Abstract
DNA barcoding of plants poses particular challenges, especially in differentiating, recently diverged taxa. The genus Gentiana (Gentianaceae) is a species-rich plant group which rapidly radiated in the Himalaya-Hengduan Mountains in China. In this study, we tested the core plant barcode (rbcL + matK) and three promising complementary barcodes (trnH-psbA, ITS and ITS2) in 30 Gentiana species across 6 sections using three methods (the genetic distance-based method, Best Close Match and tree-based method). rbcL had the highest PCR efficiency and sequencing success (100%), while the lowest sequence recoverability was from ITS (68.35%). The presence of indels and inversions in trnH-psbA in Gentiana led to difficulties in sequence alignment. When using a single region for analysis, ITS exhibited the highest discriminatory power (60%-74.42%). Of the combinations, matK + ITS provided the highest discrimination success (71.43%-88.24%) and is recommended as the DNA barcode for the genus Gentiana. DNA barcoding proved effective in assigning most species to sections, though it performed poorly in some closely related species in sect. Cruciata because of hybridization events. Our analysis suggests that the status of G. pseudosquarrosa needs to be studied further. The utility of DNA barcoding was also verified in authenticating ‘Qin-Jiao’ Gentiana medicinal plants (G. macrophylla, G. crassicaulis, G. straminea, and G. dahurica), which can help ensure safe and correct usage of these well-known Chinese traditional medicinal herbs.
Highlights
IntroductionDNA barcoding, a term first proposed by Hebert in 2003 [1], has developed as a rapid and reliable technology to identify species based on variation in the sequence of short standard DNA region(s)
DNA barcoding, a term first proposed by Hebert in 2003 [1], has developed as a rapid and reliable technology to identify species based on variation in the sequence of short standard DNA region(s). This tool is successfully used in a variety of biological applications, including discovering cryptic species [2], detecting invasive species [3], reconstructing food webs [4] and identifying medicinal plants in mixtures [5, 6]
Sequence recoverability and divergence rbcL had the highest PCR efficiency and sequencing success (100%), followed by matK (96.2%) and trnH-psbA (96.2%) (Table 1)
Summary
DNA barcoding, a term first proposed by Hebert in 2003 [1], has developed as a rapid and reliable technology to identify species based on variation in the sequence of short standard DNA region(s). This tool is successfully used in a variety of biological applications, including discovering cryptic species [2], detecting invasive species [3], reconstructing food webs [4] and identifying medicinal plants in mixtures [5, 6]. The application of DNA barcoding has been hindered by the difficulty of distinguishing closely related species, especially in PLOS ONE | DOI:10.1371/journal.pone.0153008. The application of DNA barcoding has been hindered by the difficulty of distinguishing closely related species, especially in PLOS ONE | DOI:10.1371/journal.pone.0153008 April 6, 2016
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