1
|
Menegon M, Cantaloni C, Rodriguez-Prieto A, Centomo C, Abdelfattah A, Rossato M, Bernardi M, Xumerle L, Loader S, Delledonne M. On site DNA barcoding by nanopore sequencing. PLoS One 2017; 12:e0184741. [PMID: 28977016 PMCID: PMC5627904 DOI: 10.1371/journal.pone.0184741] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/30/2017] [Indexed: 11/19/2022] Open
Abstract
Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.
Collapse
Affiliation(s)
- Michele Menegon
- Tropical Biodiversity section, Science Museum of Trento, Trento, Italy
| | - Chiara Cantaloni
- Personal Genomics s.r.l., Verona, Italy
- Functional Genomics Center, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Cesare Centomo
- Functional Genomics Center, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Marzia Rossato
- Functional Genomics Center, Department of Biotechnology, University of Verona, Verona, Italy
| | - Massimo Bernardi
- Tropical Biodiversity section, Science Museum of Trento, Trento, Italy
| | - Luciano Xumerle
- Personal Genomics s.r.l., Verona, Italy
- Functional Genomics Center, Department of Biotechnology, University of Verona, Verona, Italy
| | - Simon Loader
- Biogeography Research group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Department of Life Sciences, University of Roehampton, London, United Kingdom
| | - Massimo Delledonne
- Personal Genomics s.r.l., Verona, Italy
- Functional Genomics Center, Department of Biotechnology, University of Verona, Verona, Italy
| |
Collapse
|
2
|
Juffe-Bignoli D, Brooks TM, Butchart SHM, Jenkins RB, Boe K, Hoffmann M, Angulo A, Bachman S, Böhm M, Brummitt N, Carpenter KE, Comer PJ, Cox N, Cuttelod A, Darwall WRT, Di Marco M, Fishpool LDC, Goettsch B, Heath M, Hilton-Taylor C, Hutton J, Johnson T, Joolia A, Keith DA, Langhammer PF, Luedtke J, Nic Lughadha E, Lutz M, May I, Miller RM, Oliveira-Miranda MA, Parr M, Pollock CM, Ralph G, Rodríguez JP, Rondinini C, Smart J, Stuart S, Symes A, Tordoff AW, Woodley S, Young B, Kingston N. Assessing the Cost of Global Biodiversity and Conservation Knowledge. PLoS One 2016; 11:e0160640. [PMID: 27529491 PMCID: PMC4986939 DOI: 10.1371/journal.pone.0160640] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/24/2016] [Indexed: 11/18/2022] Open
Abstract
Knowledge products comprise assessments of authoritative information supported by standards, governance, quality control, data, tools, and capacity building mechanisms. Considerable resources are dedicated to developing and maintaining knowledge products for biodiversity conservation, and they are widely used to inform policy and advise decision makers and practitioners. However, the financial cost of delivering this information is largely undocumented. We evaluated the costs and funding sources for developing and maintaining four global biodiversity and conservation knowledge products: The IUCN Red List of Threatened Species, the IUCN Red List of Ecosystems, Protected Planet, and the World Database of Key Biodiversity Areas. These are secondary data sets, built on primary data collected by extensive networks of expert contributors worldwide. We estimate that US$160 million (range: US$116–204 million), plus 293 person-years of volunteer time (range: 278–308 person-years) valued at US$ 14 million (range US$12–16 million), were invested in these four knowledge products between 1979 and 2013. More than half of this financing was provided through philanthropy, and nearly three-quarters was spent on personnel costs. The estimated annual cost of maintaining data and platforms for three of these knowledge products (excluding the IUCN Red List of Ecosystems for which annual costs were not possible to estimate for 2013) is US$6.5 million in total (range: US$6.2–6.7 million). We estimated that an additional US$114 million will be needed to reach pre-defined baselines of data coverage for all the four knowledge products, and that once achieved, annual maintenance costs will be approximately US$12 million. These costs are much lower than those to maintain many other, similarly important, global knowledge products. Ensuring that biodiversity and conservation knowledge products are sufficiently up to date, comprehensive and accurate is fundamental to inform decision-making for biodiversity conservation and sustainable development. Thus, the development and implementation of plans for sustainable long-term financing for them is critical.
