Published November 8, 2024 | Version v1
Journal article Open

The key to bringing DNA collections to the next level

Authors/Creators

  • 1. Research Institute for Nature and Forest (INBO), Brussels, Belgium
  • 2. Ghent University, Ghent, Belgium
  • 3. Meise Botanic Garden, Meise, Belgium
  • 4. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Ostend/Merelbeke, Belgium
  • 5. Vrije Universiteit Brussel, Brussels, Belgium
  • 6. Belgian Coordinated Collections of Microorganisms / Institute of Tropical Medicine - Mycobacteriology Unit, Antwerp, Belgium
  • 7. University of Antwerp, Antwerp, Belgium|Royal Belgian Institute of Natural Sciences, Brussels, Belgium
  • 8. Flanders Marine Institute, Ostend, Belgium
  • 9. Belgian Coordinated Collections of Microorganisms / Belgian Science Policy Office, Brussels, Belgium
  • 10. Royal Zoological Society of Antwerp, Antwerp, Belgium
  • 11. Royal Museum for Central Africa, Tervuren, Belgium
  • 12. Royal Belgian Institute of Natural Sciences, Brussels, Belgium

Description

DNA collections are a valuable type of Natural Science collection, enabling the validation of past research, serving as a source for new genomic studies and supporting ex situ conservation. The DiSSCo Flanders DNA collection working group, aiming to advance and "unlock" their DNA collections, identified the need for: 1) actively sharing best practices regarding the management of DNA collections; and 2) providing guidance on how to bring theory into practice. By combining best practice examples from within the working group with available literature and brainstorming ideas, the working group co-created two outputs, referred to as: the "Challenges" and the "Key". The Challenges are a list of obstacles to DNA collection management, which shape the structure of the linked Key and can also be used to spark discussion amongst stakeholders. The Key is a tool that guides users through the maturation process of their DNA collection in a standardised way. It stimulates holistic growth, breaks down the needed work into manageable steps and helps to decide priorities during the process. Furthermore, the Key facilitates communication with both internal stakeholders and external DNA collection managers. The Key distinguishes itself from other self-assessment tools in several ways: it includes (re)investigation of the collection's purpose and context; it is specialised for DNA collections; it delivers concrete goals linked to relevant information and shared experience; and it is inclusive, targeting all Natural Science DNA collections, regardless of their context or size.

Files

RIO_article_135978.pdf

Files (462.7 kB)

Name Size Download all
md5:a9c3889a308b23df9c45a28225069f98
279.8 kB Preview Download
md5:6bd875786bdf1b867e24557da2ad830d
182.9 kB Preview Download

Additional details

Cites
Publication: 10.35035/doc-vf1a-nr22 (DOI)
Publication: 10.5281/zenodo.3949839 (DOI)
Publication: 10.3897/zookeys.365.5875 (DOI)
Publication: 10.3897/rio.10.e120483 (DOI)
Publication: 10.7554/elife.68264 (DOI)
Publication: 10.1146/annurev-genet-071719-020506 (DOI)
Publication: 10.3897/ab.e101876 (DOI)
Publication: 10.3897/arphapreprints.e103105 (DOI)
Publication: 10.1093/nar/gkab1051 (DOI)
Publication: 10.1371/journal.pbio.2002925 (DOI)
Publication: 10.3897/rio.9.e102908 (DOI)
Publication: 10.1093/database/baw125 (DOI)
Publication: 10.1155/2015/461524 (DOI)
Publication: 10.1007/s10344-018-1188-8 (DOI)
Publication: 10.1111/1755-0998.13880 (DOI)
Publication: 10.3897/bdj.5.e11625 (DOI)
Publication: 10.37044/osf.io/93qf4 (DOI)
Publication: 10.3897/biss.6.93875 (DOI)
Publication: 10.3897/biss.7.110932 (DOI)
Publication: 10.1371/journal.pone.0261130 (DOI)
Publication: 10.1371/journal.pone.0114069 (DOI)
Publication: 10.1007/978-1-4939-8935-5_2 (DOI)
Publication: 10.3897/rio.7.e67379 (DOI)
Publication: 10.1093/biosci/biac060 (DOI)
Publication: 10.4324/9780429426599 (DOI)
Publication: 10.1038/s41559-018-0614-3 (DOI)
Publication: 10.1111/1755-0998.13746 (DOI)
Publication: 10.1162/dint_a_00027 (DOI)
Publication: 10.3390/jpm12122040 (DOI)
Publication: 10.35535/pfsyst-2020-0025 (DOI)
Publication: 10.3389/fmars.2019.00277 (DOI)
Publication: 10.5194/fr-21-47-2018 (DOI)
Publication: 10.1016/j.tree.2021.07.009 (DOI)
Publication: 10.1016/j.tim.2020.06.009 (DOI)
Publication: 10.25607/obp-1653 (DOI)
Publication: 10.3390/biology12070997 (DOI)
Publication: 10.1093/nar/gkaa1023 (DOI)
Publication: 10.1093/database/baaa062 (DOI)
Publication: 10.3897/rio.7.e61664 (DOI)
Publication: 10.1371/journal.pone.0029715 (DOI)
Publication: 10.1038/sdata.2016.18 (DOI)
Publication: 10.3897/biss.6.91159 (DOI)
Publication: 10.14351/0831-0005-28.1.77 (DOI)
Has part
Other: 10.3897/rio.10.e135978.suppl1 (DOI)
Other: 10.3897/rio.10.e135978.suppl2 (DOI)

