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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Teklemariam DM, Gailing O, Siregar IZ, Amandita FY, Moura CCM. Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae. Ecol Evol 2023; 13:e9935. [PMID: 37038522 PMCID: PMC10082172 DOI: 10.1002/ece3.9935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 04/12/2023] Open
Abstract
The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.
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Affiliation(s)
- Daniel M. Teklemariam
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
- Centre of Biodiversity and Sustainable Land UseUniversity of GöttingenGöttingenGermany
| | | | | | - Carina C. M. Moura
- Department of Forest Genetics and Forest Tree BreedingUniversity of Göttingen37077GöttingenGermany
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Rakotonirina TJ, Viljoen E, Rakotonirina AH, Leong Pock Tsy JM, Radanielina T. A DNA barcode reference library for CITES listed Malagasy Dalbergia species. Ecol Evol 2023; 13:e9887. [PMID: 36937058 PMCID: PMC10015365 DOI: 10.1002/ece3.9887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
On Madagascar, the illegal and unsustainable exploitation and illegal international trade of Dalbergia (rosewood) precious woods remain a serious conservation problem. Members of this genus are at high risk of extinction as a consequence of logging, mining, and slash and burn agriculture. Morphological identification of these Malagasy species is difficult in the absence of flowers and fruits, especially in the case of cut trees, sawn wood, and finished product. In this study, we use molecular barcoding to identify the Dalbergia species with the intent to contribute to the control of their illegal trade. Thirty-six Dalbergia samples representing 12 Malagasy species of which 11 have high commercial value, were collected to test the efficacy of a region of the plastid genome (rbcL) and a nuclear-transcribed ITS for barcoding. These widely used markers, as well as DNA barcoding gaps, "best match" and "best close match" approaches, and the neighbor-joining method were employed. All samples were amplified and sequenced using the two markers. Using a single locus, the "best match" and "best close match" approaches revealed that ITS has high discriminatory power within the tested Malagasy species. The combination of rbcL + ITS revealed 100% species discrimination. This study confirms that ITS alone and in combination with chloroplast barcode rbcL allow non-ambiguous identification for the 12 species studied. The results contribute to the development of DNA barcoding as a useful tool to identify Malagasy Dalbergia and suggest that the approach developed should be expanded to all 56 potentially exploited species in reference to international CITES requirements and the sustainable management of valuable resources.
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Affiliation(s)
| | - Erika Viljoen
- Inqaba Biotechnical Industries (Pty) LtdPretoriaSouth Africa
| | | | | | - Tendro Radanielina
- Plant Molecular Biology Lab, Department of Plant Biology and EcologyUniversity of AntananarivoAntananarivoMadagascar
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Setsuko S, Yoshimura K, Ueno S, Worth JRP, Ujino-Ihara T, Katsuki T, Noshiro S, Fujii T, Arai T, Yoshimaru H. A DNA barcode reference library for the native woody seed plants of Japan. Mol Ecol Resour 2023; 23:855-871. [PMID: 36694075 DOI: 10.1111/1755-0998.13748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/08/2022] [Indexed: 01/26/2023]
Abstract
DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
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Affiliation(s)
- Suzuki Setsuko
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Kensuke Yoshimura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - James Raymond Peter Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Toshio Katsuki
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tokyo, Japan
| | - Shuichi Noshiro
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tomoyuki Fujii
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Takahisa Arai
- Tohoku University Botanical Gardens, Tohoku University, Miyagi, Japan
| | - Hiroshi Yoshimaru
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
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Brodeur A, Leblond M, Brodeur V, Taillon J, Côté SD. Investigating potential for competition between migratory caribou and introduced muskoxen. J Wildl Manage 2023. [DOI: 10.1002/jwmg.22366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alexis Brodeur
- Caribou Ungava and Centre d'Études Nordiques, Département de Biologie Université Laval 1045 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Mathieu Leblond
- Environment and Climate Change Canada 1125 Colonel By Drive Ottawa ON K1S 5B6 Canada
| | - Vincent Brodeur
- Ministère des Forêts, de la Faune et des Parcs Direction de la gestion de la faune du Nord‐du‐Québec 951 boulevard, Hamel Chibougamau QC G8P 2Z3 Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs, Direction de l'expertise sur la faune terrestre l'herpétofaune et l'avifaune 880 chemin Sainte‐Foy Québec QC G1S 4X4 Canada
| | - Steeve D. Côté
- Caribou Ungava and Centre d'Études Nordiques, Département de Biologie Université Laval 1045 Avenue de la Médecine Québec QC G1V 0A6 Canada
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Current Trends in Toxicity Assessment of Herbal Medicines: A Narrative Review. Processes (Basel) 2022. [DOI: 10.3390/pr11010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Even in modern times, the popularity level of medicinal plants and herbal medicines in therapy is still high. The World Health Organization estimates that 80% of the population in developing countries uses these types of remedies. Even though herbal medicine products are usually perceived as low risk, their potential health risks should be carefully assessed. Several factors can cause the toxicity of herbal medicine products: plant components or metabolites with a toxic potential, adulteration, environmental pollutants (heavy metals, pesticides), or contamination of microorganisms (toxigenic fungi). Their correct evaluation is essential for the patient’s safety. The toxicity assessment of herbal medicine combines in vitro and in vivo methods, but in the past decades, several new techniques emerged besides conventional methods. The use of omics has become a valuable research tool for prediction and toxicity evaluation, while DNA sequencing can be used successfully to detect contaminants and adulteration. The use of invertebrate models (Danio renio or Galleria mellonella) became popular due to the ethical issues associated with vertebrate models. The aim of the present article is to provide an overview of the current trends and methods used to investigate the toxic potential of herbal medicinal products and the challenges in this research field.
