Throughout 2025, the “ERGA – iBOL Europe Connections” blog post series addressed these and many other questions about biodiversity genomics, such as the role that citizens play in biodiversity conservation, the difference between DNA barcodes and reference genomes, and all the related disciplines. 

This series of blog posts was produced by us, the Biodiversity Genomics Europe project’s Capacity Pillar team, composed of representatives from both the iBOL Europe and ERGA Secretariats. 

Each Connection covers an aspect of biodiversity genomics and comes with a simplified-language version, the EasyConnection. The EasyConnections are intended for a lay audience and school pupils, and can be used by teachers at different levels of instruction.

Since the end of BGE is fast approaching, we decided to collect all of the EasyConnections in a single booklet, “Connections – Discovering Biodiversity Genomics.”

The booklet features eight chapters, links to extra material and media, and a “Games” section at the end to test your knowledge once you’ve read the booklet. To make it accessible to as wide an audience as possible, we have been translating it into different European languages, and for now, it is accessible in Italian and Portuguese.

We hope that “Connections” will help you get a better understanding of the fascinating world of biodiversity genomics, and that you will enjoy playing with it!

If you have been following our Connections series so far, you have learned that barcodes help us recognise which “book” of life we are holding, while reference genomes let us read every page. Today, we follow those pages out of the lab into the places where decisions are made. Biodiversity genomics has matured from proof-of-concept to a toolkit that can inform, for example, monitoring, species risk assessment, and management, and even market rules, by turning reads and assemblies into actions that matter for species, habitats, and the people depending on them.

The impact pathway usually begins with identification and baselines. DNA barcodes establish who is where. This matters when regulators need quick, reliable evidence to strengthen protection for a declining bird population in a wetland. Or when managers must separate look-alike pest species in aquaculture, or when coastal engineers test whether a beach-nourishment scheme is compatible with an endemic fish. Reference genomes deepen the story. They reveal how a species works, what its population structure is, connectivity, and adaptive variation. All clues that tell us if a population can, for instance, cope with heatwaves, if a corridor is worth restoring, and which individuals should contribute to an ex-situ programme. In other words, barcodes inform us of their presence, and genomes explain how they function.

Consider fisheries and seafood safety. Genomics applied to widely fished pelagic species can clarify stock boundaries, helping fish stock management plans align with biology rather than old assumptions. At the same time, genomics in commercially harvested clams can more precisely assess contamination risks, so that consumer guidance and coastal policies rest on data rather than speculation. In both cases, genomics can improve sustainability and trust: what gets caught, what gets sold, what gets eaten, and what the sea can afford to give.

Public health is another frontier where decisions move at the speed of evidence. Genomics of mosquito complexes that transmit West Nile virus allows us to identify cryptic lineages and chemosensory genes linked to behaviour, turning a confusing species complex into a map for outbreak-monitoring programmes. From these insights, SNP panels for routine surveillance, early detection of resistance to control measures, and area-specific interventions mandated by regional authorities can be designed.

On land, genomics can inform connectivity, reintroduction, and hybridisation policies. For example, in a rare Central European small mammal, its genomic structure showed how a modern drainage canal severed gene flow. The management recommendation is to restore corridors before populations slip past the point of recovery. Alpine chamois and butterflies reveal country-level patterns of diversity and endemism. These data now feed directly into status reviews and legally binding conservation lists. In lowland wetlands, a long-distance migratory passerine with low diversity but ongoing gene flow gains a genetic monitoring plan that guides translocation choices and post-release tracking. Where climate change pushes related hare species into contact, genomic portraits of introgression help hunting and wildlife agencies adjust seasons and safeguards to protect vulnerable mountain lineages.

Plants illustrate the same arc from data to decision. Herbs harvested from the wild, dune shrubs that stabilise coasts, and aromatic species adapting to new climates all benefit from genome-enabled surveys that distinguish clonal spread from sexual reproduction, estimate contemporary effective size, and pinpoint variants tied to heat and frost. These findings shape seed sourcing, habitat management, and Europe-wide genetic monitoring that is comparable across borders, museums, and herbaria.

What ties these stories together is not a single technology, but a way of working. Barcodes and genomes are generated in collaboration with end-users, including park services, fishery bodies, health authorities, farmers, and NGOs. Data are paired with training, screening tools, and communication adapted to local contexts. This results in a lasting impact that takes many forms, from field measurements to management plans, from genome browsers to policy briefs, and from classroom demonstrations to community-run surveys.

The book metaphor keeps us honest. Barcodes still tell us which titles we are holding, and reference genomes still let us read every page. But conservation impact starts when we file that book in the right library. We share it with the people who need it and use it to guide choices about land, water, and livelihoods. Biodiversity genomics is now doing exactly that, moving from pages to policies, with benefits that go far beyond the lab bench.

In our previous posts, we compared DNA to a book: barcodes help us identify which book we are holding, while reference genomes enable us to read every page. But here is the twist: by the time DNA leaves the wet lab, the book is broken as if we have run the pages through a “paper–shredder”. DNA extraction, library preparation, and DNA sequencing all turn the long DNA sequence into millions of pieces (we wrote about the different steps of the genomic workflow here). Bioinformatics is the art of turning that pile of shreds back into something we can read, search, and compare. It is the art that turns barcodes and reference genomes into usable knowledge.

