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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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Chen Y, Zhu X, Loukopoulos P, Weston LA, Albrecht DE, Quinn JC. Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding. Sci Rep 2021; 11:16055. [PMID: 34362980 PMCID: PMC8346583 DOI: 10.1038/s41598-021-95610-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.
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Affiliation(s)
- Yuchi Chen
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Xiaocheng Zhu
- grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - Panayiotis Loukopoulos
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Leslie A. Weston
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - David E. Albrecht
- grid.467784.e0000 0001 2231 5722Australian National Herbarium, Centre for Australian National Biodiversity Research (a Joint Venture Between Parks Australia and CSIRO), Canberra, Australian Capital Territory, Australia
| | - Jane C. Quinn
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
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Rimet F, Aylagas E, Borja Á, Bouchez A, Canino A, Chauvin C, Chonova T, Ciampor Jr F, Costa FO, Ferrari BJD, Gastineau R, Goulon C, Gugger M, Holzmann M, Jahn R, Kahlert M, Kusber WH, Laplace-Treyture C, Leese F, Leliaert F, Mann DG, Marchand F, Méléder V, Pawlowski J, Rasconi S, Rivera S, Rougerie R, Schweizer M, Trobajo R, Vasselon V, Vivien R, Weigand A, Witkowski A, Zimmermann J, Ekrem T. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.58056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
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Ecology and Environmental Impact of Myriophyllum heterophyllum, an Aggressive Invader in European Waterways. DIVERSITY 2020. [DOI: 10.3390/d12040127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The submerged evergreen aquatic plant Myriophyllum heterophyllum is among the worst invasive species in Europe, causing severe problems especially in navigation channels but also lentic systems. This review aims to provide a comprehensive overview and update on the current distribution and risks associated with this species in Europe and elsewhere. We provide an evaluation of current identification keys since misidentification can underestimate the extent of its spread. In addition, hybridization with other milfoil species has been reported in North America but seems unlikely in Europe. We further describe in detail the ecology, specifically resource requirements and biotic interactions with other plants, herbivores and pathogens as well as the spread potential of the species. Good knowledge of the autecology and synecology of this species should allow some conclusions about environmental factors possibly related to its invasive growth and is mandatory for the preparation of species-specific management measures. Finally, we outline the status of regulations coming into effect in member states of the European Union (EU) and provide an overview of applied and potential management practices.
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Amandita FY, Rembold K, Vornam B, Rahayu S, Siregar IZ, Kreft H, Finkeldey R. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecol Evol 2019; 9:1858-1868. [PMID: 30847077 PMCID: PMC6392390 DOI: 10.1002/ece3.4875] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/02/2022] Open
Abstract
The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.
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Affiliation(s)
- Fitri Y. Amandita
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- Research and Development Center for Environmental Quality and Laboratory
| | - Katja Rembold
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
- Botanical Garden of the University of BernBernSwitzerland
| | - Barbara Vornam
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
| | - Sri Rahayu
- Bogor Botanical GardenLembaga Ilmu Pengetahuan IndonesiaBogorIndonesia
| | | | - Holger Kreft
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
| | - Reiner Finkeldey
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- University of KasselKasselGermany
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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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Liu J, Jiang J, Song S, Tornabene L, Chabarria R, Naylor GJP, Li C. Multilocus DNA barcoding - Species Identification with Multilocus Data. Sci Rep 2017; 7:16601. [PMID: 29192249 PMCID: PMC5709489 DOI: 10.1038/s41598-017-16920-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.
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Affiliation(s)
- Junning Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Shuli Song
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Luke Tornabene
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ryan Chabarria
- College of Science & Engineering, Texas A&M University - Corpus Christi, Corpus Christi, TX, 78412-5806, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.
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Xu SZ, Li ZY, Jin XH. DNA barcoding of invasive plants in China: A resource for identifying invasive plants. Mol Ecol Resour 2017; 18:128-136. [PMID: 28865184 DOI: 10.1111/1755-0998.12715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/05/2023]
Abstract
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.
