Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

被引:13
|
作者
Cao, Zhengying [1 ,2 ]
Yang, Linyi [3 ]
Xin, Yaxuan [1 ,2 ]
Xu, Wenbin [4 ]
Li, Qishao [1 ,2 ]
Zhang, Haorong [1 ,2 ]
Tu, Yuxiang [1 ,2 ]
Song, Yu [5 ,6 ]
Xin, Peiyao [1 ,2 ]
机构
[1] Southwest Forestry Univ, Southwest Res Ctr Landscape Architecture Engn, Natl Forestry & Grassland Adm, Kunming, Peoples R China
[2] Southwest Forestry Univ, Key Lab Forest Resources Conservat & Utilizat Sout, Minist Educ, Kunming, Peoples R China
[3] Yunnan Forestry Vocat & Tech Coll, Kunming, Yunnan, Peoples R China
[4] Chinese Acad Sci, Wuhan Bot Garden, Wuhan, Hubei, Peoples R China
[5] Guangxi Normal Univ, Key Lab Ecol Rare & Endangered Species & Environm, Minist Educ, Guilin, Guangxi, Peoples R China
[6] Guangxi Normal Univ, Guangxi Key Lab Landscape Resources Conservat & Su, Guilin, Guangxi, Peoples R China
来源
FRONTIERS IN PLANT SCIENCE | 2023年 / 14卷
基金
中国国家自然科学基金;
关键词
Neocinnamomum; chloroplast genome; genome comparison; sequence characteristic; phylogenetic analysis; DNA BARCODES; CODON USAGE; SEQUENCE; IDENTIFICATION; MITOCHONDRIAL; ORGANIZATION; TOOLS; GENE; WILD;
D O I
10.3389/fpls.2023.1205051
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.
引用
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页数:12
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