From 7 to 9 July 2025, the Bulgarian Academy of Sciences (BAS) in Sofia hosted a regional BGE training event on biodiversity genomics. The workshop was organised by Aristotle University of Thessaloniki (AUTH) with contributions from BAS, and the University of Łódź (UniLodz). The event also aimed to build synergies between national barcoding nodes—GrBOL (Greece), BgBOL (Bulgaria), and PolBOL (Poland)—and strengthen regional capacity in biodiversity genomics.

The three-day programme combined theoretical sessions with practical training in DNA barcoding and genome-scale workflows. Day 1 focused on molecular techniques, including DNA extraction and high-molecular-weight (HMW) DNA handling. Day 2 covered barcode library preparation and sequencing using Oxford Nanopore Technologies (ONT) MinION devices. Day 3 included data analysis and submission to BOLD, as well as sessions on citizen science and community outreach. The programme concluded with a roundtable discussion on the roles and future collaboration of national barcoding initiatives in the region.

A total of 15 participants were selected via an online registration process. They represented a range of academic institutions, including Sofia University, several BAS institutes (e.g., Molecular Biology, Biodiversity and Ecosystem Research, Plant Physiology and Genetics), the National History Museum of Bulgaria, the Maritsa Vegetable Crops Research Institute, and the University of Skopje (North Macedonia). Participants included bachelor and master’s students, PhD candidates, postdoctoral researchers, and early-career scientists from fields such as molecular biology, microbial ecology, conservation, and bioacoustics.

Participants were grouped into three working teams to balance experience in laboratory and bioinformatics workflows. Training sessions were led by four instructors from AUTH (A. Triantafyllidis, S. Papakostas, E. Kaitetzidou, K. Gkagkavouzis) and one from UniLodz/PolBOL (T. Mamos), with support from the BgBOL coordination team. The training made use of BAS facilities and included newly acquired ONT reagents for practical sessions.

From 7 to 12 July 2025, the Department of Biology at the University of Florence (UNIFI), Italy, hosted an intensive BGE training event focused on whole-genome and barcode sequencing using Pacific Biosciences (PacBio) platforms. The training formed part of Work Package 12 (Joint Network Activities), under Task T12.1 (Joint Network Training), and was delivered at the Florence Genomics Facility, which is equipped with first-, second-, and third-generation sequencing platforms and associated infrastructure for high-throughput library preparation.

The aim of the training was to provide early-career researchers and technical personnel with both theoretical background and hands-on experience in DNA extraction, library preparation, and sequencing workflows. The programme emphasized the practical implementation of established protocols for de novo genome sequencing and multiplexed barcode library preparation, particularly in cases involving diverse biological materials.

Due to the technical complexity and time required for sequencing system setup and library construction, the training was designed for a small, focused group. A total of five trainees participated: three technical staff from the University of Primorska (Slovenia) and two from the University of Florence. Over the course of five days, participants engaged in lectures, practical labs, and live demonstrations of sequencing runs using the PacBio Sequel IIe platform and SMRTbell prep kit 3.0.

The training covered the full workflow from high-quality DNA extraction to barcode and whole-genome library construction, quality control, and sequencing. Labs were structured to facilitate active, hands-on learning under direct supervision from instructors, enabling participants to apply techniques and troubleshoot in real time. The event was designed to empower participating teams to independently prepare sequencing-ready libraries either in-house or for submission to external service providers.

This capacity-building activity supported BGE’s goals of enabling high-quality sequencing at scale and expanding technical expertise across European biodiversity research institutions.

From 12 to 13 February 2025, the Aristotle University of Thessaloniki (AUTh) hosted a BGE training event in Thessaloniki, focusing on DNA barcoding and applied genomics. The event was held across two venues: the Centre for Interdisciplinary Research and Innovation (CIRI) in Thermi and the School of Forestry and Natural Environment on the AUTh campus in Finikas.

The two-day programme offered a mix of theoretical input and hands-on training, addressing both laboratory and bioinformatics workflows. Day 1 focused on DNA barcoding, covering sampling protocols, DNA extraction, library preparation, and sequencing with Oxford Nanopore Technologies (ONT MinION). Participants also received training in data analysis and submission to public repositories such as BOLD.

Day 2 shifted to applied genomics and data management. Sessions included an introduction to high-performance computing (HPC) infrastructure, best practices for data archiving and version control, and workflow automation using Snakemake. The programme concluded with a session on the use of reference genomes in species conservation and trait analysis.

A total of 20 participants attended, selected through an application process to ensure a balance of backgrounds and experience. Attendees came from eight institutions across Greece, including AUTh, the International Hellenic University, University of Thessaly, Aegean University, Agricultural University of Athens, University of Patras, the Goulandris Natural History Museum, and the Hellenic Centre for Marine Research. Participants included postgraduate students, early-career researchers, and technical staff from universities, research institutes, and museums.

To support collaborative learning, participants were divided into five working groups based on their prior experience in DNA barcoding, bioinformatics, and data submission. This structure helped balance the level of support across both wet lab and computational modules.