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Affiliation(s)
- Song-Zhi Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhen-Yu Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Tang YL, Wu YS, Huang RS, Chao NX, Liu Y, Xu P, Li KZ, Cai DZ, Luo Y. Molecular identification of Uncaria (Gouteng) through DNA barcoding. Chin Med 2016; 11:3. [PMID: 26843891 PMCID: PMC4739391 DOI: 10.1186/s13020-015-0072-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 12/07/2015] [Indexed: 01/29/2023] Open
Abstract
Background While DNA barcoding is an important technology for the authentication of the botanical origins of Chinese medicines, the suitable markers for DNA barcoding of the genus Uncaria have not been reported yet. This study aims to determine suitable markers for DNA barcoding of the genus Uncaria (Gouteng). Methods Genomic DNA was extracted from the freshly dried leaves of Uncaria plants by a Bioteke’s Plant Genomic DNA Extraction Kit. Five candidate DNA barcode sites (ITS2, rbcL, psbA–trnH, ITS, and matK) were amplified by PCR with established primers. The purified PCR products were bidirectionally sequenced with appropriate amplification primers in an ABI-PRISM3730 instrument. The candidate DNA barcodes of 257 accessions of Uncaria in GenBank were aligned by ClustalW. Sequence assembly and consensus sequence generation were performed with CodonCode Aligner 3.7.1. The identification efficiency of the candidate DNA barcodes was evaluated with BLAST and nearest distance methods. The interspecific divergence and intraspecific variation were assessed by the Kimura 2-Parameter model. Genetic distances were computed with Molecular Evolutionary Genetics Analysis 6.0. Results The accessions of the five candidate DNA barcodes from 11 of 12 species of Uncaria in China and four species from other countries were included in the analysis, while 54 of total accessions were submitted to GenBank. In a comparison of the interspecific genetic distances of the five candidate barcodes, psbA–trnH exhibited the highest interspecific divergence based on interspecific distance, theta prime, and minimum interspecific distance, followed by ITS2. The distribution of the interspecific distance of ITS2 and psbA–trnH was higher than the corresponding intraspecific distance. Additionally, psbA–trnH showed 95.9 % identification efficiency by both the BLAST and nearest distance methods regardless of species or genus level. ITS2 exhibited 92.2 % identification efficiency by the nearest distance method, but 87 % by the BLAST method. Conclusion While psbA–trnH and ITS2 (used alone) were applicable barcodes for species authentication of Uncaria, psbA–trnH was a more suitable barcode for authentication of Uncaria macrophylla. Electronic supplementary material The online version of this article (doi:10.1186/s13020-015-0072-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yin-Lin Tang
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, 530021 Nanning, Guangxi China ; Clinical Laboratory, Maternal and Child Health Hospital of Guangxi, 530003 Nanning, Guangxi China
| | - Yao-Sheng Wu
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, 530021 Nanning, Guangxi China
| | - Rui-Song Huang
- Guangxi Academy of Minority Nationality Medicine and Pharmacology, 530001 Nanning, Guangxi China
| | - Nai-Xia Chao
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, 530021 Nanning, Guangxi China
| | - Yong Liu
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; School of Pharmacy, Guangdong Medical College, 523808 Dongguan, Guangdong China
| | - Peng Xu
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Liuzhou People's Hospital, 545006 Liuzhou, Guangxi China
| | - Ke-Zhi Li
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Affiliated Cancer Hospital of Guangxi Medical University, 530021 Nanning, Guangxi China
| | - Dan-Zhao Cai
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, 530021 Nanning, Guangxi China
| | - Yu Luo
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 530021 Nanning, Guangxi China ; Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, 530021 Nanning, Guangxi China
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10
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DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0854-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Corrigendum. Mol Ecol Resour 2014. [DOI: 10.1111/1755-0998.12346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLoS One 2013; 8:e77982. [PMID: 24348895 PMCID: PMC3865322 DOI: 10.1371/journal.pone.0077982] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/08/2013] [Indexed: 01/16/2023] Open
Abstract
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Paul C. Sokoloff
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Lynn J. Gillespie
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Laurie L. Consaul
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Roger D. Bull
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
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13
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Pyšek P, Hulme PE, Meyerson LA, Smith GF, Boatwright JS, Crouch NR, Figueiredo E, Foxcroft LC, Jarošík V, Richardson DM, Suda J, Wilson JRU. Hitting the right target: taxonomic challenges for, and of, plant invasions. AOB PLANTS 2013; 5:plt042. [PMCID: PMC4455668 DOI: 10.1093/aobpla/plt042] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/10/2013] [Indexed: 05/25/2023]
Abstract
Taxonomic resources are essential for the effective management of invasive plants because biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa, and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches to improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.
