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deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
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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. Appl Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Telfer AC, Young MR, Quinn J, Perez K, Sobel CN, Sones JE, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko AV, Cadel A, Brown A, Pages A, Castillo AH, Nicolai A, Glenn Mockford BM, Bukowski B, Wilson B, Trojahn B, Lacroix CA, Brimblecombe C, Hay C, Ho C, Steinke C, Warne CP, Garrido Cortes C, Engelking D, Wright D, Lijtmaer DA, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin DD, Dobias D, Sears E, Richard E, Damstra E, Zakharov EV, Laberge F, Collins GE, Blagoev GA, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton KKS, D'Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee KM, Xie L, Lu L, Penev L, Gonzalez M, Rosati ME, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova NV, Jones N, Weerasuriya N, Monkhouse N, Lavinia PD, Jannetta P, Hanisch PE, McMullin RT, Ojeda Flores R, Mouttet R, Vender R, Labbee RN, Forsyth R, Lauder R, Dickson R, Kroft R, Miller SE, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert PDN, deWaard JR. Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodivers Data J 2015; 3:e6313. [PMID: 26379469 PMCID: PMC4568406 DOI: 10.3897/bdj.3.e6313] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. NEW INFORMATION The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
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Affiliation(s)
| | | | - Jenna Quinn
- rare Charitable Research Reserve, Cambridge, Canada
| | - Kate Perez
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | | | | | | | | | - Alex Cadel
- University of Waterloo, Waterloo, Canada
| | | | - Anais Pages
- Université de Montpellier, Montpellier, France
| | | | | | | | - Belén Bukowski
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Bill Wilson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Christmas Ho
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | - Dario A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - David Gascoigne
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Dirk Neumann
- SNSB, Zoologische Staatssammlung Muenchen, Munich, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | - Emily Damstra
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Gerrie Grainge
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Ian Hogg
- University of Waikato, Hamilton, New Zealand
| | | | - Janet Topan
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Jason Bracey
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Jerry Guenther
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Joshua Persi
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Kevin Grundy
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Kirsti Nghidinwa
- Ministry of Environment and Tourism in Namibia, Windhoek, Namibia
| | | | | | - Linxi Xie
- The University of Western Ontario, London, Canada
| | - Liuqiong Lu
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | - Mailyn Gonzalez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Margaret E Rosati
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | | | | | | | | | | | - Miriam Bauman
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | | | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | - Priscila E Hanisch
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | | | - Raphaëlle Mouttet
- ANSES, Laboratoire de la Santé des Végétaux, Montferrier sur Lez, France
| | - Reid Vender
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Ross Dickson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Ruth Kroft
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Scott E Miller
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | - Sishir Panthi
- Ministry of Forests and Soil Conservation, Kathmandu, Nepal
| | | | | | - Suresh Naik
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Tatsiana Lipinskaya
- Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Thibaud Decaëns
- Université de Montpellier Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| | | | | | - Tom Woodcock
- rare Charitable Research Reserve, Cambridge, Canada
| | - Tomas Roslin
- University of Helsinki, Helsinki, Finland
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tony Zammit
- Grand River Conservation Authority, Cambridge, Canada
| | | | - Vlad Dinca
- Biodiversity Institute of Ontario, Guelph, Canada
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