Abstract
DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.
Highlights
DNA barcoding has been widely evaluated since the mitochondrial gene cytochrome c oxidase I (COI) was proposed as a DNA barcode for species identification[1]
Significant progress has been made in the DNA barcoding of higher plants, and the followingcore DNA barcodes have been proposed: matK, rbcL, internal transcribed spacer (ITS), or ITS2 and matK+rbcL[2,3,4,5,6,7,8,9,10,11]
We evaluated the effectiveness of ITS+matK for species identification in these genera by calculating genetic distance, constructing neighbor joining (NJ) trees and conducting analyses using the TaxonDNA program and compared with the core barcode proposed by the previous study
Summary
DNA barcoding has been widely evaluated since the mitochondrial gene cytochrome c oxidase I (COI) was proposed as a DNA barcode for species identification[1]. Significant progress has been made in the DNA barcoding of higher plants, and the followingcore DNA barcodes have been proposed: matK, rbcL, ITS, or ITS2 and matK+rbcL[2,3,4,5,6,7,8,9,10,11]. Many efforts have been made to establish a universal barcode for plants, these efforts have not been very successful due to the low substitution rates of mitochondrial DNA[11] and the complicated evolutionary processes and patterns of higher plants, such as genome duplication, PLOS ONE | DOI:10.1371/journal.pone.0115168. Many efforts have been made to establish a universal barcode for plants, these efforts have not been very successful due to the low substitution rates of mitochondrial DNA[11] and the complicated evolutionary processes and patterns of higher plants, such as genome duplication, PLOS ONE | DOI:10.1371/journal.pone.0115168 January 20, 2015
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