Wellcome Open Research (Jun 2024)
A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project [version 1; peer review: 2 approved]
- Silvia Salatino,
- Rebekka Uhl,
- Peter O. Mulhair,
- Freja Azzopardi,
- Jordan Beasley,
- Alex D. Twyford,
- Lucia Campos-Dominguez,
- Michelle L. Hart,
- Olga Sivell,
- David Bell,
- Gavin Broad,
- Felix Shaw,
- Piotr Cuber,
- Darren Choonea,
- Peter M. Hollingsworth,
- Laura L. Forrest,
- Sahr Mian,
- Alexandra Dombrowski,
- Mara K.N. Lawniczak,
- Claire Griffin,
- Clementine Greeves,
- Peter W.H. Holland,
- Joanna Harley,
- Owen T. Lewis,
- Amanda Jones,
- Ben W. Price,
- Raju Misra,
- Estelle Kilias,
- Ian Barnes,
- Laura Sivess,
- Heather Allen,
- Alice Minotto,
- Inez Januszczak,
- Michael Cunliffe,
- Mark L. Blaxter,
- Liam Crowley,
- Lyndall Pereira da Conceicoa,
- Brian Douglas,
- Kieran Woof,
- Ester Gaya,
- Paul Kersey
Affiliations
- Silvia Salatino
- Natural History Museum, London, England, SW7 5BD, UK
- Rebekka Uhl
- The Marine Biological Association, Plymouth, England, PL1 2PB, UK
- Peter O. Mulhair
- ORCiD
- Department of Biology, University of Oxford, Oxford, England, OX1 3SZ, UK
- Freja Azzopardi
- ORCiD
- The Marine Biological Association, Plymouth, England, PL1 2PB, UK
- Jordan Beasley
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Alex D. Twyford
- ORCiD
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, Scotland, EH9 3FL, UK
- Lucia Campos-Dominguez
- ORCiD
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, Scotland, EH9 3FL, UK
- Michelle L. Hart
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH3 5LR, UK
- Olga Sivell
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- David Bell
- ORCiD
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH3 5LR, UK
- Gavin Broad
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Felix Shaw
- Earlham Institute, Norwich, NR4 7UZ, UK
- Piotr Cuber
- Natural History Museum, London, England, SW7 5BD, UK
- Darren Choonea
- Natural History Museum, London, England, SW7 5BD, UK
- Peter M. Hollingsworth
- ORCiD
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH3 5LR, UK
- Laura L. Forrest
- ORCiD
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH3 5LR, UK
- Sahr Mian
- ORCiD
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Alexandra Dombrowski
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Mara K.N. Lawniczak
- ORCiD
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Claire Griffin
- Natural History Museum, London, England, SW7 5BD, UK
- Clementine Greeves
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Peter W.H. Holland
- ORCiD
- Department of Biology, University of Oxford, Oxford, England, OX1 3SZ, UK
- Joanna Harley
- The Marine Biological Association, Plymouth, England, PL1 2PB, UK
- Owen T. Lewis
- ORCiD
- Department of Biology, University of Oxford, Oxford, England, OX1 3SZ, UK
- Amanda Jones
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH3 5LR, UK
- Ben W. Price
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Raju Misra
- Natural History Museum, London, England, SW7 5BD, UK
- Estelle Kilias
- Department of Biology, University of Oxford, Oxford, England, OX1 3SZ, UK
- Ian Barnes
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Laura Sivess
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Heather Allen
- Natural History Museum, London, England, SW7 5BD, UK
- Alice Minotto
- ORCiD
- Earlham Institute, Norwich, NR4 7UZ, UK
- Inez Januszczak
- ORCiD
- Natural History Museum, London, England, SW7 5BD, UK
- Michael Cunliffe
- The Marine Biological Association, Plymouth, England, PL1 2PB, UK
- Mark L. Blaxter
- ORCiD
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Liam Crowley
- ORCiD
- Department of Biology, University of Oxford, Oxford, England, OX1 3SZ, UK
- Lyndall Pereira da Conceicoa
- ORCiD
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Brian Douglas
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Kieran Woof
- ORCiD
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Ester Gaya
- ORCiD
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Paul Kersey
- Royal Botanic Gardens Kew, Richmond, England, TW9 3AB, UK
- Journal volume & issue
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Vol. 9
Abstract
Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.
