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Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae)
Song, Yu1,2; Yao, Xin1,2; Tan, Yunhong1,2; Gan, Yi3; Yang, Junbo4; Corlett, Richard T.1,2
2017-12-01
发表期刊TREE GENETICS & GENOMES
ISSN1614-2942
卷号13期号:6页码:1
摘要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.
关键词Phoebe Lauraceae Chloroplast Genome Phylogenetic Relationship
语种英语
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文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/60345
专题中国西南野生生物种质资源库
作者单位1.Chinese Acad Sci, Ctr Integrat Conservat, Xishuangbanna Trop Bot Garden, Mengla 666303, Peoples R China
2.Chinese Acad Sci, Southeast Asia Biodivers Res Inst, Yezin, Nay Pyi Taw, Myanmar
3.Zhejiang A&F Univ, Sch Agr & Food Sci, Hangzhou 311300, Zhejiang, Peoples R China
4.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
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Song, Yu,Yao, Xin,Tan, Yunhong,et al. Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae)[J]. TREE GENETICS & GENOMES,2017,13(6):1.
APA Song, Yu,Yao, Xin,Tan, Yunhong,Gan, Yi,Yang, Junbo,&Corlett, Richard T..(2017).Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae).TREE GENETICS & GENOMES,13(6),1.
MLA Song, Yu,et al."Comparative analysis of complete chloroplast genome sequences of two subtropical trees, Phoebe sheareri and Phoebe omeiensis (Lauraceae)".TREE GENETICS & GENOMES 13.6(2017):1.
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