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Jamdade R, Upadhyay M, Al Shaer K, Al Harthi E, Al Sallani M, Al Jasmi M, Al Ketbi A. Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122741. [PMID: 34961211 PMCID: PMC8708657 DOI: 10.3390/plants10122741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 06/14/2023]
Abstract
Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers' reliability. Our analysis suggests that from the unsupervised method, TaxonDNA's All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.
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Affiliation(s)
- Rahul Jamdade
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximillians University, 80539 Munich, Germany;
| | - Khawla Al Shaer
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Eman Al Harthi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Mariam Al Sallani
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Mariam Al Jasmi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Asma Al Ketbi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
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Mustafa AA, Derise MR, Yong WTL, Rodrigues KF. A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology. PLANTS 2021; 10:plants10091897. [PMID: 34579429 PMCID: PMC8468032 DOI: 10.3390/plants10091897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
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Ho VT, Tran TKP, Vu TTT, Widiarsih S. Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam. J Genet Eng Biotechnol 2021; 19:93. [PMID: 34152504 PMCID: PMC8217478 DOI: 10.1186/s43141-021-00188-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/01/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. RESULTS The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. CONCLUSION The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.
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Affiliation(s)
- Viet The Ho
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam.
| | - Thi Kim Phuong Tran
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam
| | - Thi Thanh Tram Vu
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam
| | - Sasanti Widiarsih
- Plant Mutation Breeding Division, Centre for Isotopes and Radiation Application, National Nuclear Energy Agency, Jl. Lebakbulus Raya No. 49, South Jakarta, Indonesia
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Shadrin DM. DNA Barcoding: Applications. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542104013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fu LF, Yang* TG, Lan DQ, Wen F, Liu H. Chrysosplenium sangzhiense (Saxifragaceae), a new species from Hunan, China. PHYTOKEYS 2021; 176:21-32. [PMID: 33958936 PMCID: PMC8065015 DOI: 10.3897/phytokeys.176.62802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Chrysosplenium sangzhiense Hong Liu, a new species from Hunan, China, is described and illustrated. The phylogenetic analysis revealed that the new species belongs to subgen. Chrysosplenium and is closely related to C. grayanum, C. nepalense and C. sinicum. The chromosome number of the new species is 2n = 46, indicating a novel basic number x = 23 in Chrysosplenium that is different from other species. This also suggests that C. sangzhiense is probably an allopolyploid derivative of a species with x = 11 and one with x = 12. Morphologically, C. sangzhiense can be easily distinguished from C. grayanum, C. nepalense, C. sinicum and C. cavaleriei, a species not included in our phylogenetic analysis by a suite of characters relating to the sterile shoots, basal leaves, cauline leaves, flowering stem, sepals, disc, capsule and seed. A global conservation assessment is performed, and classifies C. sangzhiense as Least Concern (LC).
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Affiliation(s)
- Long-Fei Fu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, ChinaGuangxi Institute of Botany, Chinese Academy of SciencesGuilinChina
| | - Tian-Ge Yang*
- College of Life Sciences & Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of Hubei Province, South-Central University for Nationalities, Wuhan 430074, Hubei Province, ChinaSouth-Central University for NationalitiesWuhanChina
| | - De-Qing Lan
- College of Life Sciences & Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of Hubei Province, South-Central University for Nationalities, Wuhan 430074, Hubei Province, ChinaSouth-Central University for NationalitiesWuhanChina
| | - Fang Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, ChinaGuangxi Institute of Botany, Chinese Academy of SciencesGuilinChina
| | - Hong Liu
- College of Life Sciences & Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of Hubei Province, South-Central University for Nationalities, Wuhan 430074, Hubei Province, ChinaSouth-Central University for NationalitiesWuhanChina
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Shadrin D, Valuyskikh O, Kanev V. A checklist of the flowering plants of Komi Republic (northeast of European Russia) and their representation in BOLD and GenBank databases. ACTA BIOLOGICA SIBIRICA 2020. [DOI: 10.3897/abs.6.e54572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We presented the updated list of flowering plants (Angiosperms) of the Komi Republic that comprises 1211 taxa (including subspecies), 401 genera, and 80 families. This checklist based on the authors field collections data, materials from the Scientific Herbarium of the Institute of Biology of the Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences, published data and open-access databases. For each taxon of flowering plants, we provided a presence-absence checklist of nucleotide sequences (rbcL, matK, ITS2 and trnH-psbA) that is available in BOLD and GenBank databases of DNA barcode data. The presented dataset will promote the identification of potentially new species (including endemic taxa) for molecular taxonomy and including of new sequences into the global database of BOLD Systems using the regional flora as model object.
