Phylogenomics of <i>Keteleeria</i> (Pinaceae) based on plastome and nuclear sequence data

Abstract Keteleeria is a conifer genus of Pinaceae mainly distributed in China with significant ecological and economic value. It is widely used as an ornamental, in construction, and for furniture‐making. However, Keteleeria is challenging in taxonomy due to high morphological polymorphism and variation. In this study, we performed genome skimming sequencing on 39 Keteleeria accessions, along with 9 publicly available plastomes and Sequence Read Archive datasets, covering all acknowledged Keteleeria species. We then assembled plastomes, nuclear ribosomal DNAs, and single‐copy orthologs. Comparative plastome analysis indicates that Keteleeria plastomes have lost an inverted repeat region but are conserved in terms of size, structure, gene content, and organization. Phylogenetic analysis revealed that Keteleeria is a robust monophyletic group with low internal resolution. Nevertheless, plastome‐based phylogenetic trees resolved Keteleeria into two strongly supported clades. Our phylogenetic results do not support any previously proposed Keteleeria classification system. We observed widespread nonmonophyly of Keteleeria taxa and phylogenetic conflicts, which may be attributed to factors such as incomplete lineage sorting, hybridization, introgression, identification, and taxonomic treatment issues. Molecular dating indicates that extant Keteleeria diverged around the late Miocene and is younger than suggested by fossil records, but this accords with historical geographic and climate events.