When referring to Natural Science collections (Addink et al. 2020), one might think of a myriad of pinned butterflies in a museum drawer, a huge reconstructed skeleton of a Brachiosaurus, a sparkling Lapis Lazuli or a beautifully dried and mounted herbarium specimen, to name but a few. A much less conspicuous and relatively young type of Natural Science collection is a DNA collection, preserving DNA extracted from (non-human) organisms or environmental specimens such as water, soil or air. A common synonym is "DNA bank(s)" (de Vicente and Andersson 2006, Corrales et al. 2023). A DNA collection can be categorised under the overarching concepts of a “biological or environmental repository'' (ISBER 2023), a “biodiversity biobank” (Corrales and Astrin 2023) or a “molecular collection” (de Mestier et al. 2023). Natural Science DNA collections are typically associated with genetic laboratories within research institutes. The DNA specimens themselves are either extracted from museum specimens or actively gathered during sampling events by collecting tissue, organisms or environmental samples to extract the DNA from.

Natural Science DNA collections are considered valuable because:

• DNA specimens often contain much unexplored genetic information.

• DNA specimens often have enough volume left after their original research purpose for additional analyses.

• DNA specimens contain DNA molecules that are stable information carriers.

• DNA specimens avoid repeated destructive sampling of the source material.

• DNA specimens can be used to carry out alternative versions of genetic and genomic studies (e.g. molecular taxonomy, conservation genetic research, population genetics and phylogenetics) by using different techniques (e.g. other molecular markers, other sequencing techniques) than were used in the original study.

• DNA specimens allow research validation (i.e. repetition using the same techniques as the original study).

• DNA specimens allow investigation into completely new research questions (e.g. “museum genomics” (Card et al. 2021) and “museomics” (Raxworthy and Smith 2021).

• DNA specimens are extremely valuable when it comes to generating barcoding reference libraries (i.e. molecular vouchers (Astrin et al. 2013)).

• DNA specimens are crucial in the context of rapidly evolving research fields, such as eDNA (environmental DNA) biomonitoring (Jarman et al. 2018), metabarcoding and metagenomics (Ryan et al. 2021, Lazareva et al. 2022).

• DNA specimens allow storage of genetic diversity information during a global biodiversity crisis as a potential source of ex-situ conservation (Corrales and Astrin 2023).

Of course, the value of each individual DNA specimen depends on its specific (data) context and quality (Veltjen et al. in preparation).

Although all types of Natural Science collections have their own associated management challenges, biodiversity biobanks, including DNA collections, have received extra attention in recent years. This is evident when looking at recent publications, such as the “Policies Handbook on Using Molecular Collections” (de Mestier et al. 2023), “Biodiversity biobanking - a Handbook on Protocols and Practices” (Corrales and Astrin 2023) and “Biodiversity biobanks: a landscape analyses” (Corrales et al. 2023). Similarly, there are specialised communities that focus on DNA collection and data management, such as the "International Society for Biological and Environmental Repositories (ISBER)", publishing the “ISBER Best Practices: Recommendations for Repositories” (ISBER 2023), the Global Genome Biodiversity Network (GGBN, created in 2013) and the Biodiversity Genomics Data Hub (Forsdick et al. 2023). These developments are largely expected for the three main reasons, discussed in the next paragraphs.

Firstly, given the context in which DNA specimens are generated:

• Genetic research is relatively young compared to other research disciplines, such as morphological studies (Durmaz et al. 2015).

• Genetic research is becoming more accessible and less costly (Ferreira et al. 2018).

• Identification by DNA sequencing is being increasingly used: the methods for DNA-based taxonomy and identification can largely be applied across taxonomic groups (however, see Keck et al. (2022)).

• Sequencing techniques continue to evolve quickly (Satam et al. 2023).

• Various high-profile agreements, such as the Convention on Biological Diversity (CBD), Access and Benefit Sharing (ABS) and the Nagoya protocol have attracted more attention to, and regulations for, the utilisation of genetic resources.

• DNA collections are a particularly challenging type of Natural Science collection, as their specimens are often linked to a wide variety of related data, such as:

  • The initial source sample from which the DNA was obtained, which can subsequently be linked to a specimen voucher (e.g. herbarium specimens, see Funk et al. (2017)).

  • The resulting DNA sequence data (e.g. deposited on ENA (Cummins et al. 2021)) and genetic/genomic datasets.

  • A match to a molecular voucher (and linked specimen voucher) from a reference database (Astrin et al. 2013).