Bioinformatics is the product of molecular biology meeting computing. Bioinformatics facilitated the development of the first sequence alignments and substitution matrices, dynamic programming, the creation of searchable databases, and the first “find-it-fast” tools that supercharged homology searches. As sequencing scaled, assembly algorithms emerged, followed by hybrid approaches for long-read platforms. Alongside the algorithms came various file formats (FASTA/FASTQ/BAM/CRAM/GFF/GTF), workflow engines, and the hard-won lesson that reproducibility matters more than quick fixes.

For barcoding, the task is targeted: extract a standard marker (or “abstract”), check its quality, align it against a trusted database, and report the most accurate match with confidence. Think of well-indexed catalogues and fast look-ups, ideal for monitoring and quick assessments. For reference genomes, the task is editorial. Correct sequencing errors, assemble the million pieces into chromosomes, phase haplotypes, polish with multiple evidence tracks (long reads, linked reads, Hi-C, RNA-seq), and annotate genes and repeats. That finished “book” enables population genomics, local adaptation, and conservation genomics studies.

Modern analyses involve dozens of steps, quality checks, trimming, deduplication, mapping, variant calling, assembly, scaffolding, annotation, all wrapped in containers and workflows to make sure a colleague can re-run them on Tuesday and get an answer on the same day. Good metadata is the structure that holds all the pages: sample, permit, locality, preservation, instrument, kit, and version numbers (we discussed the importance of metadata with Joana Castro Pauperio in this episode of Genomic Connections). Without that structure, even the finest assembly becomes a vague curiosity.

A few field notes from the trenches

Everyone has a story of a 2 a.m. run that failed because a file was called final_FINAL_reallyFinal.fastq.gz. We have all been rescued by checksums, saved by containerised toolchains, and learned never to delete intermediate files before the multi-QC report is green. We name scripts after pets, we comment our code (eventually), and we celebrate the day a 500 GB BAM shrinks elegantly into a reproducible VCF.

Why does this matter to BGE and the communities tied to the project? For iBOL Europe, robust bioinformatics means clean barcode libraries, sound assignments, and credible trend analyses. For ERGA, it means reference genomes that stand up to re-analysis and can power subsequent population, functional, and comparative genomics, the applications stakeholders care about (from conservation planning to bioeconomy uses).

Bioinformatics is not an afterthought: it is a research field itself! It is the bridge from sequencer output to decisions. Treat pipelines as publishable methods, treat metadata as data, and treat your future self as a collaborator who deserves clarity. In the next post, we will demonstrate how these computational foundations are applied in practical settings, including monitoring, policy, and management, without losing sight of the overall context (or the pages).

In our earlier “Connections” posts, we explored how DNA technologies, collaborative networks, and international policies shape biodiversity genomics. Today, we turn to another key element: the important role that non-professionals can have in science, or what is often called citizen science. We will unpack what this term means, clarify common misconceptions, and highlight why citizen scientists are vital to projects like Biodiversity Genomics Europe (BGE). It is a story about terminology and teamwork.

The term citizen science is surprisingly recent. One of the earliest recorded uses dates back to 1989, when 225 volunteers collected rain samples as part of a U.S. project aimed at raising awareness about acid rain (Wikipedia). The term “citizen science” was formally added to the Oxford English Dictionary only in 2014,  defining it as 

“a scientific work undertaken by members of the general public, often in collaboration with or under the direction of professional scientists and scientific institutions.”

A citizen scientist, likewise, is defined as a member of the public who engages in such work alongside professionals. Interestingly, “citizen” here simply means anyone; in other words, science by citizens of the world. Thus, a citizen scientist is anyone who is not a scientist but actively participates in real research.

Citizen scientists are:

• Members of the public from all walks of life who voluntarily contribute to scientific research.
• Collaborators at any stage of the scientific project lifecycle.
• Individuals driven by curiosity, passion for nature, community interest, or the desire to make a difference by helping scientists answer questions.
• Partners who expand the reach of research to locations unreachable by professional scientists.
  

Citizen scientists are not:

• Only field workers who collect, for example, environmental DNA, in rivers or soil. While some do help with sampling, citizen science is also about other activities like observing wildlife in your backyard. It also includes classifying images online or transcribing museum records. Outdoor sampling is just one part of it.
• Formally trained scientists or PhDs. No advanced degree or lab coat is required to participate.
• A single stereotype of a person. They can be of any age, background, and living anywhere.
• Replacements for professional scientists. Instead, they complement and work under the guidance of experts, together improving the scope and quality of research.

Biodiversity genomics relies on citizen scientists because the task is far larger than any research team can achieve alone. As species are vanishing at record speed, only a constant stream of data will give us the power to detect and address threats in time. Volunteers support this reach in different ways, such as hobby entomologists who photograph and submit insects for DNA barcoding, park rangers and hiking clubs who keep Malaise traps operating, or even coastal residents who filter seawater to capture the eDNA of invasive species. Their local knowledge reveals hidden habitats, while the DNA they collect flows directly into reference libraries and genome databases. The exchange is two-way. Participants gain new skills, a genuine sense of ownership, and a front‑row seat to cutting‑edge science. In return, they become ambassadors who share information about genomics, conservation, and responsible sampling within their communities. 

