Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae)
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Phoebe is an economically important genus from the family Lauraceae. It is widely distributed in tropical and subtropical Asia, but systematics of the genus is unclear, and currently there is no species-level phylogeny. Here, we determined the complete chloroplast genome sequences of two species with long-range PCR and next genome sequencing technologies, and identified mutation sites and highly variable regions. These highly variable sites were used to reconstruct the phylogeny. The plastomes of Phoebe sheareri and P. omeiensis were 152, 876, and 152, 855 bp, respectively. Comparative genomic analysis indicated that there are 222 mutation sites including 146 substitutions, 73 indels, and 3 microinversions in both plastomes. Fifty-six single-nucleotide changes were identified in gene-coding regions, and 45 microsatellite sites were found for use in species identification. Fourteen divergence hotspots of 38 variable regions were located. Phylogeny was reconstructed using a Bayesian and maximum likelihood approach for 12 Phoebe species and other five related Lauraceae based on 15 of the highly variable regions including accD-psaI, atpB-rbcL, ndhC-trnV, ndhF-rpl32, petA-psbJ, psaA, psbA-trnH, rbcL, rps8-rpl14, rps16-trnQ, rpl32-trnL, trnC-petN, trnL-trnF, trnS-trnG, and ycf1 indicated that variability in the chloroplast regions proposed as variable is enough to detect divergence events among 12 taxa of Phoebe, and that maybe also useful to help to elucidate further relationships among other taxa of the genus.
KeywordsPhoebe Lauraceae Chloroplast Genome Phylogenetic relationship
We would like to acknowledge Jing Yang, Juan-hong Zhang, Chun-yan Lin, and Ji-xiong Yang at Germplasm Bank of Wild Species of Kunming Institute of Botany, Chinese Academy Sciences, for sequencing technology. This work was supported by the National Natural Science Foundation of China (No. 31600531), the CAS “Light of West China” Program, the 1000 Talents Program (WQ20110491035), the scientific research fund of Zhejiang A&F University (2014FR007), and the Zhejiang Provincial Natural Science Foundation of China (LQ15C020002). We sincerely thank five anonymous referees and Dr. Giovanni Vendramin for their critical and invaluable comments that greatly improved our manuscript.
Compliance with ethical standards
Data archiving statement
The complete chloroplast genome sequence data of Phoebe sheareri and Phoebe omeiensis and the Sanger sequence data of accD-psaI, atpB-rbcL, ndhC-trnV, ndhF-rpl32, petA-psbJ, psaA, psbA-trnH, rbcL, rps8-rpl14, rps16-trnQ, rpl32-trnL, trnC-petN, trnL-trnF, trnS-trnG, and ycf1 of 12 Phoebe species will be submitted to GenBank of NCBI through the revision process. All of the accession numbers from NCBI must be supplied prior to final acceptance of the manuscript.
Conflict of interest statement
The authors declare that they have no conflicts of interest. The authors alone are responsible for the content and writing of this article.
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