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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
Fu, Chao-Nan1,2,3; Wu, Chung-Shien4; Ye, Lin-Jiang2,3; Mo, Zhi-Qiong1,3; Liu, Jie1; Chang, Yu-Wen4; Li, De-Zhu2,3; Chaw, Shu-Miaw4; Gao, Lian-Ming1
2019-02-26
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume9Pages:11
Abstract

Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by "trnQ-IRs". These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.

Indexed BySCI
Language英语
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/64602
Collection中国西南野生生物种质资源库
中国科学院东亚植物多样性与生物地理学重点实验室
Corresponding AuthorChaw, Shu-Miaw; Gao, Lian-Ming
Affiliation1.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
4.Acad Sinica, Biodivers Res Ctr, Taipei 11529, Taiwan
Recommended Citation
GB/T 7714
Fu, Chao-Nan,Wu, Chung-Shien,Ye, Lin-Jiang,et al. Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide[J]. SCIENTIFIC REPORTS,2019,9:11.
APA Fu, Chao-Nan.,Wu, Chung-Shien.,Ye, Lin-Jiang.,Mo, Zhi-Qiong.,Liu, Jie.,...&Gao, Lian-Ming.(2019).Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide.SCIENTIFIC REPORTS,9,11.
MLA Fu, Chao-Nan,et al."Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide".SCIENTIFIC REPORTS 9(2019):11.
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