Instead of being an optional extra, citizen science now powers the large‑scale, inclusive approach that modern biodiversity genomics demands. Science conducted with the public, for the lasting benefit of both people and the planet.
Stay tuned for our next post, where we will continue to explore the ever-expanding connections in the world of biodiversity genomics.

Within BGE, both ERGA and iBOL Europe carried out many activities involving citizen scientists, including, for instance, the Bioblitz in the Croatian Caves we talked about in our previous blog post. You can learn more about BGE’s involvement with citizen scientists here.

What is a Biodiversity Hotspot? 

Biodiversity hotspots are regions that are exceptionally rich in endemic species (those found nowhere else), in relatively small areas, but face important threats. Consequently, these Hotspots are global conservation priorities because they harbour a large portion of Earth’s biodiversity.

The European continent hosts such hotspots, and Biodiversity Genomics Europe, under a dedicated partnership agreement led by CSIC, the Spanish National Research Council, chose six priority countries to boost the generation of genomic resources for their most distinctive species:

BioBlitzes are coordinated sampling efforts that unite taxonomists, genomicists, and volunteers. They are beneficial in two ways. First, they act as a field classroom, immersing citizen scientists, from local residents to school students into science, strengthening community awareness. Second, DNA barcodes generated during an event provide information about which species are present, while reference-quality genomes built from those same species help us understand how they work, adapt, or decline. Data from barcodes and genomes are tightly coupled: barcodes provide real-time monitoring, while genomes reveal functional variation that informs management.

Croatia – Genomes in the dark – collecting in a hidden biodiversity hotspot

The Dinaric mountain range of Croatia is home to the world’s richest subterranean biomes and is the historical cradle of biospeleology (cave biology). 

Cave species evolved in remarkably stable conditions, which makes them highly vulnerable to rising temperatures and other disturbances. Their subterranean habitats are isolated, and the organisms cannot survive on the surface, leaving them with no migration possibilities when the environment changes. This ecological trap makes genomic studies and the protection of their subterranean refuges increasingly urgent.

To date, over 900 cave species have been discovered in the Dinarides, with more than 150 new ones reported in Croatia since 2002. 

Two cave-focused BioBlitzes took place in April and October 2024, one on the island of Mljet, the other in Velebit’s Cerovac caves. Participants learned how to locate invertebrates, recognise different species, and preserve specimens for barcoding and genome sequencing. More than forty cave species were secured. In addition, park staff and school groups were introduced to biodiversity genomics and learned more about how genomic resources can support biodiversity assessment, conservation, and restoration efforts by providing scientific evidence for informed management decisions. This outcome demonstrates how local partnerships and the use of genomic data can advance subterranean biodiversity conservation.

Photo credits: Martina Pavlek, Iva Cupic, Jana Bedek, TIn Rozman, Alen Kirin, Nikolina Kuharic

In our earlier posts, we celebrated the technical wizardry that empowers iBOL Europe’s DNA barcoding and ERGA’s reference-genome pipelines. Today, we zoom out from bench top and bioinformatics queues to the rules for using those pipelines responsibly. The conversation here is based on two elements: the Nagoya Protocol on Access and Benefit Sharing (ABS) and the debate over Digital Sequence Information (DSI). Both are under the umbrella of the United Nations Convention on Biological Diversity (CBD), and both are poised to shape every barcoding run and every reference genome we produce.

The Nagoya Protocol, adopted in 2010 and enforced in 2014, translated the Convention’s promise of fair and equitable benefit‐sharing into operational obligations. Field teams who collect specimens must secure Prior Informed Consent and negotiate Mutually Agreed Terms before any genetic resource crosses a border. These administrative steps aim to curb scientific colonialism, foster respect for Indigenous knowledge systems, and channel royalties or capacity‐building back to the nation where the specimen was collected. iBOL Europe and ERGA already navigate this protocol daily, because each barcode voucher and each specimen used for the generation of a reference genome must carry a transparent legal pedigree.

Source: https://www.cbd.int/convention/articles/default.shtml?a=cbd-01

The CBD entered into force in 1993, and the boom of sequence databases soon revealed a gap in the Convention. Indeed, the CBD focuses on physical samples, while genomic data travels instantly across digital platforms. The policy community coined the term Digital Sequence Information (DSI) to highlight this distinction – DSI refers to raw reads, assemblies, and barcodes. Since 2016, Parties to the Convention have sought a mechanism that extends benefit-sharing to these ‘files’ without impairing open science principles. Negotiators progressed at the Kunming–Montreal Conference of the Parties in 2022. This process led to the establishment of the Cali Fund for the Fair and Equitable Sharing of Benefits from the Use of Digital Sequence Information on Genetic Resources during COP16 in 2024/2025, aimed at collecting contributions from commercial users of DSI. COP16 laid the groundwork for implementing these mechanisms, and ongoing discussions will continue to fine-tune the system.

