Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

Wang, De‐Yi; Wang, Qiang; Wang, Yingli; Xiang, Xiao‐Guo; Huang, Luqi; Jin, Xiao‐Hua

doi:10.1371/journal.pone.0170286

Cited by 13 publications

(13 citation statements)

References 56 publications

(101 reference statements)

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“…It took nearly five years from the time of publication of the first papers suggesting candidates for plant DNA barcode markers (e.g., Kress et al, 2005) for the botanical community to reach some consensus on the regions that showed the highest promise of success (Lahaye et al, 2008;CBOL Plant Working Group, 2009;Chen et al, 2010;China Plant BOL Group, 2011;Hollingsworth, 2011). It is still not uncommon to see publications testing various markers in specific group of plants (Wang et al, 2017). Yet, even before universal plant markers were accepted systematists, ecologists, evolutionary biologists, and conservationists were already speculating and providing initial tests of the application of plant DNA barcodes to address critical questions in organismal biology (e.g., Kress & Erickson, 2008b;Valentini et al, 2009).…”

Section: Hotspots In the Application Of Plant Dna Barcodes Todaymentioning

confidence: 99%

“…Two additional avenues for developing the library for plants include lineage‐based efforts and floristic efforts. Individual taxonomists are also generating DNA barcodes for specific groups of plants as either trials for sequencing success using the standard markers (e.g., Chen et al, , ; Wang et al, ) or as part of their basic molecular phylogenetic investigations in which the DNA barcode markers are used for understanding evolutionary relationships. Although many of these “DNA barcodes” may not receive the official GenBank DNA barcode designation, they are all adding to the library of sequences that complement the standard DNA barcode markers.…”

Section: Tomorrow's Outlook For Plant Dna Barcodingmentioning

confidence: 99%

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Plant DNA barcodes: Applications today and in the future

Kress

2017

J of Sytematics Evolution

222

146

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DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, matK, trnHpsbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and costeffective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors.

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Section: Hotspots In the Application Of Plant Dna Barcodes Todaymentioning

confidence: 99%

Section: Tomorrow's Outlook For Plant Dna Barcodingmentioning

confidence: 99%

Plant DNA barcodes: Applications today and in the future

Kress

2017

J of Sytematics Evolution

222

146

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“…DNA barcoding has become instrumental in plant research for identification of cryptic species ( Bickford et al, 2007 ; Miwa et al, 2009 ; Liu et al, 2011 ), biodiversity assessments ( Lahaye et al, 2008 ; Gonzalez et al, 2009 ; von Cräutlein et al, 2011 ; Yan et al, 2015 ), community phylogeny ( Kress et al, 2009 , 2010 ), conservation biology ( Laiou et al, 2013 ; Veldman et al, 2014 ; Liu et al, 2015 ; Shapcott et al, 2015 ), invasive biology ( Armstrong and Ball, 2005 ; Bleeker et al, 2008 ; Newmaster and Ragupathy, 2009 ; Van De Wiel et al, 2009 ), and disease and pest management ( Ball and Armstrong, 2006 ; Lee et al, 2012 ; Montecchio and Faccoli, 2014 ; Shapcott et al, 2015 ). At present, the resolution of several candidate DNA barcodes has been tested in many plant groups ( Clerc-Blain et al, 2010 ; Gao et al, 2010 ; Liu et al, 2011 ; Yu et al, 2011 ; Wang D.Y. et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

et al. 2018

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The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia – Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.

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“…The SCAR technique is much more useful and less costly than the DNA barcoding technique (65). Yet, DNA barcoding is anticipated to be one of the biological taxonomy's most successful instruments, and it is regarded as an essential key barcode for Codonopsis barcoding at the species level (66).…”

Section: Random Amplified Polymorphic Dna (Rapd)mentioning

confidence: 99%

The application of DNA molecular markers in the study of Codonopsis species genetic variation, a review

Yang

Abdalrahman

Sonia

et al. 2020

Cell Mol Biol (Noisy-le-grand)

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Codonopsis genus is comprised of species that are perennial plants primarily distributed across all east, southeast, and Central Asia. The most famous species of Codonopsis are C. tangshen, C. lanceolate, and C. pilosula. The records showed that they have a long story usage as traditional Chinese medicines, as they were alleged to be able to intensify the spleen and the lung as well as enriching blood and engendering liquid. Certain species have a culinary value in southern China and Southeast Asia, where they are considered as tea, wine, soup, plaster, and porridge. Codonopsis species were shown to be of great importance in medicine, due to their broad biological activity. Therefore, a clear understanding of their genetic diversity is needed. Adequate distinctions and descriptions of those species are necessary to preserve plant reservoir, investigations of genes associated with desirable traits, and understanding of evolutionary relationships.Subsequently, various molecular marker techniques such as Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeats (SSR), and Inter Simple Sequence Repeat (ISSR), Single Nucleotide Polymorphism (SNP), internal transcribed spacer (ITS), and Sequence-Characterized Amplified Region (SCAR) have been improved to provide detailed informations about genomes, that historically were not possible to obtain based on only phenotypic methods. This review represents the usage of DNA molecular markers for molecular diversity analysis of medically important species belonging to the genus Codonopsis.

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Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

Cited by 13 publications

References 56 publications

Plant DNA barcodes: Applications today and in the future

Plant DNA barcodes: Applications today and in the future

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

The application of DNA molecular markers in the study of Codonopsis species genetic variation, a review

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