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Oyebanji OO, Chukwuma EC, Bolarinwa KA, Adejobi OI, Adeyemi SB, Ayoola AO. Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers. J Biosci 2020. [DOI: 10.1007/s12038-020-00061-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Chisholm C, Becker MS, Pollard WH. The Importance of Incorporating Landscape Change for Predictions of Climate-Induced Plant Phenological Shifts. FRONTIERS IN PLANT SCIENCE 2020; 11:759. [PMID: 32670312 PMCID: PMC7329987 DOI: 10.3389/fpls.2020.00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Warming in the high Arctic is occurring at the fastest rate on the planet, raising concerns over how this global change driver will influence plant community composition, the timing of vegetation phenological events, and the wildlife that rely on them. In this region, as much as 50% of near-surface permafrost is composed of thermally sensitive ground ice that when melted produces substantial changes in topography and microbiome conditions. We take advantage of natural variations in permafrost melt to conduct a space-for-time study on Ellesmere Island in northern Canada. We demonstrate that phenological timing can be delayed in thermokarst areas when compared to stable ground, and that this change is a function of shifting species composition in these vegetation communities as well as delayed timing within species. These findings suggest that a warming climate could result in an overall broadening of blooming and leafing windows at the landscape level when these delayed timings are taken into consideration with the projected advance of phenological timings in ice-poor areas. We emphasize that the impacts of geomorphic processes on key phenological drivers are essential for enhancing our understanding of community response to climate warming in the high Arctic, with implications for ecosystem functioning and trophic interactions.
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Affiliation(s)
- Chelsea Chisholm
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael S. Becker
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Geography, McGill University, Montreal, QC, Canada
| | - Wayne H. Pollard
- Department of Geography, McGill University, Montreal, QC, Canada
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15
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Li B, Lin F, Huang P, Guo W, Zheng Y. Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biol Res 2020; 53:21. [PMID: 32410692 PMCID: PMC7227249 DOI: 10.1186/s40659-020-00289-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/29/2020] [Indexed: 01/25/2023] Open
Abstract
Background Liriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm. Results We performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79. Conclusions The genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Wenying Guo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China. .,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.
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16
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Pang X, Liu H, Wu S, Yuan Y, Li H, Dong J, Liu Z, An C, Su Z, Li B. Species Identification of Oaks ( Quercus L., Fagaceae) from Gene to Genome. Int J Mol Sci 2019; 20:ijms20235940. [PMID: 31779118 PMCID: PMC6928813 DOI: 10.3390/ijms20235940] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 11/30/2022] Open
Abstract
Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.
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Affiliation(s)
- Xinbo Pang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Hongshan Liu
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Suran Wu
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Yangchen Yuan
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Haijun Li
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Junsheng Dong
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Zhaohua Liu
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Chuanzhi An
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Zhihai Su
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
| | - Bin Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Administration Bureau of Hongyashan State Owned Forest Farm in Yixian County, Yixian 074200, China; (H.L.); (S.W.); (Y.Y.); (H.L.); (J.D.); (Z.L.); (C.A.); (Z.S.)
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China
- Correspondence:
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Li S, Qian X, Zheng Z, Shi M, Chang X, Li X, Liu J, Tu T, Zhang D. DNA barcoding the flowering plants from the tropical coral islands of Xisha (China). Ecol Evol 2018; 8:10587-10593. [PMID: 30464830 PMCID: PMC6238132 DOI: 10.1002/ece3.4545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/19/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
AIM DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future. LOCATION Xisha Islands, China. METHODS This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic-based method to assess the barcoding resolution. RESULTS All the three DNA barcodes showed high levels of PCR success (96%-99%) and sequencing success (98%-100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%-90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes. MAIN CONCLUSIONS This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
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Affiliation(s)
- Shengchun Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zexin Zheng
- South China Agricultural UniversityGuangzhouChina
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaoyu Chang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaojuan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
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18
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Han K, Wang M, Zhang L, Wang C. Application of Molecular Methods in the Identification of Ingredients in Chinese Herbal Medicines. Molecules 2018; 23:E2728. [PMID: 30360419 PMCID: PMC6222746 DOI: 10.3390/molecules23102728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/16/2022] Open
Abstract
There are several kinds of Chinese herbal medicines originating from diverse sources. However, the rapid taxonomic identification of large quantities of Chinese herbal medicines is difficult using traditional methods, and the process of identification itself is prone to error. Therefore, the traditional methods of Chinese herbal medicine identification must meet higher standards of accuracy. With the rapid development of bioinformatics, methods relying on bioinformatics strategies offer advantages with respect to the speed and accuracy of the identification of Chinese herbal medicine ingredients. This article reviews the applicability and limitations of biochip and DNA barcoding technology in the identification of Chinese herbal medicines. Furthermore, the future development of the two technologies of interest is discussed.