ABS permits are NOT “boring compliance forms” to rush through on the eve of submission. They are architectural blueprints for an equitable, reproducible, and future-proof research culture. The sooner biodiversity researchers integrate Nagoya thinking and prepare for DSI benefit-sharing, the smoother the path for publishing, sharing, and reusing our data sets will be. So, the next time you plan a field expedition or start assembling a genome, remember: ethics is not a speed bump; it’s the on-ramp to a legacy of science that everyone can share.

Now, “Connections” has also turned into a podcast, “Genomic Connections,” further expanding ways to reach our audience.  We will release an episode of “Genomic Connections” per month, starting in April 2025, and here you can listen to the show’s trailer. Each episode will explore a different step of the genomic workflow, always highlighting the many connections between the two communities and the advantages of joining forces for better outcomes for biodiversity. For each “Genomic Connection” episode, the podcast hosts Christian de Guttry (ERGA Project Manager) and Kasia Fantoni (iBOL Europe Community Manager) interview experts who help boost genomic science and infrastructure in Europe: the challenges they face, the innovations they develop, and the impact of their work.

You can listen to Genomic Connections on Spotify and PocketCast.

For the first episode of Genomic Connections, “Frozen Futures – The role of Biobanking in Biodiversity Genomics,” Kasia and Christian are joined by Jonas Astrin and Camilla Di Nizo from the Leibniz Institute for the Analysis of Biodiversity Change (LIB) to talk about the essential role of Biobanking. 

The episode’s full Transcript (AI-generated) is available below the credits.

Credits

The episode is licensed under a CC-BY 4.0 license. 

“Genomic Connections” is written and produced by Christian de Guttry, Kasia Fantoni, Luisa Marins and Chiara Bortoluzzi.

Graphic design by Luisa Marins. Postproduction by Kasia Fantoni.

Music (intro and outro): “⁠Nostalgic Reflections⁠” by Ant.Survila (c) copyright 2025 Licensed under a CC-BY-NC 4.0 license. Ft: airtone.

Biodiversity Genomics Europe is a Horizon Europe project funded by the European Commission, the Swiss Confederation and the United Kingdom.

Episode #1, “Frozen Futures” Transcript

Kasia: 

Oh, Chris, I had a bit of a rough return home because my fridge broke. Luckily, most of the stuff inside didn’t spoil, but I had to throw some tiramisu leftovers in the trash.

Christian: 

Oh, yes, that sounds like a rocky welcome home. And while it’s horrible that you had to throw out your tiramisu, it’s good that most of your food didn’t spoil,

Kasia: 

yes, indeed, it mainly was food that wouldn’t risk much deterioration, 

Christian:

Good for you; differently from your food, the samples Biogenomic Europe work with are very sensitive to outside temperatures, and would have suffered way worse than your tiramisù. 

Kasia:

Indeed, we need to store them very safely and as soon as possible, to make sure that they preserve their genomic information. And that’s where biobanking comes in. In today’s episode, we will talk about bio banking with Jonas Astrin and Camila Di Nizo.

I am Kasia Fantoni iBOL Europe Community Manager,

Christian:

I’m Christian de Guttry, ERGA project manager, and you’re listening to Genomic Connections, a podcast about Biodiversity Genomics.

Kasia:

For this episode, we are joined by Jonas Astrin and Camila Di. Both of them are from the Leibniz Institute of the analysis of biodiversity change in short, LIB. Jonas Astrin is the head of the section and curator of the biobank of LIB and he is also responsible for the strategic development of the biobank. He is also active in various biobanking networks such as the global genome biodiversity network and the International Society for biological and environmental resources. Jonas is also engaged in biospecimen research. Camilla di Nizo oversees the cell culture lab at lib and there she manages daily Sample Acquisition. Her work includes developing protocols for obtaining cryopreserving cells from non model species and conducting karyotype analysis where needed.

Christian:
LIB was created by joining forces between the zoological research Museum in Koenig in Bonn and the Museum of Nature of Hamburg. So this organization is dedicated to studying how biodiversity changes over time, supporting conservation effort and sharing knowledge with the public. The Lib biobank stores many kind of samples, including DNA from animals tissues, living cells, small organisms and even environmental samples in liquid nitrogen at minus 190 degrees Celsius, and personally, I find it wonderful to know that these samples and the associated data are available for researchers

worldwide. 

Kasia:

Fantastic. Let’s get started. So bio banking can sound like a fancy cold storage system in your own words, what is so exciting about it and why it is so critical for Biodiversity Genomics?

Jonas:
Well, hello, thanks for the question. And yeah, why is it exciting? If you are a nerd, it definitely is exciting because science is exciting to nerds. If you’re not a nerd, then you should tune out, probably, but being a nerd as we are, bio banking is great because it enables science. You can do some proper scientific research, at least at the molecular level, without having biobanks. Biobanks make research repeatable in a way, because they archive the samples that have been used, you can prove the research wrong using those samples. You can repeat the research, and as long as we have the material, the collection, that can be accessed over and over again. Bio banks are just one component, because you also have morphological collections, as we call them, where the whole animals are usually stored, or, yeah, parts of the organisms at least, that can help identify them. So yeah, apart from repeating or making science repeatable, biobanks also make it possible to expand on previous research, so you can use specimens that have been amply described or analyzed and the results published on them, and use them in another context. And this just grows the knowledge net and makes knowledge or makes the samples more meaningful every time they are reused. Also you can completely or base completely new studies on the material so it’s more sustainable. You don’t have to go out and recollect every single time and just use the material that has been already collected and. And use that in new studies.

