Comparative chloroplast genomes of Hamamelidaceae: genome evolution and phylogenomic implications

Hamamelidaceae, a family within the core eudicots and the order Saxifragales, represents a characteristic lineage of the East Asian flora and holds considerable ecological and economic importance. However, molecular phylogenetic studies based on single or a few genetic loci have failed to resolve certain phylogenetic relationships among species, genera, and tribes within the family. Besides, less knowledge on the chloroplast genome evolution of Hamamelidaceae has known to us so far. In this study, we first sequenced and de novo assembled the complete chloroplast genomes of 37 representative species with comprehensive genus-level sampling within Hamamelidaceae. The whole length of chloroplast genomes of the 37 Hamamelidaceae species ranged from 158,090 bp to 160,814 bp with typical quadripartite structure. Minor visible divergences exhibited in the inverted repeat (IR)/single-copy (SC) boundary regions, which leading to the size variations in Hamamelidaceae chloroplast genomes. Four DNA barcodes (ndhC/rps18/trnT-GGU/trnR-UCU) and 6,084 chloroplast microsatellites were identified for Hamamelidaceae. Comparative chloroplast genomes analysis revealed that the genome structure, gene arrangement, gene and GC content, codon usage bias, and core genes of Hamamelidaceae species were highly conserved, while clpP gene exhibited significant positive selection (dN/dS > 1) in Hamamelidaceae. Chloroplast genome-based phylogeny of Hamamelidaceae supported the monophyly of the majority of extant genera and all Hamamelidaceae species were divided into four subfamilies with high resolution. Exbucklandioideae was the earliest-diverging lineage, followed by Mytilarioideae, Disanthoideae, and Hamamelidoideae. Moreover, chloroplast capture events through hybridization or introgression may lead to the cytonuclear discordance. Overall, our study not only illuminate the chloroplast genome evolution but also provide a robust phylogenetic framework for constructing a more resolved “Tree of Life” of Hamamelidaceae.