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Affiliation(s)
- Ke Han
- School of Computer and Information Engineering, Harbin University of Commerce, Harbin 150028, China.
| | - Miao Wang
- Life sciences and Environmental Sciences Development Center, Harbin University of Commerce, Harbin 150010, China.
| | - Lei Zhang
- Life sciences and Environmental Sciences Development Center, Harbin University of Commerce, Harbin 150010, China.
| | - Chunyu Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
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19
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Speranskaya AS, Krinitsina AA, Shipulin GA, Khafizov KF, Logacheva MD. High-Throughput Sequencing for the Authentication of Food Products: Problems and Perspectives. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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21
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Tan S, Luo Y, Hollingsworth PM, Burgess KS, Xu K, Li D, Gao L. DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China. Ecol Evol 2018; 8:7195-7205. [PMID: 30073078 PMCID: PMC6065341 DOI: 10.1002/ece3.4254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 01/13/2023] Open
Abstract
Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH-psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree-based method. Amplification and sequencing success were highest for rbcL, followed by trnH-psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH-psbA (86.01%). The addition of trnH-psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co-occurring con-generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.
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Affiliation(s)
- Shao‐Lin Tan
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Ya‐Huang Luo
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
| | | | - Kevin S. Burgess
- Department of BiologyCollege of Letters and SciencesColumbus State UniversityUniversity System of GeorgiaColumbusGeorgia
| | - Kun Xu
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Lian‐Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
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22
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Wu Y, Li M, Yang Y, Jiang L, Liu M, Wang B, Wang Y. Authentication of Small Berry Fruit in Fruit Products by DNA Barcoding Method. J Food Sci 2018; 83:1494-1504. [DOI: 10.1111/1750-3841.14177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/01/2018] [Accepted: 04/06/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Yajun Wu
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Meige Li
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Yange Yang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Li Jiang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Mingchang Liu
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Bin Wang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Yingchun Wang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
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Kuzmina ML, Braukmann TWA, Fazekas AJ, Graham SW, Dewaard SL, Rodrigues A, Bennett BA, Dickinson TA, Saarela JM, Catling PM, Newmaster SG, Percy DM, Fenneman E, Lauron-Moreau A, Ford B, Gillespie L, Subramanyam R, Whitton J, Jennings L, Metsger D, Warne CP, Brown A, Sears E, Dewaard JR, Zakharov EV, Hebert PDN. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700079. [PMID: 29299394 PMCID: PMC5749818 DOI: 10.3732/apps.1700079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/26/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. METHODS Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery. RESULTS Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae). DISCUSSION Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
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Affiliation(s)
- Maria L. Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Aron J. Fazekas
- The Arboretum, University of Guelph, 50 Stone Road East, Ontario N1G 2W1, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephanie L. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Anuar Rodrigues
- Office of the Vice-Principal Academic and Dean, University of Toronto, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Bruce A. Bennett
- Yukon Conservation Data Centre (CDC), Whitehorse, Yukon Territory Y1A 2C6, Canada
| | - Timothy A. Dickinson
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Paul M. Catling
- The Agriculture and Agri-Food Canada Collection of Vascular Plants (DAO), 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Steven G. Newmaster
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Diana M. Percy
- Natural History Museum, Cromwell Road, Kensington, London SW75BD, United Kingdom
| | - Erin Fenneman
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aurélien Lauron-Moreau
- Institut de recherche en biologie végétale, Université de Montréal, 2900 Edouard Montpetit Boulevard, Montréal, Québec H3T 1J4, Canada
| | - Bruce Ford
- University of Manitoba Vascular Plant Herbarium (WIN), Department of Biological Sciences, University of Manitoba, 66 Chancellors Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lynn Gillespie
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Ragupathy Subramanyam
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Jeannette Whitton
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Linda Jennings
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deborah Metsger
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
| | - Connor P. Warne
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Allison Brown
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Elizabeth Sears
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Jeremy R. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
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Birch JL, Walsh NG, Cantrill DJ, Holmes GD, Murphy DJ. Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia. PLoS One 2017; 12:e0186259. [PMID: 29084279 PMCID: PMC5662090 DOI: 10.1371/journal.pone.0186259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/28/2017] [Indexed: 01/09/2023] Open
Abstract
In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.