References

  • Abarenkov K, Andersson A, Bissett A, Finstad AG, Fossøy F, Grosjean M, Hope M, Jeppesen TS, Kõljalg U, Lundin D, Nilsson H, Prager M, Provoost P, Schigel D, Suominen S, Svenningsen C, Frøslev TG (2023) Publishing DNA-derived data through biodiversity data platforms. GBIF Secretariat https://doi.org/10.35035/doc-vf1a-nr22
  • Access to Biological Collection Data task group (2007) Access to Biological Collection Data (ABCD), Version 2.06. Biodiversity Information Standards (TDWG). http://www.tdwg.org/standards/115. Accessed on: 2024-8-26.
  • Addink W, Hardisty A, Islam S, Weiland C, Glöckner F, Güntsch A (2020) Advancing the Catalogue of the World's Natural History Collections - 10 recommendations from DiSSCo. Zenodo https://doi.org/10.5281/zenodo.3949839
  • Astrin J, Zhou X, Misof B (2013) The importance of biobanking in molecular taxonomy, with proposed definitions for vouchers in a molecular context. ZooKeys 365: 67‑70. https://doi.org/10.3897/zookeys.365.5875
  • Borisenko A, Young R, Hanner R (2024) A lab-centric, workflow-based data management system for environmental DNA research. Research Ideas and Outcomes 10 https://doi.org/10.3897/rio.10.e120483
  • Buckner JC, Sanders RC, Faircloth BC, Chakrabarty P (2021) The critical importance of vouchers in genomics. eLife 10 https://doi.org/10.7554/elife.68264
  • Card D, Shapiro B, Giribet G, Moritz C, Edwards S (2021) Museum Genomics. Annual Review of Genetics 55 (1): 633‑659. https://doi.org/10.1146/annurev-genet-071719-020506
  • CETAF Legislations and Regulations Group (2019) CETAF Code of Conduct and Best Practice for Access and Benefit Sharing, Annex 5: Practice Guidance. URL: https://cetaf.org/resources/best-practices/
  • Corrales C, Astrin JJ (2023) Biodiversity Biobanking – a Handbook on Protocols and Practices. Pensoft, Advanced Books https://doi.org/10.3897/ab.e101876
  • Corrales C, Luciano S, Astrin J (2023) Biodiversity biobanks: a landscape analysis. ARPHA Preprints https://doi.org/10.3897/arphapreprints.e103105
  • Crop Trust (2020) Seeds for Resilience Genebank reviews. https://www.croptrust.org/work/projects/seeds-for-resilience/#c7192. Accessed on: 2024-8-19.
  • Cummins C, Ahamed A, Aslam R, Burgin J, Devraj R, Edbali O, Gupta D, Harrison PW, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu V, Kay S, Kumar M, Lathi A, Leinonen R, Madeira F, Madhusoodanan N, Mansurova M, O'Cathail C, Pearce M, Pesant S, Rahman N, Rajan J, Rinck G, Selvakumar S, Sokolov A, Suman S, Thorne R, Totoo P, Vijayaraja S, Waheed Z, Zyoud A, Lopez R, Burdett T, Cochrane G (2021) The European Nucleotide Archive in 2021. Nucleic Acids Research 50 https://doi.org/10.1093/nar/gkab1051
  • Deck J, Gaither M, Ewing R, Bird C, Davies N, Meyer C, Riginos C, Toonen R, Crandall E (2017) The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PLOS Biology 15 (8). https://doi.org/10.1371/journal.pbio.2002925
  • de Mestier A, Mulcahy D, Harris D, Korotkova N, Long S, Häffner E, Paton A, Schiller E, Leliaert F, Mackenzie-Dodds J, Fulcher T, Stahls G, von Rintelen T, Martín M, Lücking R, Williams C, Lyal C, Güntsch A, Aronsson H, Castelin M, Pielach A, Poczai P, Ruiz-León Y, Sanmartin Bastida I, Thines M, Droege G (2023) Policies Handbook on Using Molecular Collections. Research Ideas and Outcomes 9 https://doi.org/10.3897/rio.9.e102908