Secondly, some DNA collections have come into being in an "ad-hoc" manner as a by-product of a genetic research laboratory, rather than being carefully planned. Sometimes, the DNA collections themselves have only recently been identified and treated as Natural Science collections.

Thirdly, the communities of researchers and laboratory technicians that manage DNA collections (especially those not linked to Natural Science museums, such as universities or governmental institutes), are often relatively new to, or not (yet) involved in the larger Natural Science collection community or the biobanking community. They may consequently miss certain useful guidance and knowledge when managing DNA collections.

The members of the DiSSCo Flanders consortium, with the common goal of maturing their DNA collections to be included in DiSSCo Europe, identified: 1) a need for actively sharing best practices regarding the management of (Natural Science) DNA collections and 2) a need for guidance on how to bring management theory into practice, given that each DNA collection varies in maturity, context and size. The context of DNA collections varies in terms of diverse factors, such as the available means (time, money, manpower), the geographical scope of the specimens, the organisation of the genetic laboratory associated with the DNA collection and the number of people (e.g. scientists, students, technicians) associated with the DNA collections that generate specimens for deposit. The consortium’s Collection Self-Assessment Tool (CSAT) scores on the benchmark statements of the molecular collections (CSAT taken around January 2023), supported this need and showed that many of the best practices circulating at the time of the assessment were not (yet) put into practice.

Using the shared experience of the consortium members and the available literature linked to DNA collection management, the consortium aimed to co-create a resource that addresses the question: “How can a DNA collection be matured as efficiently as possible, taking into account the collections’ diversity in context and size?”.

During the DiSSCo Flanders project, the DiSSCo Flanders DNA collection working group was created. The working group is open to all Natural Science DNA collection associates in Belgium: researchers, lab technicians, collection managers, data managers etc. Around 50 people were brought together, with 13 different affiliations: Meise Botanic Garden, the Flanders Research Institute for Agriculture, Fisheries and Food, the Research Institute for Nature and Forest, the Belgian Coordinated Collections of Microorganisms, the Institute of Tropical Medicine, the Royal Zoological Society of Antwerp, KU Leuven, the Royal Belgian Institute of Natural Sciences, the University of Antwerp, the Royal Museum for Central Africa, Ghent University, the Flanders Marine Institute and the Vrije Universiteit Brussel. Most of the organizations represented here do not have a DNA-collection-only biodiversity biobank: tissues or (micro-)organisms are often stored in parallel. The various DNA collections are handled in a variety of contexts: universities, governmental and museum institutes; organised in both decentralised or centralised manners; using cold storage or room temperature storage; managed by an appointed curator or a dedicated lab technician and so on. The working group will have met 10 times over the course of 4 years (2021-2024, last meeting is in October 2024). Topics that have already been covered include: brainstorming and sharing of good practices, digital management, physical storage, data standards, legal challenges, standard operating procedures, linkage and the co-creation of this tool. During some of these topics, invited speakers joined in to share their expertise. The members of the working group also communicated interesting literature, events or courses via a mailing list and shared their workflows, to stimulate discussion and receive feedback from peers.

The working group co-created two main products: "the Challenges" and "the Key". Firstly, we compiled a “List of challenges for improving DNA collection management”; from this point onwards, these will be referred to as: the Challenges. Secondly, we co-created a tool to tackle these Challenges in a more strategic, standardised way: “The key to bringing DNA collections to the next level”; from this point onwards referred to as: the Key. These two products result from consulting and discussing current best practice literature and sharing in-house best practices and ideas.

Definitions used throughout this document are given in Suppl. material 1. The following works have inspired us to address multiple topics included in the main text, as well as the in-depth information given in Suppl. material 2: Zimkus and Ford (2014), Huxley et al. (2020), Corrales and Astrin (2023), de Mestier et al. (2023), ISBER (2023), the SPNHC wiki and the GGBN wiki. The in-depth information given in Suppl. material 2 cites inspiring work such as: Access to Biological Collection Data task group (2007), Wieczorek et al. (2012), Guralnick et al. (2014), Droege et al. (2016), Deck et al. (2017), Petersen et al. (2018), CETAF Legislations and Regulations Group (2019), Pearlman et al. (2019), Crop Trust (2020), Sayers et al. (2020), Schoch et al. (2020), Güntsch et al. (2021), Luger et al. (2021), Santi et al. (2021), Ståhls et al. (2021), Grosjean et al. (2022), Hardisty et al. (2022), Hardisty et al. (2022), Woodburn et al. (2022), Abarenkov et al. (2023), Grosjean et al. (2023), Borisenko et al. (2024), Norton et al. (2024).