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Affiliation(s)
- Joanne L. Birch
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
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Yao PC, Gao HY, Wei YN, Zhang JH, Chen XY, Li HQ. Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size. PLoS One 2017; 12:e0185311. [PMID: 28934362 PMCID: PMC5608404 DOI: 10.1371/journal.pone.0185311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022] Open
Abstract
Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01). These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11–15.
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Affiliation(s)
- Peng-Cheng Yao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hai-Yan Gao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Ya-Nan Wei
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian-Hang Zhang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiao-Yong Chen
- School of Ecological and Environmental Sciences, Tiantong National Station of Forest Ecosystem, East China Normal University, Shanghai, China
- * E-mail: (HQL); (XYC)
| | - Hong-Qing Li
- School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail: (HQL); (XYC)
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Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Comput Biol Chem 2017; 71:20-31. [PMID: 28961510 DOI: 10.1016/j.compbiolchem.2017.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 02/01/2023]
Abstract
The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated and sequenced 15 rbcL and six matK fragments, but our analysis of the resultant sequences demonstrated a limited ability of matK and rbcL in distinguishing between Triticum accessions. Therefore, we pursued a bioinformatics approach to determine the most useful loci which may be used as DNA barcodes for the Triticum spp. We obtained the 10 available chloroplast genomes of the 10 Triticum species and sub-species from NCBI, and performed chloroplast genome-wide analysis to find the potential barcode loci. A total of 134 chloroplast genes, gene combinations, intergenic regions and intergenic region combinations were tested using a Tree-based method. We were unable to discriminate between Triticum species by using chloroplast genes, gene combinations and intergenic regions. However, a combination of the intergenic region (trnfM-trnT) with either (trnD-psbM), (petN-trnC), (matK-rps16) or (rbcL-psaI) demonstrated a very high discrimination capacity, suggesting their utilization as DNA barcodes for the Triticum plants. Furthermore, our novel DNA barcodes demonstrated high discrimination capacity for other Poaceae members.
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Mezzasalma V, Bruni I, Fontana D, Galimberti A, Magoni C, Labra M. A DNA barcoding approach for identifying species in Amazonian traditional medicine: The case of Piri-Piri. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Pei N, Chen B, Kress WJ. Advances of Community-Level Plant DNA Barcoding in China. FRONTIERS IN PLANT SCIENCE 2017; 8:225. [PMID: 28270824 PMCID: PMC5318406 DOI: 10.3389/fpls.2017.00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/06/2017] [Indexed: 05/31/2023]
Abstract
DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation. Lastly, we raised five possible directions; specifically, proposing a "purpose-driven barcode" fit for multi-level applications, developing new integrative sequencing strategies, pushing DNA barcoding beyond terrestrial ecosystem, constructing national-level DNA barcode sequence libraries for special plant groups, and establishing intelligent identification systems or online server platforms. These efforts will be potentially valuable to explore large-scale biodiversity patterns, the origin and evolution of life, and will also facilitate preservation and utilization of biodiversity resources.
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Affiliation(s)
- Nancai Pei
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of ForestryGuangzhou, China
| | - Bufeng Chen
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of ForestryGuangzhou, China
| | - W. J. Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian InstitutionWashington, DC, USA
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O. Elansary H, Ashfaq M, Ali HM, Yessoufou K. The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry. PLoS One 2017; 12:e0172170. [PMID: 28199378 PMCID: PMC5310869 DOI: 10.1371/journal.pone.0172170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/31/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance. The sequence recovery was similar for rbcL (96.4%) and matK (84%), but the number of specimens assigned correctly to the respective genera and species was lower for rbcL (75% and 29%) than matK (85% and 40%). The combination of rbcL and matK brought the number of correct generic and species assignments to 83.4% and 40%, respectively. Individually, the efficiency of both markers varied among different plant families; for example, all palm specimens (Arecaceae) were correctly assigned to species while only one individual of Asteraceae was correctly assigned to species. Further, barcodes reliably assigned ornamental horticultural and medicinal plants correctly to genus while they showed a lower or no success in assigning these plants to species and cultivars. For future, we recommend the combination of a complementary barcode (e.g. ITS or trnH-psbA) with rbcL + matK to increase the performance of taxa identification. By aiding species identification of horticultural crops and ornamental palms, the analysis of the barcode regions will have large impact on horticultural industry.