Christian:

That’s wonderful. So basically, for what I understood, biobank, biobanks are a legacy for the future of research, and we mentioned before that within the biobank, you can also store DNA at those super low temperatures, and we often talk about DNA as the book of life. So if your bio bank were a library, how would you describe your cataloging system and the rail collections you are most proud of?

Jonas: 

Okay, so that’s yeah, two parts of the question. Our catalog that we have is not too different, different, actually, from a library catalog, although, strictly speaking, we would rather be an archive than a library, because a library has copies of the same media that exists several times, and everything that we have are unique objects, so more of an archive of life, and yeah, the catalog is a database that’s maybe not too exciting to look at if you’re not a nerd in another area and in the data area, but it enables a lot of data sharing. This database is structured by common data standards, and we deal out the data to both our own portal at the lib website, and to the ggbm the that is the global biodiversity biobanking network. That’s an aggregated aggregator site where lots of different biobanks from throughout the world show their data and make it accessible. Yeah, the second part of the questions, a question about our holdings. So we have, in general, generally speaking, we have mostly animals. We have also quite a few environmental samples, like sediment samples or filtered water samples. But from those animals, it’s mostly vertebrates and arthropods, insects, spiders, crabs, etc. In terms of material, it’s either tissue or cells or DNA and yeah, regionally, they come a lot of them, our samples, come from Central Europe and particularly Germany, mostly probably based on the fact that we have been working in the German bucker life project for over a decade, and has accumulated lots of samples regionally. And it makes sense to structure collections regionally. But we also, through other projects, have lots of samples, for example, from the Caucasus area. We have quite a few samples from Africa, few from Latin America and basically worldwide, where we collaborate with lots of different partners. The most exciting sample, I had to think a bit about it, but I think I would say maybe a wooly mammoth. We got a hair sample from a wooly mammoth that was came from the permafrost and Todd, and we were able to extract DNA from it and did a DNA barcode on the mammoth. So if you see a hairy elephant walking around and want to snatch a hair and DNA barcode it to make sure it is a wooly mammoth, you can compare it against our data.

Camilla: 

Yeah, can I compliment a little bit and talk about some other special samples that we We are also proud of? So we had sales from the Soho dove, which is unfortunately already extinct in the wild, as well as other critically endangered species such as the European eel or the yellow crested cacao or the Madagascar spider tortoise. And some of these species are still poorly known, despite their threat in its status, which we believe that’s very important to have this in our collections.

Kasia: 

Thanks so much both. It seems like you need a lot of technological advancement and technology and technology, generally speaking, to preserve all these very precious samples. And we know that technological advancement is running pretty fast. So is there any recent innovation on storage methodologies that made you think like, this is the game changing methodology or technology for bio banking?

Camilla: 

Well, I think what we consider an innovation in our bio bank is the recent creation of our cell culture bank. Although it’s not a it’s a an old technique. We only recent people are realizing the importance of archiving sales due to the range of possibilities that sales provide. It because cells can carry identical copies of the genetic information, giving high quality material for genomic studies, which is particularly reported nowadays, doing due to the increase number of these projects. And additionally, because cells can provide chromosome information, we have observed a recent increase in interest in cytogenetic studies, which is also old, but now people, it’s becoming more popular because it’s complementing these genomic projects. 

Christian:

I have the impression that the permafrost was our planet biobank for a long time, but now we are little by little, losing it. Unfortunately, I have a question about iBOL Europe and ERGA. So both rely on high quality samples, and we know that the cold chain is quite important for high quality sample, but these two communities, they do different kind of research. And how do you tailor if you tailor biobanking practices to meet the needs of these two communities?

Jonas: 

So generally speaking, I would say that to be properly set up as a biobank will make will enable you to cater to all kinds of different communities, including the bar coding and the genome sequencing community. And there’s nothing special we need to do now to adapt to these projects. But you need a proper database. You need good temperature monitoring, ideally redundant temperature monitoring in your collections, you need good service instruments, and my take is that you would also need liquid nitrogen to to make sure that you have the best possible preservation, particularly for samples that go to the genome stream, and definitely for the cells that Camilla mentioned, and yeah, you also need to be in a network, and you need to be able to show your data through through portals like GGBN. For us, the situation is pretty good. We were lucky that we had been approved a new building that we’re moving into this year, and we have a big new cryo facility with lots of shiny, huge liquid nitrogen tanks that even our DNA goes into minus 190 degrees storage. So we could make sure that everything is really perfectly stored, and that helps for bringing samples in so we have cryo cards that move around and cryo pots that we can use to solve the samples, all at liquid nitrogen temperatures, and that helps with the cold chain that Camilla is now going to comment on, yeah. 

