i>C. songarica</i> drove the formation of European species. <i>C. cuneata</i> may represent the earliest lineage of Chinese <i>Crataegus</i>. The uplift of the Qinghai-Tibet Plateau (QTP) and the Asian monsoon system may have led the ancestors of <i>C. cuneata</i> in south-western China to migrate toward the northeast, giving rise to other Chinese <i>Crataegus</i> species. This study offers crucial insights into the origins of <i>Crataegus</i> and proposes an evolutionary model for the genus.