  • de Vicente MC, Andersson M (Eds) (2006) DNA banks-providing novel options for genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. URL: https://cgkb.cgiar.croptrust.org/images/file/learning_space/dnabanks.pdf
  • Droege G, Barker K, Seberg O, Coddington J, Benson E, Berendsohn WG, Bunk B, Butler C, Cawsey EM, Deck J, Döring M, Flemons P, Gemeinholzer B, Güntsch A, Hollowell T, Kelbert P, Kostadinov I, Kottmann R, Lawlor RT, Lyal C, Mackenzie-Dodds J, Meyer C, Mulcahy D, Nussbeck SY, O'Tuama É, Orrell T, Petersen G, Robertson T, Söhngen C, Whitacre J, Wieczorek J, Yilmaz P, Zetzsche H, Zhang Y, Zhou X (2016) The Global Genome Biodiversity Network (GGBN) Data Standard specification. Database 2016 https://doi.org/10.1093/database/baw125
  • Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J, Cogulu O (2015) Evolution of Genetic Techniques: Past, Present, and Beyond. BioMed Research International 2015: 1‑7. https://doi.org/10.1155/2015/461524
  • Ferreira CM, Sabino-Marques H, Barbosa S, Costa P, Encarnação C, Alpizar-Jara R, Pita R, Beja P, Mira A, Searle J, Paupério J, Alves PC (2018) Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. European Journal of Wildlife Research 64 (4). https://doi.org/10.1007/s10344-018-1188-8
  • Forsdick N, Wold J, Angelo A, Bissey F, Hart J, Head M, Liggins L, Senanayake D, Steeves T (2023) Journeying towards best practice data management in biodiversity genomics. Molecular Ecology Resources https://doi.org/10.1111/1755-0998.13880
  • Funk V, Gostel M, Devine A, Kelloff C, Wurdack K, Tuccinardi C, Radosavljevic A, Peters M, Coddington J (2017) Guidelines for collecting vouchers and tissues intended for genomic work (Smithsonian Institution): Botany Best Practices. Biodiversity Data Journal 5 https://doi.org/10.3897/bdj.5.e11625
  • Groom QJ, Dillen M, Huybrechts P, Johaadien R, Kyriakopoulou N, Fernandez FJQ, Trekels M, Wong WY (2021) Connecting molecular sequences to their voucher specimens. Biohackrxiv https://doi.org/10.37044/osf.io/93qf4
  • Grosjean M, Høfft M, Gonzalez M, Hahn A, Robertson T (2022) GRSciColl: What is the Global Registry of Scientific Collections and How to Contribute? Biodiversity Information Science and Standards 6 https://doi.org/10.3897/biss.6.93875
  • Grosjean M, Robertson T, Gonzalez M, Høfft M, Hahn A (2023) Ongoing Work with the Global Registry of Scientific Collections. Biodiversity Information Science and Standards 7 https://doi.org/10.3897/biss.7.110932
  • Güntsch A, Groom Q, Ernst M, Holetschek J, Plank A, Röpert D, Fichtmüller D, Shorthouse DP, Hyam R, Dillen M, Trekels M, Haston E, Rainer H (2021) A botanical demonstration of the potential of linking data using unique identifiers for people. PLOS ONE 16 (12). https://doi.org/10.1371/journal.pone.0261130
  • Guralnick R, Conlin T, Deck J, Stucky B, Cellinese N (2014) The Trouble with Triplets in Biodiversity Informatics: A Data-Driven Case against Current Identifier Practices. PLOS ON 9 (12). https://doi.org/10.1371/journal.pone.0114069
  • Harati M, Williams R, Movassaghi M, Hojat A, Lucey G, Yong W (2018) An Introduction to Starting a Biobank. Methods in Molecular Biology7‑16. https://doi.org/10.1007/978-1-4939-8935-5_2
  • Hardisty A, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2022) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7 https://doi.org/10.3897/rio.7.e67379