Since April 2025, Karazin Kharkiv National University (KKNU) has been implementing a series of decentralized, rolling training events as a way to sustain training activities while ensuring participant safety and accessibility under unstable conditions. Sessions have been held in both Lviv and Kharkiv, targeting early-career researchers, including PhD students, university graduates, and war veterans with backgrounds in biology re-entering the scientific workforce.

 

The rolling format allowed for individualized support and continuity of engagement at times when centralized events were not feasible. Participants have included researchers from diverse backgrounds and institutions, such as Anastasiia Zabolotnia (private sector, Ternopil), Olga Komarnytska and Solomyia Dyka (Lviv National University), Andrii Tupikov (independent), Marta Kulyk (Lviv National University), and several trainees from Kharkiv National University, including Mykhailo Pereverzev, Oleksandr Surma, Mariia Sidorova, Serhii Sidorovsky, and Georgii Turaziani.

 

Three structured in-person training events were conducted to reach broader audiences:

• A one-day training for biodiversity monitoring experts from the Ukrainian Hydrometeorological Center in Kyiv (9 April 2025, 7 participants);
• A hybrid workshop for entomologists from Natural Reserves and National Parks, hosted by the State Natural History Museum in Lviv (21–23 May 2025), with 15 in-person and over 50 online participants;
• A two-day training at Kyiv National University (31 May – 1 June 2025) involving six participants from the Department of Ecology, including staff and PhD students.

These mission-driven training efforts have been instrumental in maintaining Ukraine’s participation in biodiversity genomics and capacity building despite the ongoing conflict.

 

From 21 to 23 May 2025, the Naturalis Biodiversity Center in Leiden, the Netherlands, hosted a BGE training event focused on biodiversity genomics. The programme combined theoretical lectures with hands-on sessions, addressing both the DNA barcoding (iBOL) and reference genome (ERGA) components of the project.

The first day featured theoretical lectures attended by 22 participants, while the second day offered laboratory training and data analysis sessions for 18 participants. Practical components included DNA extraction, quantification, PCR, and visualization using Qubit fluorometers, gel electrophoresis systems, and the Agilent TapeStation. An Oxford Nanopore Technologies (ONT) MinION device was also used, with new flow cells and ligation kits procured for the training.

Participants were primarily PhD students and postdoctoral researchers from Naturalis and Dutch institutions such as Leiden University, selected through a targeted registration process launched one month prior to the event. Applicants provided information on institutional affiliation, academic position, and prior molecular biology experience.

During the hands-on sessions, participants processed biological samples using the Naturalis ONT DNA-barcoding pipeline and learned to analyze barcode data for submission to BOLD. They also explored the basics of whole genome sequencing data processing using Galaxy and were introduced to FAIR data management principles. The training provided a full workflow overview, from experimental design to data interpretation.

From February 3 to 7, 2025, the ‘BGE joint network training: Biodiversity Research Integrating barcoding, Genomics and High-throughput Technologies (BRIGHT)’ took place at the Faculty of Biology and Environmental Protection at the University of Lodz, Poland. The training brought together 24 in person participants (selected based on application process) and 31 online participants, mostly students (master and PhD students), early career researchers and stakeholders: GO’s (National Parks and Gene Banks representatives), and NGO’s (private companies representatives). The main goal was to train the audience in biodiversity studies employing molecular methods.

Additionally, the attendees had the opportunity to work in an actual scientific project which involved: preparation of DNA barcodes for 500 pollinators specimens from Impatiens spp. from different sampling sites in Poland and genome reconstruction of keystone species in freshwater habitats, the crustacean Gammarus jazdzewkii.

BGE joint network training: Biodiversity Research Integrating barcoding, Genomics and High-throughput Technologies (BRIGHT). Image by: Piotr Gadawski

Overview of the event 

Thanks to the synergy of DNA barcoding, genomics methods and high-throughput sequencing technologies, recognition of biodiversity from individuals through populations to species levels became available for everyone. 

During the workshop both theoretical and practical aspects of application of molecular methods in biodiversity studies were explored. The classes were given by 19 instructors and covered various topics from the basic concepts of biodiversity organisation, through molecular laboratory methods, genomic research, databases (eg. ENA, BOLD, UNITE, COPO) to examples of citizen science involvement in scientific projects. The practical part included training in sampling, DNA isolation for barcoding and genomic research, DNA amplification and quality control, ONT sequencing, molecular data management and analysis and a visit to DNA sequencing centre and biobank.

BGE joint network training: Biodiversity Research Integrating barcoding, Genomics and High-throughput Technologies (BRIGHT). Image by: Piotr Gadawski

Feedback summary 

The attendees received a questionnaire to assess all the sessions and provide feedback. In general, the sessions received very high scores with marks “excellent” in all the cases, the number of instructors was sufficient for all the parts. The attendees also very positively assessed all the instructors and the handbook prepared for the workshop.