RESULT 1: List of all the identified challenges for DNA collections (the Challenges). Each challenge is individually numbered purely for ease of identification: there is no associated priority.

1. Execute strategic management of the DNA collection: have a vision, define actions to achieve that vision, monitoring and managing of the progress.

2. Ensure participation in DNA collection management within institutes, including: the management of the institute, the external parties (e.g. visiting scientists) that generate and re-use DNA specimens, the students that generate and re-use DNA specimens, the researchers that generate and re-use DNA specimens.

3. Ensure a mind shift towards data sharing and FAIR data (Wilkinson et al. 2016) and working “as open as possible, as closed as necessary” (Landi et al. 2020).

4. Demystify legal aspects surrounding genetic research and DNA collections.

5. Establish a good workflow that ensures successful material and data transfer between the field, lab and archiving activities.

6. Formulate and maintain successful communication procedures which ensure that the workflow and responsibilities are clear at the start and throughout each project/collaboration.

7. Centralise and structure DNA collection data, for example in a Collection Management System (CMS) and/or Laboratory Information Management System (LIMS).

8. Select or customise Collection Management Systems to meet the needs of DNA collections.

9. Digitally unlock DNA collection data and physically unlock the DNA specimens for re-use, for example, via the GGBN portal, DiSSCo or GBIF.

10. Store (the large volumes of) genetic/genomic data (unpublished) in a standardised and centralised manner and properly link them with the DNA collection data.

11. Unlock genetic/genomic data (published) via dedicated (open) data repositories, such as ENA.

12. Link DNA sequence data and DNA specimens to all related specimens, such as source specimens and voucher specimens (Buckner et al. 2021, Groom et al. 2021).

13. Determine minimal required data at the start of research projects which will lead to the addition of new DNA specimens to the DNA collection.

14. Good documentation of all the material and methods preceding the addition of a DNA sample to a collection.

15. Ensure good management of the documentation surrounding DNA specimens, such as Standard Operating Procedures (SOPs), workflows and/or guidelines.

16. Manage the rapid expansion of the number of specimens within DNA collections.

17. Enable efficient retrieval of DNA specimens within the collection.

18. Mitigate the risks of DNA sample degradation.

19. Foresee back-up solutions for physical and digital storage.

20. Minimise the consequences of destructive sampling of DNA specimens: quality loss due to handling (e.g. freeze-thaw cycles) and (theoretically) ultimately consumed specimens.

21. Track sample quality, usage, storage location and data.

22. Balance resources (time, money, people) for achieving the best possible DNA collection management.

23. Make decisions on physical storage methods, based on limited and/or scattered information and data about their consequences on the quality of the DNA collection.

RESULT 2: The key to bringing DNA collections to the next level (the Key). An interactive format of the Key, including guidance documentation for the seven Key-questions and 11 Key-categories is available in Suppl. material 2.

Start situation: There is a DNA collection in your organisation that you would like to mature. (Tip: If you are looking into starting a new DNA collection, read: Harati et al. (2018) and/or ISBER (2023)).

1. Do you have an up-to-date overview of all direct, internal stakeholders of the institute’s DNA collection and are you involving them in the (current) intent to “bring the DNA collection to the next level”?
   • Yes: continue to 2.
   • No or I need help: go to Suppl. material 2 "1. Involving the stakeholders".
2. Is preserving a DNA collection within the scope of the institute and is the DNA collection officially recognised within the institute?
   • Yes: continue to 3.
   • No or I need help: go to Suppl. material 2 "2. Having the DNA collection within the institute's vision".
3. Do you have, on paper, a clear description of the scope of the DNA collection?
   • Yes: continue to 4.
   • No or I need help: go to Suppl. material 2 "3. Outlining a scope".
4. Have you outlined the current overarching workflow of the DNA collection?
   • Yes: continue to 5.
   • No or I need help: go to Suppl. material 2 "4. Outlining the current workflow".
5. Go to Table 1, establish and log the starting level. Have you been able to establish the starting level and is the assessment properly logged?
   • Yes: continue to 6.
   • No or I need help: go to Suppl. material 2 "5. Establishing the starting level".
6. Level up, one level at a time and log the process. Have you reached all of the goals in level 3?
   • Yes: continue to 7.
   • No or I need help: go to Suppl. material 2 "6. Levelling up".
7. Do you have a re-evaluation strategy for the DNA collection?
   • Yes: Perfect, all done … for now!
   • No or I need help: go to Suppl. material 2 "7. Re-using the Key".