  • Hardisty AR, Ellwood ER, Nelson G, Zimkus B, Buschbom J, Addink W, Rabeler RK, Bates J, Bentley A, Fortes JAB, Hansen S, Macklin JA, Mast AR, Miller JT, Monfils AK, Paul DL, Wallis E, Webster M (2022) Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet. BioScience 72 (10): 978‑987. https://doi.org/10.1093/biosci/biac060
  • Huxley R, Quaisser C, Butler CR, Dekker RW (2020) Managing Natural Science Collections. 1. Routledge https://doi.org/10.4324/9780429426599
  • ISBER (2023) ISBER Best Practices: Recommendations for Repositories. 5. ISBER, Vancouver, 19 pp. URL: https://www.isber.org/page/BPR
  • Jarman S, Berry O, Bunce M (2018) The value of environmental DNA biobanking for long-term biomonitoring. Nature Ecology & Evolution 2 (8): 1192‑1193. https://doi.org/10.1038/s41559-018-0614-3
  • Keck F, Couton M, Altermatt F (2022) Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses. Molecular Ecology Resources 23 (4): 742‑755. https://doi.org/10.1111/1755-0998.13746
  • Landi A, Thompson M, Giannuzzi V, Bonifazi F, Labastida I, da Silva Santos LOB, Roos M (2020) The "A" of FAIR – As Open as Possible, as Closed as Necessary. Data Intelligence 2: 47‑55. https://doi.org/10.1162/dint_a_00027
  • Lazareva T, Barbitoff Y, Changalidis A, Tkachenko A, Maksiutenko E, Nasykhova Y, Glotov A (2022) Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. Journal of Personalized Medicine 12 (12). https://doi.org/10.3390/jpm12122040
  • Lücking R, Nadel M, Araujo E, Gerlach A (2020) Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS? Plant and Fungal Systematics 65 (2): 303‑357. https://doi.org/10.35535/pfsyst-2020-0025
  • Luger T, Maes S, Milkers A, Bergmans B (2021) Een collectieplan schrijven? Dat doe je zo! [Writing a collection plan? Like this!]. OBT, leiden, 88 pp. URL: https://www.cultureelerfgoed.nl/publicaties/publicaties/2021/01/01/een-collectieplan-schrijven-dat-doe-je-zo [ISBN 978-90-5799-343-5]
  • Norton B, Woodburn M, Grant S, Jones J, Webbink K, Vincent S, Trekels M, Buschbom J, Baskauf S, Biodiversity Information Standards (TDWG) (2024) Latimer Core (LtC) GitHub Repository. https://github.com/tdwg/ltc. Accessed on: 2024-4-09.
  • Pearlman J, Bushnell M, Coppola L, Karstensen J, Buttigieg PL, Pearlman F, Simpson P, Barbier M, Muller-Karger F, Munoz-Mas C, Pissierssens P, Chandler C, Hermes J, Heslop E, Jenkyns R, Achterberg E, Bensi M, Bittig H, Blandin J, Bosch J, Bourles B, Bozzano R, Buck JH, Burger E, Cano D, Cardin V, Llorens MC, Cianca A, Chen H, Cusack C, Delory E, Garello R, Giovanetti G, Harscoat V, Hartman S, Heitsenrether R, Jirka S, Lara-Lopez A, Lantéri N, Leadbetter A, Manzella G, Maso J, McCurdy A, Moussat E, Ntoumas M, Pensieri S, Petihakis G, Pinardi N, Pouliquen S, Przeslawski R, Roden N, Silke J, Tamburri M, Tang H, Tanhua T, Telszewski M, Testor P, Thomas J, Waldmann C, Whoriskey F (2019) Evolving and Sustaining Ocean Best Practices and Standards for the Next Decade. Frontiers in Marine Science 6 https://doi.org/10.3389/fmars.2019.00277
  • Petersen M, Glöckler F, Kiessling W, Döring M, Fichtmüller D, Laphakorn L, Baltruschat B, Hoffmann J (2018) History and development of ABCDEFG: a data standard for geosciences. Fossil Record 21 (1): 47‑53. https://doi.org/10.5194/fr-21-47-2018
