Nuclear phylogeny of Malus with increased sampling provides new insights into biogeography and character evolution.

Background: Malus is one of the most widespread genera of Rosaceae and includes several economically and ornamentally significant plants (e.g., apple and crabapple). The extensive genome and transcriptome data for Malus available in public databases offer a great opportunity for phylogenomic, biogeographical, and character evolution analyses in this group.

Results: We utilized nuclear genes from 45 transcriptomes/genomes, comprising 32 ingroup taxa (Malus and related species), to reconstruct a comprehensive and well-supported phylogeny and to investigate biogeography and character evolution. Our coalescent-based phylogenies from 12,835 gene families and 1,597 orthologs indicate that Malus encompasses Eriolobus and Docynia, and they identified six well-supported clades within Malus. Malus originated in Northern and Southern East Asia during the early Miocene (~ 20 Ma) and subsequently dispersed to other regions. The persistent calyx in the fruit, lobed leaves, and stone cells represent ancestral traits. A strong phylogenetic signal was detected in three traits: calyx, leaf morphology, and stone cell. Additionally, fruit size showed a significant correlation with calyx morphology.

Conclusion: Our findings offer new insights into the phylogeny of Malus, its biogeography, and morphological evolution.