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

Wenbo Shi; Weicai Song; Zimeng Chen; Haohong Cai; Qin Gong; Jin Liu; Chao Shi; Shuo Wang

doi:10.7717/peerj.14573

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

PeerJ. 2023 Feb 3:11:e14573. doi: 10.7717/peerj.14573. eCollection 2023.

Authors

Wenbo Shi^#¹, Weicai Song^#¹, Zimeng Chen¹, Haohong Cai¹, Qin Gong¹, Jin Liu², Chao Shi^{1

3}, Shuo Wang¹

Affiliations

¹ College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China.
² Yunnan Institute of Tropical Crops, Xishuangbanna, China.
³ Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China.

^# Contributed equally.

Abstract

The genus Phoebe (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 Phoebe 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 Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe 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 Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.

Keywords: Chloroplast genome; Comparative analysis; Conservation; Phoebe; Phylogeny; Phylogeographical origin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

China
Genome, Chloroplast* / genetics
Lauraceae* / genetics
Phylogeny
Phylogeography

Grants and funding

This work was supported by the National Natural Science Foundation of China (NO. 31801022) and the Shandong Province Natural Science Foundation of China (NO. ZR2019BC094). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.