DNA Barcoding the Dioscorea in China, a Vital Group in the Evolution of Monocotyledon: Use of matK Gene for Species Discrimination

Sun, Xiepeng; Zhu, Yingjie; Guo, Jing; Peng, Bin; Bai, Ming; Hang, Yue‐Yu

doi:10.1371/journal.pone.0032057

Cited by 38 publications

(37 citation statements)

References 47 publications

(51 reference statements)

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“…The distribution of intra-specific versus interspecific variability was evaluated by assessment of the presence of DNA barcoding gaps. Moreover, BLAST 1 and the nearest distance method were used to test the power of species identification as described previously (Sun et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Applying DNA barcodes for identification of economically important species in Brassicaceae

Yao

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Brassicaceae is a large plant family of special interest; it includes many economically important crops, herbs, and ornamentals, as well as model organisms. The taxonomy of the Brassicaceae has long been controversial because of the poorly delimited generic boundaries and artificially circumscribed tribes. Despite great effort to delimitate species and reconstruct the phylogeny of Brassicaceae, little research has been carried out to investigate the applicability and effectiveness of different DNA regions as barcodes -a recent aid for taxonomic identification -to identify economically important species in Brassicaceae. In this study, we evaluated the feasibility of five intensively recommended regions [rbcL, matK, trnH-psbA, internal transcribed spacer (ITS), ITS2] as candidate DNA barcodes to discriminate economic species of Brassicaceae in China and try to establish a new digital identification method for economic plants of Brassicaceae. All sequences of 58 samples from 27 economic species (Brassicaceae) in China were assessed in the success rates of PCR amplifications, intra-and inter-specific divergence, DNA barcoding gaps, and efficiency of identification. Compared with other markers, ITS showed superiority in species discrimination with an accurate identification of 67.2% at the species level. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS was a powerful but not perfect barcode for Brassicaceae identification. We further discuss the discrimination power of different loci due to inheritance pattern, polyploidization and hybridization in species-specific evolution. Further screening of other nuclear genes related to species isolation as plant barcode candidates is also proposed.

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Section: Discussionmentioning

confidence: 99%

Applying DNA barcodes for identification of economically important species in Brassicaceae

Yao

et al. 2015

Genet. Mol. Res.

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“…The use of a combination of DNA sequences with existing morphological characters can facilitate fast and reliable identification of species (Smith et al, ; Will et al, ; DeSalle, ; Hajibabaei et al, ). In plants, several single‐locus or multi‐loci candidate DNA barcodes have been tested and proven to be useful for plant identification (Thomas, ; Gao, ; Li et al, ; Sun et al, ). These markers include the nuclear ribosomal internal transcribed spacer (ITS) and plastid gene regions ( rpoB , rpoC1, rbcL , matK ) and plastid non‐coding regions ( atpH‐atpI , psbK‐psbI , trnH‐psbA ).…”

mentioning

confidence: 99%

Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae)

Mao

Zhang

Nakamura

et al. 2014

J of Sytematics Evolution

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Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identification of the species of these four genera is crucial to their medicinal uses. In this study, we tested the utility of nine barcodes (matK, rbcL, atpH-atpI, rpl32-trnL UAG , rps18-clpp, trnL-trnF, trnL-ndhJ, trnS-trnfM, and internal transcribed spacer (ITS)) to discriminate different species of Podophylloideae. Thirty-six individuals representing 12 species of Podophylloideae were collected from different locations in China, Japan, and North America. We assessed the feasibility of amplification and sequencing of all markers, examined the levels of the barcoding gap based on DNA sequence divergence between ranges of intra-and interspecific variation using pairwise distances, and further evaluated successful identifications using each barcode by similarity-based and tree-based methods. Results showed that nine barcodes, except rps18-clpp, have a high level of primer universality and sequencing success. As a single barcode, ITS has the most variable sites, greater intra-and interspecific divergences, and the highest species discrimination rate (83%), followed by matK which has moderate variation and also high species discrimination rates. However, these species can also be discriminated by ITS alone, except Dysosma versipellis (Hance) M. Cheng ex T. S. Ying and D. pleiantha (Hance) Woodson. The combination of ITS þ matK did not improve species resolution over ITS alone. Thus, we propose that ITS may be used as a sole region for identification of most species in Podophylloideae. The failure of ITS to distinguish D. versipellis and D. pleiantha is likely attributed to incomplete lineage sorting due to recent divergence of the two species.