  • Raxworthy C, Smith BT (2021) Mining museums for historical DNA: advances and challenges in museomics. Trends in Ecology & Evolution 36 (11): 1049‑1060. https://doi.org/10.1016/j.tree.2021.07.009
  • Ryan MJ, Schloter M, Berg G, Kostic T, Kinkel LL, Eversole K, Macklin JA, Schelkle B, Kazou M, Sarand I, Singh BK, Fischer D, Maguin E, Ferrocino I, Lima N, McClure RS, Charles TC, de Souza RS, Kiran GS, Krug HL, Taffner J, Roume H, Selvin J, Smith D, Rybakova D, Sessitsch A (2021) Development of Microbiome Biobanks – Challenges and Opportunities. Trends in Microbiology 29 (2): 89‑92. https://doi.org/10.1016/j.tim.2020.06.009
  • Santi I, Casotti R, Comtet T, Cunliffe M, Koulouri P(, Macheriotou L, Not F, Obst M, Pavloudi C, Romac S, Thiebaut E, Vanaverbeke J, Pade N (2021) European Marine Omics Biodiversity Observation Network (EMO BON) Handbook (Version 1.0). EMBRC-ERIC https://doi.org/10.25607/obp-1653
  • Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare R, Banday S, Mishra A, Das G, Malonia S (2023) Next-Generation Sequencing Technology: Current Trends and Advancements. Biology 12 (7). https://doi.org/10.3390/biology12070997
  • Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Schoch CL, Sherry ST, Karsch-Mizrachi I (2020) GenBank. Nucleic Acids Research 49 https://doi.org/10.1093/nar/gkaa1023
  • Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I (2020) NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020 https://doi.org/10.1093/database/baaa062
  • Ståhls G, Aleixo A, Hyvärinen M, Kuusijärvi A, Myllys L, Väre H, Sihvonen P, Luttinen A, Kröger B, Oinonen M, Schulman L, Juslén A (2021) The Genomic Resources Collection Policy of the Finnish Museum of Natural History. Research Ideas and Outcomes 7 https://doi.org/10.3897/rio.7.e61664
  • Veltjen E, Brosens D, Cools C, De Cuyper B, De Vos B, D'hondt B, Herr C, Lambeens I, Maebe K, Lettens S, Pollet M, Soors J, Teunen L, Vanden Broeck A, Van Driessche C, Verstraeten A, De Wever A (in preparation) INBO-beslissingsboom: Archiveren van natuurwetenschappelijke specimens (of niet)? INBO.
  • Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R, Robertson T, Vieglais D (2012) Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7 (1). https://doi.org/10.1371/journal.pone.0029715
  • Wilkinson M, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J, da Silva Santos LB, Bourne P, Bouwman J, Brookes A, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo C, Finkers R, Gonzalez-Beltran A, Gray AG, Groth P, Goble C, Grethe J, Heringa J, 't Hoen PC, Hooft R, Kuhn T, Kok R, Kok J, Lusher S, Martone M, Mons A, Packer A, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S, Schultes E, Sengstag T, Slater T, Strawn G, Swertz M, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3 (1). https://doi.org/10.1038/sdata.2016.18
  • Woodburn M, Buschbom J, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2022) Latimer Core: A new data standard for collection descriptions. Biodiversity Information Science and Standards 6 https://doi.org/10.3897/biss.6.91159
  • Zimkus BM, Ford LS (2014) Best practices for genetic resources associated with natural history collections: Recommendations for practical implementation. Collection Forum 28: 77‑112. https://doi.org/10.14351/0831-0005-28.1.77