Collapse
Affiliation(s)
- Diego Juffe-Bignoli
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
- * E-mail:
| | - Thomas M. Brooks
- International Union for Conservation of Nature (IUCN), 28 rue Mauverney, 1196 Gland, Switzerland
- World Agroforestry Center (ICRAF), University of the Philippines Los Baños, Laguna 4031, Philippines
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart TAS 7001, Australia
| | - Stuart H. M. Butchart
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Richard B. Jenkins
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Kaia Boe
- Nature-based Solutions Group, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland
| | - Michael Hoffmann
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
- International Union for Conservation of Nature (IUCN), 28 rue Mauverney, 1196 Gland, Switzerland
| | - Ariadne Angulo
- IUCN Species Survival Commission, Amphibian Specialist Group, Toronto M8W 1R2, Canada
| | - Steve Bachman
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, Regent’s Park, London NW1 4RY, United Kingdom
| | - Neil Brummitt
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Kent E. Carpenter
- IUCN Marine Biodiversity Unit, Global Species Programme/ Biological Sciences, Old Dominion University, Norfolk, Virginia, United States of America
| | - Pat J. Comer
- NatureServe, 4600 N. Fairfax Dr., Arlington, VA 22203, United States of America
| | - Neil Cox
- IUCN CI Biodiversity Assessment Unit, IUCN Global Species Programme, c/o Conservation International, 2011 Crystal Drive, Suite 500, Arlington, VA 22202, United States of America
| | - Annabelle Cuttelod
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - William R. T. Darwall
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Moreno Di Marco
- ARC Centre of Excellence for Environmental Decisions, Centre for Biodiversity and Conservation Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
- School of Geography, Planning and Environmental Management, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Lincoln D. C. Fishpool
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Bárbara Goettsch
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Melanie Heath
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Craig Hilton-Taylor
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Jon Hutton
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
- Luc Hoffmann Institute, WWF International, 1196 Gland, Switzerland
| | - Tim Johnson
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
| | - Ackbar Joolia
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - David A. Keith
- Centre for Ecosystem Science, University of New South Wales, Sydney, New South Wales 2052, Australia
- New South Wales Office of Environment and Heritage, Hurstville, New South Wales 2220, Australia
| | - Penny F. Langhammer
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ 85287, United States of America
| | - Jennifer Luedtke
- IUCN Species Survival Commission, Amphibian Specialist Group, Toronto M8W 1R2, Canada
| | | | - Maiko Lutz
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Ian May
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Rebecca M. Miller
- Nature-based Solutions Group, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland
- IUCN Global Ecosystem Management Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | | | - Mike Parr
- American Bird Conservancy, 1731 Connecticut Avenue, Washington DC 20009, United States of America
| | - Caroline M. Pollock
- IUCN Global Species Programme, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Gina Ralph
- IUCN Marine Biodiversity Unit, Global Species Programme/ Biological Sciences, Old Dominion University, Norfolk, Virginia, United States of America
| | - Jon Paul Rodríguez
- International Union for Conservation of Nature (IUCN), 28 rue Mauverney, 1196 Gland, Switzerland
- Provita, Apdo. 47552, Caracas 1041-A, Venezuela
- Centro de Ecología, Instituto Venezolano de Investigaciones Científicas, Apdo. 20632, Caracas 1020-A, Venezuela
| | - Carlo Rondinini
- Global Mammal Assessment Program, Department of Biology and Biotechnologies, Sapienza University of Rome, Viale dell'Università 32, I-00185 Rome, Italy
| | - Jane Smart
- International Union for Conservation of Nature (IUCN), 28 rue Mauverney, 1196 Gland, Switzerland
- Biodiversity Conservation Group, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland
| | - Simon Stuart
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
- International Union for Conservation of Nature (IUCN), 28 rue Mauverney, 1196 Gland, Switzerland
| | - Andy Symes
- BirdLife International, David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, United Kingdom
| | - Andrew W. Tordoff
- Critical Ecosystem Partnership Fund, 2011 Crystal Drive, Suite 500, Arlington, VA 22202, United States of America
| | - Stephen Woodley
- World Commission on Protected Areas IUCN, 64 Juniper Road, Chelsea, QC J9B1T3, Canada
| | - Bruce Young
- NatureServe, 4600 N. Fairfax Dr., Arlington, VA 22203, United States of America
| | - Naomi Kingston
- United Nations Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, CB3 0DL Cambridge, United Kingdom
| |
Collapse
|