Camilla:

Now what I wanted to comment is that having these standardized procedures for collecting, transporting, storing samples, applies to all genomic projects. So we we try to encourage, whenever possible, to have step frozen tissues or trying cell culture, because it’s two approaches, yeah, the high quality DNA for any Genome Project, either iBOL (Europe) or ERGA.

Kasia: 

I think that when talking about bio banking, so we talk about storage, but also logistics, I think they play an important role. So we have different specimens coming from different region of Europe, at least to LIB so and what is the biggest challenge that you face when shipping or receiving samples, especially when we talk about remote out of permafrost or international locations?

Camilla:

Yeah, I think regarding the transport of flash frozen samples or frozen cells is very challenging, because not everybody has access to dry ice or a dry shipper with liquid nitrogen, especially if we are talking about collecting remote and bringing to the to the bio bank, to the lab and additionally specialized couriers are normally very expensive and subject to specific regulations, which makes more difficult, I would say, thinking about the cells. So transporting tissues to grow from the field, to grow the cells in the lead requires a specific type of medium with antibiotics to prevent contamination. And this can be an obstacle because it has to be kept at constant temperature, four degrees, not less than that. And also, in my case, what. Is a little bit challenging is that the time limit to process this, these samples, to grow the cells, so I have to process as soon as possible to increase the chance of having cells. So finally, it’s important to mention that we need all the pyramids, and this sometimes could be quite challenging, especially depending on the country

Christian:

To keep pace with time, we could discuss, we should discuss about artificial intelligence and machine learning that basically are two similar concepts. Do you think that this kind of technology, I mean, all of the genomic lab in the world are now thinking on how to apply these technologies to their own research. And do you think that this technology play your role in how you organize or monitor the specimen, or in any other aspects within your facility?

Camilla:

Yes, I we believe that artificial artificial intelligence would help us to ensure accurate sample tracking and prevent misleading for example. Also, we think that in the future, we will benefit from AI to the text, sample contamination, degradation, cell viability. So

the so far, we don’t foresee that much need, actually, because lots of stuff is done manually and needs eye control. So it’s also a risk to apply AI to an unlimited extent. So for bio banking, we’re a bit old school on that.

Kasia: 

So do you know, like, there is a lot of thing going on, I guess, in your lab, but is, is, can you give us a glimpse of the road ahead that you have, for instance, if you have any be important milestone or project you want or hope to tackle at your biobank?

Jonas: 

Yes, so an important challenge for the future of biobanking in general is to work towards the harmonization of biobanks and to grow the network, particularly biodiversity, because we have some catching up to do, but also generally, I mean biobanking is most widespread in the human biobanking area with which we interact as well, and it’s important to interact with those biobanks, because technologically, they’re usually more advanced, and best practices are usually done together with those biobanks, as we do in isper But yeah, I mean in biodiversity, we have lots of small communities storing frozen samples in their own Way, and in part, they need their own way, because they are also particularly collected and need to be preserved in a particular way. But still, there are some chances to better standardize how we’re doing this, how we’re collecting information on them, how we’re sharing that information, and how we are talking about options to strengthen the bio banking community, so we have all these little tribes of bio banks and molecular collections that we need to bring closer together, get them to talk more, interact more, use synergies and build better joint projects, and GGBN can be a key player to do that and harmonize and streamline the processes. And, yeah, this is about protocols. This is about data. This is about graph writing and also science policy, I guess.

Camilla: 

Yeah, regarding the cell, the plan is to archive the largest number of species, especially those that are considered more difficult to obtain the cells. In the case of vertebrates, for example, amphibians, the group that suffers more now in that we are living this climate crisis, reptiles and fishes are also difficult to get cells, so the goal is to develop protocols to have more of these in our collection. And one of our wishes is to Coronavirus their cells from invertebrates, particularly arthropods, to cover this group with the largest number of species, we have already started some tests, which has proven very difficult, but I’m positive that this could be our next big step.

Christian:

That’s super interesting. Actually, bio banking is a an evolving field of research, we can say, given that we are talking talking about the future. So imagine a future scientist stumbling on one of your stored viads 50 years from now. So in 2075 What do you hope they will be able to discover or be able to do with that sample?

Camilla: 

Yeah, I mean, my first thought would would be that that person doesn’t stumble, that he or she would, in a very organized, very neat way, go to the dgbm portal, look worldwide for where they can find which sample and have the appropriate metadata with it. And then they would see, oh, okay, I can go to LIB biobank and they will have this and that cell culture or DNA, or whatever I’m looking for. But no one knows. So maybe it is going to be a stumbling because politically, it’s not very clear where we’re going. And for that option, we’re also trying to to gear up and quite a few samples, DNA samples that we have, we have been sealing in metal capsules and keeping as a backup storage at room temperature, without water, without oxygen, in inert gasses, to really help people stumble on post apocalyptic biobank samples. I don’t think we have the wooly mammoth there, but lots of red listed species, protected species that may, by then, not be around anymore. But yes, what should people be able to do with that sample? So they should be able to reconstruct research that has been done, and they should be able to open up a window in time for species, for populations, and this is what collections are for, to understand how these species and populations have changed over time, why maybe they got extinct, or why maybe that population has flourished. What was it genetically maybe that made that possible? And infer from this material, useful information, valuable information, both for society and for basic knowledge and yeah, understand biodiversity better and protect better biodiversity better. Camilla, did you want to add anything about?