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Affiliation(s)
- Hosam O. Elansary
- Floriculture, Ornamental Horticulture and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- * E-mail: ,
| | - Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, ON, Guelph, Canada
| | - Hayssam M. Ali
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Timber Trees Research Department, Sabahia Horticulture Research Station, Horticulture Research Institute, Agriculture Research Center, Alexandria, Egypt
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK campus, Johannesburg, South Africa
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Saarela JM, Sokoloff PC, Bull RD. Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora. PeerJ 2017; 5:e2835. [PMID: 28194307 PMCID: PMC5300018 DOI: 10.7717/peerj.2835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/30/2022] Open
Abstract
The Coppermine River in western Nunavut is one of Canada's great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km2, extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014. Results are presented in an annotated checklist, including citation of all specimens examined, comments on taxonomy and distribution, and photographs for a subset of taxa. The vascular plant flora comprises 300 species (311 taxa), a 36.6% increase from the 190 species documented by previous collections made in the area over the last century, and is considerably more diverse than other local floras on mainland Nunavut. We document 207 taxa for Kugluk (Bloody Falls) Territorial Park, an important protected area for plants on mainland Nunavut. A total of 190 taxa are newly recorded for the study area. Of these, 14 taxa (13 species and one additional variety) are newly recorded for Nunavut (Allium schoenoprasum, Carex capitata, Draba lonchocarpa, Eremogone capillaris subsp. capillaris, Sabulina elegans, Eleocharis quinqueflora, Epilobium cf. anagallidifolium, Botrychium neolunaria, Botrychium tunux, Festuca altaica, Polygonum aviculare, Salix ovalifolia var. arctolitoralis, Salix ovalifolia var. ovalifolia and Stuckenia pectinata), seven species are newly recorded for mainland Nunavut (Carex gynocrates, Carex livida, Cryptogramma stelleri, Draba simmonsii, Festuca viviparoidea subsp. viviparoidea, Juncus alpinoarticulatus subsp. americanus and Salix pseudomyrsinites) and 56 range extensions are reported. The psbA-trnH and rbcL DNA sequence data were used to help identify the three Botrychium taxa recorded in the study area. Three new combinations are proposed: Petasites frigidus subsp. sagittatus (Banks ex Pursh) Saarela, Carex petricosa subsp. misandroides (Fernald) Saarela and Carex simpliciuscula subsp. subholarctica (T. V. Egorova) Saarela.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section and Centre for Arctic Knowledge & Exploration, Research and Collections, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Paul C. Sokoloff
- Botany Section and Centre for Arctic Knowledge & Exploration, Research and Collections, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Roger D. Bull
- Botany Section and Centre for Arctic Knowledge & Exploration, Research and Collections, Canadian Museum of Nature, Ottawa, ON, Canada
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Braukmann TWA, Kuzmina ML, Sills J, Zakharov EV, Hebert PDN. Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. PLoS One 2017; 12:e0169515. [PMID: 28072819 PMCID: PMC5224991 DOI: 10.1371/journal.pone.0169515] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/18/2016] [Indexed: 01/30/2023] Open
Abstract
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.
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Affiliation(s)
- Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Maria L. Kuzmina
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jesse Sills
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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More RP, Mane RC, Purohit HJ. matK-QR classifier: a patterns based approach for plant species identification. BioData Min 2016; 9:39. [PMID: 27990177 PMCID: PMC5148893 DOI: 10.1186/s13040-016-0120-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/02/2016] [Indexed: 12/24/2022] Open
Abstract
Background DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK (matK) and ribulose-1, 5-bisphosphate carboxylase (rbcL) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification. Methods In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. Results Due to the higher discrimination success obtained with the matK as compared to the rbcL, we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK-QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species. Conclusions This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK-QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0120-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravi Prabhakar More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India ; Present Institute: Division of Molecular Entomology, ICAR- National Bureau of Agricultural Insect Resources (NBAIR), Hebbal, Bengaluru, 560024 Karnataka India
| | | | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India
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Hollingsworth PM, Li DZ, van der Bank M, Twyford AD. Telling plant species apart with DNA: from barcodes to genomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150338. [PMID: 27481790 PMCID: PMC4971190 DOI: 10.1098/rstb.2015.0338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 12/17/2022] Open
Abstract
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China
| | - Michelle van der Bank
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Roslin T, Majaneva S. The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite! Genome 2016; 59:603-28. [PMID: 27484156 DOI: 10.1139/gen-2015-0229] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.
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Affiliation(s)
- Tomas Roslin
- a Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden.,b Spatial Foodweb Ecology Group, Department of Agricultural Sciences, PO Box 27, (Latokartanonkaari 5), FI-00014 University of Helsinki, Finland
| | - Sanna Majaneva
- c Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden
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35
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Liu J, Yan HF, Ge XJ. The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China. PLoS One 2016; 11:e0153008. [PMID: 27050315 PMCID: PMC4822852 DOI: 10.1371/journal.pone.0153008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
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.