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Affiliation(s)
- Petr Pyšek
- Institute of Botany, Department of Invasion Ecology, Academy of Sciences of the Czech Republic, CZ-252 43 Průhonice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Prague, Czech Republic
| | - Philip E. Hulme
- The Bio-Protection Research Centre, Lincoln University, PO Box 84, Canterbury, New Zealand
| | - Laura A. Meyerson
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Road, Kingston, RI 02881, USA
| | - Gideon F. Smith
- South African National Biodiversity Institute, Biosystematics Research and Biodiversity Collections Division, Private Bag X101, Pretoria 0001, South Africa
- H. G. W. J. Schweickerdt Herbarium, Department of Plant Science, University of Pretoria, Pretoria 0002, South Africa
- Centre for Functional Ecology, Departamento de Ciências da Vida, Universidade de Coimbra, 3001-455 Coimbra, Portugal
| | - James S. Boatwright
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Belville 7535, Cape Town, South Africa
| | - Neil R. Crouch
- Ethnobotany Unit, South African National Biodiversity Institute, PO Box 52099, 4007 Berea Road, Durban, South Africa
- School of Chemistry, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Estrela Figueiredo
- Centre for Functional Ecology, Departamento de Ciências da Vida, Universidade de Coimbra, 3001-455 Coimbra, Portugal
- Department of Botany, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth 6031, South Africa
| | - Llewellyn C. Foxcroft
- Conservation Services, South African National Parks, Skukuza 1350, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
| | - Vojtěch Jarošík
- Institute of Botany, Department of Invasion Ecology, Academy of Sciences of the Czech Republic, CZ-252 43 Průhonice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Prague, Czech Republic
| | - David M. Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
- Institute of Botany, Laboratory of Flow Cytometry, Academy of Sciences of the Czech Republic, CZ-252 43 Průhonice, Czech Republic
| | - John R. U. Wilson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Invasive Species Programme, Claremont 7735, South Africa
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Pellicer J, Kelly L, Magdalena C, Leitch I. Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies). Genome 2013; 56:437-49. [DOI: 10.1139/gen-2013-0039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nymphaeales are the most species-rich lineage of the earliest diverging angiosperms known as the ANA grade (Amborellales, Nymphaeales, Austrobaileyales), and they have received considerable attention from morphological, physiological, and ecological perspectives. Although phylogenetic relationships between these three lineages of angiosperms are mainly well resolved, insights at the whole genome level are still limited because of a dearth of information. To address this, genome sizes and chromosome numbers in 34 taxa, comprising 28 species were estimated and analysed together with previously published data to provide an overview of genome size and chromosome diversity in Nymphaeales. Overall, genome sizes were shown to vary 10-fold and chromosome numbers and ploidy levels ranged from 2n = 2x = 18 to 2n = 16x = ∼224. Distinct patterns of genome diversity were apparent, reflecting the differential incidence of polyploidy, changes in repetitive DNA content, and chromosome rearrangements within and between genera. Using model-based approaches, ancestral genome size and basic chromosome numbers were reconstructed to provide insights into the dynamics of genome size and chromosome number evolution. Finally, by combining additional data from Amborellales and Austrobaileyales, a comprehensive overview of genome sizes and chromosome numbers in these early diverging angiosperms is presented.
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Affiliation(s)
- J. Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - L.J. Kelly
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- Queen Mary University of London, School of Biological and Chemical Science, London E1 4NS, UK
| | - C. Magdalena
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - I.J. Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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