The Challenges and Key are two outputs which the international community of DNA collections can apply where needed and expand upon going forwards. The Challenges can be used to spark debate on DNA collection management outside the DiSSCo Flanders working group. They can be adapted and complemented as the global discussion continues. DNA collections that use the Key will mature their DNA collection in a standardised way regardless of their context, considering all different aspects in DNA collection management (i.e. the categories), stimulating a holistic growth (i.e. respecting the levels), breaking down the maturation work into manageable steps (i.e. the goals) and setting priorities (i.e. the categories with the lowest level). Additionally, the Key is a tool that can facilitate overall communication. Firstly, between different stakeholders, such as management and researchers, as the tool allows both a “helicopter view” of the maturation process (i.e. Table 1), as well as being able to zoom in on one concrete goal at a time (i.e. Suppl. material 2). Secondly, the tool allows clear communication across different DNA collections regarding their current maturation level and (near) future ambitions, which facilitates easier sharing of experiences that can inspire, give perspective on what is realistic or even allow different DNA collections to collaborate more intensively for a set period of time when working towards the same goal. This is especially valuable given the often encountered issues with limited availability of resources and personnel: better communication between collections allows for better resource pooling and avoidance of ineffective strategies.

The Challenges and Key are focused on DNA collections only, yet it is important to acknowledge that DNA collections are often embedded in a wider context, in the first place often including a parallel “source material collection” (i.e. tissues, environmental specimens or organisms the DNA specimens were created from) and, in the second place, being part of a larger institutional Natural Science collection. On the one hand, many of the Challenges and goals in the Key can be generalised as being challenges or goals linked to managing molecular collections, (biodiversity and/or environmental) biobanks or even Natural Science collections: they are transferable to many other types of Natural Science collections. Yet, on the other hand, remaining specific to DNA collections increases the relevance of the tool for DNA collection managers and avoids "scope creep". Working with the broader scope of (biodiversity) biobanks has given more generalised results; for example, having to conclude that biobank curation practices vary greatly and that they experience more broadly defined challenges (Corrales et al. 2023). Notwithstanding that learning from different types of Natural Science or biodiversity biobank collections is extremely valuable, a next step is the translation of these results into tangible actions tailored to collection managers, which will further foster their implementation. Such translation is crucial for any recommendations to be applicable in real-life collection management, but it is also especially arduous given the ongoing limitations in available resources (e.g. personnel), one of the (current) challenges. The Challenges and Key, as presented in the results, are intended to empower one or a few individuals wanting to make a difference, in a manageable (i.e. step-wise), progressive and learning-while-doing manner. If a demand for it develops, the concept of the Challenges and Key can be recycled for other types of biodiversity biobank collections, such as living microorganisms, tissue collections, environmental specimen collections or even seedbanks. The resulting parallel tools can also link to the goals and guidance documentation (Suppl. material 2) of this document when they are overlapping, to avoid duplication of effort.

DNA collections, as well as all types of Natural Science collections, cannot be uncoupled from research practices. Research relies heavily on good practices being applied in collection management in order for the DNA specimens to be of value for reuse and vice versa: DNA collections rely heavily on good practices being applied during the collection of the specimens the DNA specimens are derived from, as well as good research practices overall. Research practices, such as the usage of proper sampling techniques, detailed (meta)data documentation, data management planning, project planning, fieldwork planning and application of the FAIR principles (Wilkinson et al. 2016), will positively benefit the quality and the data management of DNA collections. This is also apparent from Corrales and Astrin (2023) dedicating multiple chapters of their book to best practices in specimen collection and preservation, as well as other literature advocating the need for investing in training on the importance of specimen collecting and linking to specimen vouchers (Lücking et al. 2020, Buckner et al. 2021, de Mestier et al. 2023).

As the tool draws from many of the recently-compiled literature resources on the topic, its first version is expected to be complete. Nonetheless, it is worth noting that there was not an exhaustive search of (best practice) literature of DNA collections, nor is the information written in the guidance documentation (Suppl. material 2) as comprehensive as certain more elaborate guidelines or handbooks (e.g. ISBER (2023), de Mestier et al. (2023), Corrales and Astrin (2023)). It is expected that this tool will evolve as it is used, with updates being published as new versions are enriched by users. It is therefore anticipated that any currently missing information will be identified and (links to) the missing information will be added.