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Affiliation(s)
- Juan Liu
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Jiangxi Agriculture University, Nanchang, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
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36
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Affiliation(s)
- Michael S. Becker
- Department of Geography; McGill University; 805 Sherbrooke Street W Montreal QC H3A 0B9 Canada
- Center for Macroecology, Evolution and Climate; The Natural History Museum of Denmark; University of Copenhagen; Universitetsparken 15 Copenhagen DK-2100 Denmark
| | - Wayne H. Pollard
- Department of Geography; McGill University; 805 Sherbrooke Street W Montreal QC H3A 0B9 Canada
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37
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Pinar MS, Dizkirici A, Yigit O. Understanding taxonomic position of local endemic Agropyron deweyi (Poaceae) using morphological characters and sequences of nuclear and chloroplast DNA regions. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Bello A, Daru BH, Stirton CH, Chimphango SBM, van der Bank M, Maurin O, Muasya AM. DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera. AOB PLANTS 2015; 7:plv124. [PMID: 26507570 PMCID: PMC4670488 DOI: 10.1093/aobpla/plv124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) data set as a better barcode than single regions. We found a high score (100 %) of correct identification of individuals to their respective genera but a very low score (<50 %) in identifying them to species. We found a considerable match (54 %) between genetic species and morphologically delimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of the phylogenetic signal in recently diverged lineages of the CFR.
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Affiliation(s)
- Abubakar Bello
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Barnabas H Daru
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - Charles H Stirton
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Samson B M Chimphango
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Olivier Maurin
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - A Muthama Muasya
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
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Pei N, Erickson DL, Chen B, Ge X, Mi X, Swenson NG, Zhang JL, Jones FA, Huang CL, Ye W, Hao Z, Hsieh CF, Lum S, Bourg NA, Parker JD, Zimmerman JK, McShea WJ, Lopez IC, Sun IF, Davies SJ, Ma K, Kress WJ. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots. Sci Rep 2015; 5:15127. [PMID: 26456472 PMCID: PMC4601009 DOI: 10.1038/srep15127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.
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Affiliation(s)
- Nancai Pei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - David L. Erickson
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Bufeng Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Xuejun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Nathan G. Swenson
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Jin-Long Zhang
- Flora Conservation Department, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, N.T., Hong Kong
| | - Frank A. Jones
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
| | - Chun-Lin Huang
- Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Wanhui Ye
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Zhanqing Hao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Chang-Fu Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Roosevelt Road 1, Taipei, Taiwan
| | - Shawn Lum
- National Institute of Education of Nanyang Technological University, Singapore 637616
| | - Norman A. Bourg
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - John D. Parker
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Jess K. Zimmerman
- Institute for Tropical Ecosystem Studies, University of Puerto Rico, San Juan Puerto Rico, 00936-8377, USA
| | | | - Ida C. Lopez
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Stuart J. Davies
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - W. John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
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Gillespie LJ, Saarela JM, Sokoloff PC, Bull RD. New vascular plant records for the Canadian Arctic Archipelago. PHYTOKEYS 2015; 52:23-79. [PMID: 26311505 PMCID: PMC4549883 DOI: 10.3897/phytokeys.52.8721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/15/2015] [Indexed: 06/04/2023]
Abstract
The Canadian Arctic Archipelago is a vast region of approximately 1,420,000 km(2), with a flora characterized by low species diversity, low endemicity, and little influence by alien species. New records of vascular plant species are documented here based on recent fieldwork on Victoria and Baffin Islands; additional records based on recent literature sources are mentioned. This paper serves as an update to the 2007 publication Flora of the Canadian Arctic Archipelago, and brings the total number of vascular plants for the region to 375 species and infraspecific taxa, an increase of 7.7%. Three families (Amaranthaceae, Juncaginaceae, Pteridaceae) and seven genera (Cherleria L., Cryptogramma R. Br., Platanthera Rich., Sabulina Rchb., Suaeda Forssk. ex J.F. Gmel., Triglochin L., Utricularia L.) are added to the flora, and one genus is deleted (Minuartia L.). Five species are first records for Nunavut (Arenarialongipedunculata Hultén, Cryptogrammastelleri (S.G. Gmel.) Prantl, Puccinelliabanksiensis Consaul, Saxifragaeschscholtzii Sternb., Utriculariaochroleuca R.W. Hartm.).