Camilla: 

Yeah, In the cell perspective, I think people would be able to perform comparative studies or virology or disease that we have now and would maybe have in the future, or use the sales or eco toxicological studies in different organisms, comparing human environmental impact now and in the future, or use the cell to recover biodiversity.

Kasia:

Why not talking about stumbling still, I would like to come up with the last question, which is a bit more on the funny side, and I would like to ask both of you if you could preserve a sample from any mythological or extinct creatures. Which one would you pick and why? 

Camilla: 

I think this is the most difficult question.

The first thing that I thought was a unicorn, because my daughter loves unicorns. But now, giving a second thought, maybe the dodo, this big bird that was extinct from Mauritius Island, because I think it’s very sad that we had the chance to co exist with this animal and ended up driving it to extinction,

Jonas:

I guess for me to just name something, I could name a few things that I would love to have at the biobank. But what I thought of first thing the top of my head was Europe, to read a sea scorpion, those up to several meter long, swimming Scorpion related giants and the seas. And would be really cool to understand their their metabolism, their Yeah, evolution better by having DNA from them, at least. Maybe even better if we do invertebrates, one of cells and maybe grow a little at some point.

Kasia: 

Wonderful. Thank you so much. Camila and Jonas for joining us. This podcast is brought together by Biodiversity Genomics. Europe project founded by the European Union, the Swiss Confederation and the United Kingdom.

Would you like to suggest a topic for an upcoming episode, or would you like to reach out? Send us an email.

In our first post, we explored the importance of biodiversity genomics. In the second post, we met iBOL Europe and ERGA, the two communities that power the Biodiversity Genomics Europe project (BGE) by studying biodiversity using different but complementary genomic techniques. Today, we will look at how these two communities perform many similar steps to achieve their goals. This includes collecting biological samples, analyzing genomic data, and applying their findings to support biodiversity conservation initiatives.

Sampling: Both iBOL Europe and ERGA start with the first step of collecting material in the field. For iBOL Europe, this involves obtaining tissue samples from both museums and the field, where environmental DNA (eDNA) samples from soil and water are also gathered in addition to flying insects from tools like Malaise traps. Alternatively, ERGA typically obtains tissue samples (for example, leaf cuttings, biopsies, or whole organisms) that require immediate freezing, often in liquid nitrogen, to keep the biological material as intact as possible. This extra layer of care ensures the highest-quality DNA available for in-depth genomic analyses

From the top of the Alps (left) to the lowlands of the Biebrza Marshes (right), finding samples for barcoding and DNA sequencing often feels like an adventure. However, field sampling must always be carried out with an extra layer of care to ensure that specimens are stored in the most appropriate ways to optimise the time and costs associated with field sampling. This is exemplified by the small tank filled with liquid nitrogen shown on the left-hand figure, which is used to transport and preserve the precious samples down the mountain.
Photos by Brad Carlson and Szczepan Skibicki. 

Sample Processing: Once in the lab, both communities make use of molecular techniques to extract DNA. However, while barcoding involves DNA extractions from both individual specimens and bulk or environmental samples (that contain multiple organisms), reference genome sequencing is solely focussed on high quality DNA extractions from individual specimens. DNA from individual specimens.

Sample Processing at Naturalis Biodiversity Center. Courtesy of Naturalis Biodiversity Center.

Sequencing: After DNA extraction, both initiatives use next-generation sequencing platforms to decode the genetic material. iBOL Europe often relies on targeted DNA sequencing approaches, but also uses short-read ‘skimming’ for museum specimens, to generate DNA barcodes from environmental samples and reference samples. Meanwhile, ERGA leverages several different types of short-read and long-read data to assemble chromosome-level reference genomes that capture complex genomic regions more effectively.

Sequencing centers, along with the sequencing machines depicted here, are crucial components of the infrastructure needed to support biodiversity genomics initiatives such as BGE.
Picture by David Levene, courtesy of Wellcome Sanger Institute.

Data analysis: Both iBOL Europe and ERGA handle large amounts of genomic data. Artificial intelligence (AI) methods increasingly help compare unknown DNA snippets against huge digital libraries or refine the final genome assembly. For iBOL Europe, the goal is to generate DNA barcode reference libraries and use these for accurate species identifications to enable presence/absence monitoring at scale. For ERGA, the data analysis aims at unraveling full genomic architectures from reference genomes, offering clues for evolutionary studies and potential “genetic rescue” strategies for threatened species.

Biodiversity conservation impact: ultimately, the information obtained from both DNA barcoding and reference genome assembly informs conservation actions. DNA barcoding data can help pinpoint hotspots of species diversity or track the spread of invasive species. On the other hand, ERGA’s high-quality genomic resources can guide genetic rescue efforts, revealing which populations have enough genetic diversity to adapt to pressing environmental changes. Although iBOL Europe and ERGA focus on different levels of detail, their workflows share many parallels, with high quality references central to both endeavours, underscoring the collaborative spirit of the BGE project.

