Accurate authentication of and its closely related species by comparative analysis of complete plastomes.
10.1016/j.apsb.2018.05.009
- Author:
Shuying ZHU
1
;
Zhitao NIU
1
;
Qingyun XUE
1
;
Hui WANG
1
;
Xuezhu XIE
1
;
Xiaoyu DING
1
Author Information
1. College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
- Publication Type:Journal Article
- Keywords:
Authentication;
BS, bootstrap value;
CE, capillary electrophoresis;
Complete plastome sequence;
Dendrobium officinale;
Genetic marker;
HPLC, high-pressure liquid chromatography;
IR, inverted repeat region;
Indels, insertions/deletions;
LSC, large single copy region;
ML, maximum likelihood;
NGS, next-generation sequencing;
Plastomic comparison;
SNPs, single nucleotide polymorphisms;
SSC, small single copy region;
SV, sequence variability.
- From:
Acta Pharmaceutica Sinica B
2018;8(6):969-980
- CountryChina
- Language:English
-
Abstract:
Owing to its great medicinal and ornamental values, is frequently adulterated with other species on the market. Unfortunately, the utilization of the common DNA markers ITS, ITS2, and + is unable to distinguish from 5 closely related species of it (, , , and ). Here, we compared 63 plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of genes. Furthermore, the intraspecific sequence variability among different species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different species. By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate species.