The Key differentiates itself from the current plethora of self-assessment tools, such as the BBMRI Self-Assesment-Service (SAS), the ISBER Biobank-Assessment Tool (BAT) and the SYNTHESYS+ Collections Self-Assessment Tool in a number of ways. Firstly, the Key obliges the collection manager(s) to (re)investigate the purpose and hence importance of the collection, prior to even thinking about adhering to good or best practices or "levelling up", as well as re-evaluating the context of the collection (e.g. stakeholders and hosting institute). Secondly, levelling up is made as tangible as possible, facilitated by: 1) the narrow scope (i.e. its being limited to one type of Natural Science collection compared to other tools), 2) defining clear goals that are achievable for any DNA collection regardless of its context, 3) immediate linking to relevant information and 4) actively sharing experiences. Thirdly, the Key is openly published and can be used for free, building on the Open Science and community mindset and aiming for (Natural Science) DNA collections of all shapes, sizes and contexts to be included.

The next step is that the Challenges and Key are tested and improved, based on user feedback. As they are hereby published openly in their first version, all (user) feedback is welcomed. The Challenges and Key can be used independently in their current format (cf. self-assessments) or their usage can be embedded in community-driven initiatives. Such community initiatives could include the organisation of user-support-sessions which allow direct engagement with the users and create inspiring and supportive interactions between DNA collection managers. The DiSSCo Flanders DNA collections working group plans to adopt this community approach and invest in testing, updating and improving the Challenges and Key, whereby developing a more interactive format of the outputs will also be considered.

A holistic, yet realistic approach with tangible goals facilitates the maturation of a DNA collection in an efficient, durable manner, regardless of the collections’ context, size and available resources. One way to carry out this approach is to use "The key to bringing DNA collections to the next level”, presented here. During the maturation process, investment in (internal) stakeholder inclusion, as well as in exchanging experiences with the local or global DNA community, is considered important for achieving real, concrete progress in the management of a DNA collection, especially when the collection's resources are limited.

We’d like to thank all the participants of the DiSSCo Flanders DNA collection working group for their contributions during the on-site and online meetings, as well as sharing relevant information in between meetings about relevant courses or literature. We are also grateful to the invited speakers who have shared information on either different digital solutions or legal expertise. Lastly, we also want to thank the passive members of the working group for having interest in this initiative.

Research Foundation Flanders - International Research Infrastructure (FWO-IRI)

I001721: DiSSCo Flanders: Towards a collection management infrastructure for Flanders

Meise Botanic Garden

All shared experiences are included in this document with the informed consent of the co-authors and the collections they represent.

Author contributions follow the CRediT author statements (Allen, O’Connell & Kiermer, 2019). Participation in at least one working group meeting is considered “Investigation”. Participation in the working group meeting that conceptualised this output is considered “Conceptualisation”. Emily Veltjen: Conceptualisation, Investigation, Writing - Original Draft, Writing - Review & Editing, Supervision. Pieter Asselman: Investigation, Writing - Review & Editing. Wim Baert: Conceptualisation, Investigation, Writing - Review & Editing. Steve Baeyen: Investigation, Writing - Review & Editing. Lise Beirinckx: Investigation, Writing - Review & Editing. Liselot Breyne: Investigation, Writing - Review & Editing. Dimitri Brosens: Investigation, Writing - Review & Editing. Tim Claerhout: Investigation, Writing - Review & Editing. Sari Cogneau: Conceptualisation, Investigation, Writing - Review & Editing. Karen Cox: Investigation, Writing - Review & Editing. Laura Cuypers: Conceptualisation, Investigation, Writing - Review & Editing. Lynn Delgat: Conceptualisation, Investigation, Writing - Review & Editing. Philippe Desmeth: Investigation, Writing - Review & Editing. Jordi de Raad: Conceptualisation, Investigation, Writing - Review & Editing. Lore Esselens: Investigation, Writing - Review & Editing. Maria-Rose Eves Down: Investigation, Writing - Review & Editing. Frederik Leliaert: Investigation, Writing - Review & Editing, Funding acquisition. Kenny Meganck: Investigation, Writing - Review & Editing. Zjef Pereboom: Investigation, Writing - Review & Editing, Funding acquisition. Nathalie Smitz: Conceptualisation, Investigation, Writing - Review & Editing. Gontran Sonet: Conceptualisation, Investigation, Writing - Review & Editing. Maarten Trekels: Investigation, Writing - Review & Editing. An Vanden Broeck: Investigation, Writing - Review & Editing, Funding acquisition. Charlotte Van Driessche: Writing - Review & Editing. Aaike De Wever: Conceptualisation, Investigation, Writing - Review & Editing, Supervision, Funding acquisition.