Following similar steps, from field sampling to sequencing and analysis, these two communities bring diverse genomic data under one roof. Thus, biodiversity is understood faster and deeper, and there is a stronger scientific basis for protecting life on Earth. Stay tuned for our next post, where we continue to explore the synergies between DNA barcoding and reference genomes.

In our first blog post, we introduced Biodiversity Genomics and its importance. Today, we highlight the two growing communities powering the Biodiversity Genomics Europe (BGE) project: iBOL Europe and ERGA. Each of these pan-European networks brings its unique approach to understanding and protecting the living world, yet both share a common mission: safeguarding Earth’s biodiversity at a critical moment in our planet’s history.

iBOL Europe is the European regional node of the global International Barcode of Life consortium (iBOL). Its core method, DNA barcoding, relies on short, standardised segments of DNA to identify species accurately and efficiently, much like human fingerprints can be used to identify individuals. With a broad network of more than 500 members from 173 institutions across 29 European countries, iBOL Europe is building an interconnected system that can rapidly detect and monitor species, offering critical insights into their distributions and interactions. iBOL Europe’s work also links into iBOL’s global BIOSCAN initiative, which aims to track species worldwide, discover novel ones, and deepen our understanding of ecosystem dynamics.

ERGA (the European Reference Genome Atlas) tackles biodiversity from another angle: assembling high-quality reference genomes. As the European node of the Earth BioGenome Project (EBP), ERGA’s goal is to coordinate the sequencing and assembly of the complete genomic “blueprints” of all eukaryotic species across Europe, offering extraordinary details about each organism’s genetic makeup. These chromosome-level genomes serve as foundational resources, allowing researchers to explore complex biological processes and evolutionary histories. Beyond generating genomes, ERGA’s pan-European community works on best-practice guidelines, training materials, and community-based actions that strengthen the entire biodiversity genomics ecosystem.

Despite their distinct approaches, one focusing on rapid species identification through barcoding, the other on in-depth genomic assemblies, iBOL Europe and ERGA both endorse the urgent need to address biodiversity loss. Together, they form complementary pillars under the BGE project, accelerating our collective capacity to observe and protect life on Earth.

In our next post, we will explore how barcoding and reference genomes intersect, overlap, and collectively expand our understanding of biodiversity genomics. We hope you enjoyed this exploration of the two key communities, and we look forward to sharing more insights soon!

Biodiversity is such a popular term that it’s easy to assume that it has been around for centuries, but, in fact, it is relatively new. The word “Biodiversity” was first coined in 1985 during the National Forum on Biodiversity held in Washington, D.C. Before this, the term “biological diversity” was used, but it was not until the Forum that the term “Biodiversity” took on its current meaning. 

Biodiversity itself is a combination of two roots: “Bios” (Βίος), from the Greek word for life, and “Diversity,” derived from the Latin word “Diversitas,” meaning variety or difference. 

Together, these two words describe the richness of life forms on Earth, including ecosystems, species – from plants and animals to bacteria, fungi, and microscopic organisms – and the genetic makeup of individual organisms. It is also about how life forms interact and build intricate communities, with each part contributing to something greater than the sum of its parts.

While the concept of biodiversity has existed in scientific circles for years, it was not until the Earth Summit in Rio de Janeiro (Brazil) in 1992 that it gained political traction. At the Summit, representatives from 150 countries signed the Convention on Biological Diversity (CBD). This marked a turning point, with biodiversity being recognised as an environmental issue and a critical factor in economic, social, and cultural well-being. The signing of the CBD was a major step in the international community’s commitment to the preservation and sustainable use of biodiversity, outlining three main objectives: the conservation of biological diversity, the sustainable use of its components, and the fair and equitable sharing of benefits arising from genetic resources. In 2022, the CBD was implemented to conserve the genetic diversity of all species within the Kunming-Montreal Global Biodiversity Framework – until then, it focused on domesticated and farmed species, cultivated plants, their wild relatives and other socioeconomically and culturally important species.

Genomics What exactly is genomics? Genomics is the study of an organism’s genome, which is its entire set of genetic material, and how this information influences its biology. Every single organism within the domain of Eukaryota (which includes plants, animals, fungi, and more) has a genome made up of DNA – the fundamental blueprint of life. Compared to genetics, genomics takes a broader scientific approach: it looks at all the DNA in an organism’s genome, including both the genes that code for proteins and the non-coding regions that do not directly code for proteins but still play essential roles in gene regulation and function. What sets genomics apart from genetics is its comprehensive scope and the level of resolution it offers, allowing us to dive deeper into the complex genetic structure that defines every living being. However, it is worth noting that over recent years, the term genomics has been used more loosely to include areas of genetics and even DNA-barcoding research that use ‘genomics’ technologies.
Genomics is closely tied to biodiversity because it helps us better understand a key overlooked component: “genetic diversity.”

In our next blog post, we will take a closer look at how iBOL Europe and ERGA are advancing our understanding of biodiversity and genomics, shedding light on the complexity of life.

We hope you have enjoyed this brief introduction to the concepts of “Biodiversity” and “Genomics.” Stay tuned for more exciting insights in the upcoming posts!