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Affiliation(s)
- Lynn J. Gillespie
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Jeffery M. Saarela
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Paul C. Sokoloff
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Roger D. Bull
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
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Xu C, Dong W, Shi S, Cheng T, Li C, Liu Y, Wu P, Wu H, Gao P, Zhou S. Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques. Mol Ecol Resour 2015; 15:1366-74. [DOI: 10.1111/1755-0998.12413] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 03/21/2015] [Accepted: 04/04/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shuo Shi
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- College of Life Science; Hebei Normal University; Shijiazhuang 050024 China
| | - Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Ping Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Hongkun Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Peng Gao
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
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Schneider SC, Rodrigues A, Moe TF, Ballot A. DNA barcoding the genus Chara: molecular evidence recovers fewer taxa than the classical morphological approach. JOURNAL OF PHYCOLOGY 2015; 51:367-380. [PMID: 26986531 DOI: 10.1111/jpy.12282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 11/25/2014] [Indexed: 06/05/2023]
Abstract
Charophytes (Charales) are benthic algae with a complex morphology. They are vulnerable to ecosystem changes, such as eutrophication, and are red-listed in many countries. Accurate identification of Chara species is critical for understanding their diversity and for documenting changes in species distribution. Species delineation is, however, complicated, because of high phenotypic plasticity. We used barcodes of the ITS2, matK and rbcL regions to test if the distribution of barcode haplotypes among individuals is consistent with species boundaries as they are currently understood. The study included freshly collected and herbarium material of 91 specimens from 10 European countries, Canada and Argentina. Results showed that herbarium specimens are useful as a source of material for genetic analyses for aquatic plants like Chara. rbcL and matK had highest sequence recoverability, but rbcL had a somewhat lower discriminatory power than ITS2 and matK. The tree resulting from the concatenated data matrix grouped the samples into six main groups contrary to a traditional morphological approach that consisted of 14 different taxa. A large unresolved group consisted of C. intermedia, C. hispida, C. horrida, C. baltica, C. polyacantha, C. rudis, C. aculeolata, and C. corfuensis. A second unresolved group consisted of C. virgata and C. strigosa. The taxa within each of the unresolved groups shared identical barcode sequences on the 977 positions of the concatenated data matrix. The morphological differences of taxa within both unresolved groups include the number and length of spine cells, stipulodes, and bract cells. We suggest that these morphological traits have less taxonomic relevance than hitherto assumed.
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Affiliation(s)
- Susanne C Schneider
- Norwegian Institute for Water Research, Gaustadalleen 21, Oslo, 0349, Norway
| | - Anuar Rodrigues
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Therese Fosholt Moe
- Norwegian Institute for Water Research, Gaustadalleen 21, Oslo, 0349, Norway
| | - Andreas Ballot
- Norwegian Institute for Water Research, Gaustadalleen 21, Oslo, 0349, Norway
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TALLEI TRINAEKAWATI, KOLONDAM BEIVYJONATHAN. DNA Barcoding of Sangihe Nutmeg ( Myristica fragrans ) using mat K Gene. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.4308/hjb.22.1.41] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Yan LJ, Liu J, Möller M, Zhang L, Zhang XM, Li DZ, Gao LM. DNA barcoding ofRhododendron(Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains. Mol Ecol Resour 2014; 15:932-44. [DOI: 10.1111/1755-0998.12353] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/22/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Michael Möller
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Lin Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xue-Mei Zhang
- Landscape and Horticultural College; Yunnan Agricultural University; Kunming 650201 Yunnan China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
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Liu J, Yan HF, Newmaster SG, Pei N, Ragupathy S, Ge XJ. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12276] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Nancai Pei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Subramanyam Ragupathy
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
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Nithaniyal S, Newmaster SG, Ragupathy S, Krishnamoorthy D, Vassou SL, Parani M. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India. PLoS One 2014; 9:e107669. [PMID: 25259794 PMCID: PMC4178033 DOI: 10.1371/journal.pone.0107669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
- Interdisciplinary School of Indian System of Medicine, SRM University, Chennai, India
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
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Wang XC, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang JH, Cai D, Li JQ. ITS1: a DNA barcode better than ITS2 in eukaryotes? Mol Ecol Resour 2014; 15:573-86. [PMID: 25187125 DOI: 10.1111/1755-0998.12325] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 11/30/2022]
Abstract
A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
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Affiliation(s)
- Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, 151 MaLianWa North Road, Beijing, 100193, China
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Ojeda DI, Santos-Guerra A, Oliva-Tejera F, Jaen-Molina R, Caujapé-Castells J, Marrero-Rodríguez A, Cronk Q. DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa. AOB PLANTS 2014; 6:plu050. [PMID: 25147310 PMCID: PMC4168286 DOI: 10.1093/aobpla/plu050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.
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Affiliation(s)
- Dario I Ojeda
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
| | | | - Felicia Oliva-Tejera
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Ruth Jaen-Molina
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Aguedo Marrero-Rodríguez
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Quentin Cronk
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
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Peterson PM, Romaschenko K, Soreng RJ. A laboratory guide for generating DNA barcodes in grasses: a case study ofLeptochloas.l. (Poaceae: Chloridoideae). ACTA ACUST UNITED AC 2014. [DOI: 10.1080/00837792.2014.927555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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