Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

Dan Zong; Anpei Zhou; Yao Zhang; Xinlian Zou; Dan Li; Anan Duan; Chengzhong He

doi:10.7717/peerj.6386

Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

PeerJ. 2019 Feb 20:7:e6386. doi: 10.7717/peerj.6386. eCollection 2019.

Authors

Dan Zong^{1

2}, Anpei Zhou^{1

2}, Yao Zhang^{1

2}, Xinlian Zou^{1

2}, Dan Li³, Anan Duan^{1

2

4}, Chengzhong He^{1

2

4}

Affiliations

¹ Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.
² Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China.
³ Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan, China.
⁴ Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.

Abstract

Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.

Keywords: Chloroplast genome; Phylogenetic relationship; Populus; Western Sichuan Plateau.

Grants and funding

This work was supported by the National Natural Science Foundation of China (Grant No. 31460205, 31860219, 31360184) and the Forestry Public Benefit Research Program (No. 201104076). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.