| Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny | |
Yu, Xiang-Qin1,2; Drew, Bryan T.3; Yang, Jun-Bo1; Gao, Lian-Ming2 ; Li, De-Zhu1
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| 2017-06-02 | |
| 发表期刊 | PLoS ONE
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| 卷号 | 12期号:6页码:e0178026 |
| 摘要 | Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima. |
| DOI | 10.1371/journal.pone.0178026 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000402624300025 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.kib.ac.cn/handle/151853/51345 |
| 专题 | 中国西南野生生物种质资源库 |
| 作者单位 | 1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species Southwest China, Kunming, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming, Yunnan, Peoples R China 3.Univ Nebraska, Dept Biol, Kearney, NE USA |
| 推荐引用方式 GB/T 7714 | Yu, Xiang-Qin,Drew, Bryan T.,Yang, Jun-Bo,et al. Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny[J]. PLoS ONE,2017,12(6):e0178026. |
| APA | Yu, Xiang-Qin,Drew, Bryan T.,Yang, Jun-Bo,Gao, Lian-Ming,&Li, De-Zhu.(2017).Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.PLoS ONE,12(6),e0178026. |
| MLA | Yu, Xiang-Qin,et al."Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny".PLoS ONE 12.6(2017):e0178026. |
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| 2017-PLoS ONE_Yu XQ.（3146KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 下载 | |
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