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“…[68] On the contrary, insertions, deletions, and short sequence repeats were common and often more numerous than single base pair substitution that has been the limitation on the part of trnH-psbA , hence remained unable to fulfill the criteria of plant DNA barcoding. [7] Nevertheless, in the present study, intergenic spacer trnH-psbA also exhibited persistent problem in obtaining constant bidirectional sequences.…”

Section: Discussionmentioning

confidence: 99%

“…[1234] The technique utilizes ~650 bp region of mitochondrial COI in animals[5] and various chloroplast regions ( matK, rbcL , and trnH-psbA ) in plants. [678] The application of the technique emphasizes some thrust areas, like documentation of the important and vulnerable ethnomedicinal plant bio-resources, dealing with which is recently defined as the subject “Ethnobotany Genomics.”[9] The principal issues in ethnobotany emphasized the importance of correct species identification and deciphering of indigenous and conventional knowledge of restorative plant usage and their transfer for the promotion of bio-prospect in human health care. Apocynaceae is one of the 10 largest angiosperm families (including Asclepiadaceae) and comprises of several prominent medicinal plants, like Rauvolfioideae subfamily of Apocynaceae is known for the rich source of typical laticiferous tissues, which produce various alkaloids and cardenolides being used in traditional medicines for stomach ulcer, fever, asthma, whooping cough, etc.…”

Section: Introductionmentioning

confidence: 99%

Identification of ethnomedicinal plants (Rauvolfioideae: Apocynaceae) through DNA barcoding from northeast India

2013

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Background:DNA barcode-based molecular characterization is in practice for plants, but yet lacks total agreement considering the selection of marker. Plant species of subfamily Rauvolfioideae have long been used as herbal medicine by the majority of tribal people in Northeast (NE) India and at present holds mass effect on the society. Hence, there is an urgent need of correct taxonomic inventorization vis-à-vis species level molecular characterization of important medicinal plants.Objective:To test the efficiency of matK in species delineation like DNA barcoding in Rauvolfiadae (Apocynaceae).Materials and Methods:In this study, the core DNA barcode matK and trnH-psbA sequences are examined for differentiation of selected ethnomedicinal plants of Apocynaceae. DNA from young leaves of selected species was isolated, and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification.Results:The ~758 bp matK sequence in comparison to the trnH-psbA showed easy amplification, alignment, and high level of discrimination value among the medicinal Rauvolfioidae species. Intergenic spacer trnH-psbA is also exhibited persistent problem in obtaining constant bidirectional sequences. Partial matK sequences exhibited 3 indels in multiple of 3 at 5 end. Evidently, generated matK sequences are clustered cohesively, with their conspecific Genbank sequences. However, repeat structures with AT-rich regions, possessing indels in multiple of 3, could be utilized as qualitative molecular markers in further studies both at the intra-specific and shallow inter-specific levels like the intergenic spacers of CpDNA.Conclusion:matK sequence information could help in correct species identification for medicinal plants of Rauvolfioideae.

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DNA Barcoding the Dioscorea in China, a Vital Group in the Evolution of Monocotyledon: Use of matK Gene for Species Discrimination

Cited by 38 publications

References 47 publications

Applying DNA barcodes for identification of economically important species in Brassicaceae

Applying DNA barcodes for identification of economically important species in Brassicaceae

Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae)

Identification of ethnomedicinal plants (Rauvolfioideae: Apocynaceae) through DNA barcoding from northeast India

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