Comparative chloroplast genome analyses of diverse <i>Phoebe</i> (Lauraceae) species endemic to China provide insight into their phylogeographical origin

Abstract

The genus <i>Phoebe</i> (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered <i>Phoebe</i> species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse <i>Phoebe</i> species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (<i>petA-psbE</i>, <i>ndhF-rpl32</i>, and <i>psbM-trnD</i>-GUC) as well as three highly divergent genes (<i>rbcL</i>, <i>ycf1</i>, and <i>ycf2</i>) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various <i>Phoebe</i> species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of <i>Phoebe</i> species. In addition, based on the phylogeographical analysis of <i>Phoebe</i> species in China, we inferred that the <i>Phoebe</i> species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of <i>Phoebe</i> species and have the potential to contribute to the conservation of <i>Phoebe</i> species that are in danger of extinction.