Also, the attendees suggested having smaller groups during the laboratory practicals (the groups were 4-5 people) and to extend time for the bioinformatic sessions.

Header image and image above: BGE joint network training: Biodiversity Research Integrating barcoding, Genomics and High-throughput Technologies (BRIGHT). Image by: Piotr Gadawski

Text by Luisa Marins

From September 23 to 27, 2024, the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) hosted a BGE workshop, focusing on DNA barcoding and high-quality reference genomes – the project’s two main research streams. The workshop brought together early-career researchers and students with diverse backgrounds in biology and bioinformatics, offering hands-on training with state-of-the-art technologies. Participants included master’s and PhD students as well as postdoctoral researchers from institutions in the Berlin area, such as the Free University Berlin (FU), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), and the Natural History Museum Berlin (MfN). A total of 28 participants were selected through an application process, ensuring a diverse range of research focuses and career stages.

The 5-day workshop was designed to cover two main topics: DNA barcoding and whole genome sequencing, assembly and annotation. The barcoding module was led by Amrita Srivathsan and her team from the Natural History Museum Berlin (MfN), while the genome assembly module was led by researchers from the Leibniz Institute for Zoo and Wildlife Research Camila Mazzoni, Diego De Panis and Tom Brown.

 

Genomics starts in the field: the workshop included theoretical and practical sessions on sampling for genomics analysis – participants learned how to set a malaise trap. Image by: BGE/ERGA

 

The workshop was very successful and participants reported that they learned a lot in the intense training week. All six groups were able to barcode their samples, with five of them achieving a success rate of over 80%. In the genome assembly module, participants produced high-quality chromosome-level genome assemblies, as well as annotations, and became familiar with Galaxy – a web-based platform that allows users to run bioinformatic workflows and analysis in an accessible and reproducible way.

 

For sequencing during the barcoding module, an Oxford Nanopore MinION Mk1B device was used. The portable sequencer that enabled participants to observe sequencing in real-time. Image by: BGE/ERGA

 

Curious to hear what the participants had to say about the workshop?
Check out this video for an inside look at the event and the feedback from some participants:

 

Header image: In the lab: participants had hands-on experience sampling specimens, extracting DNA, preparing it for sequencing, and finally analyzing the sequences. Image by: BGE/ERGA

Text by Oleksandr Zinenko

Last 28-29 September 2024, a training event for early career scientists on mass DNA barcoding and genomics had taken place in V. N. Karazin Kharkiv National University. It’s the first such event held completely in person in the Karazin Safe Space in Kharkiv, Ukraine.

The event has gathered all participants of the BGE project and early career scientists: master (3) and PhD (2) students, young professionals from state institutions(2) and advanced bachelor students (3). During two days the methods of biological sample collections, preservation, express and low cost DNA extraction, amplification and sequencing individual barcodes and basics of genomics (the idea of HMW, DNA extraction and quantification) were covered in mixed lecture and hands-on activities.

The number of participants (15) was limited by the Safe space capacity and was restricted due to the safety situation in Kharkiv (several raid alerts were announced, but due to the venue of the workshop being a bomb shelter, the training did not interrupt). 

The training was very positively met: participants noted great value of hands-on workshops, in person participation and presentation of modern methods.

The training event took place at the Center for Interdisciplinary Research and Innovation. A total of 22 participants joined in the event, all of them coming from a wide array of academic institutes in Greece: Aristotle University (12), University of Thessaly (1), University of Patras (1), Athens Kapodistrian University (1), CERTH (3), ELGO-Dimitra (1), HCMR (2), and Agricultural University of Athens (1). Participants were grouped into five groups with equally represented research backgrounds. Two participants brought their own samples, specifically exoparasitic arthropods and zooplankton samples.

The facilities included all the necessary equipment for training on the Barcoding (iBOL) and Genome (ERGA) components of the event (e.g., Qubit, gel electrophoresis, TapeStation, PCR). For the purposes of the training, an Oxford Nanopore MinION and associated consumables (flow cell, ligation kit, etc.) were purchased.

The work program for the 2-day training covered both aspects of the DNA barcoding (iBOL) and genomic (ERGA) communities, with a concluding session on Citizen Science and the development of the National Barcoding Node (Gr-BOL).

By Luisa Marins (European Reference Genome Atlas, ERGA)

One of the main goals of BGE is to support the new generation of researchers in biodiversity genomics by promoting training and knowledge sharing activities across Europe. Well-qualified trainers and training materials are essential assets to achieve this objective. Representatives of many BGE partners institutions met last week at the Aristotle University Thessaloniki, Greece, for an intensive workshop focused on developing a foundational training framework in biodiversity genomics.

Above: The workshop gathered representatives from 13 BGE partner institutions, offering an excellent opportunity for exchanging knowledge and integrating the barcoding and reference-genome streams of BGE.

The workshop also aimed at aligning activities and sharing knowledge between the reference-genomes and reference-barcodes communities of BGE. The sessions were distributed across 3 days of theoretical presentations and hands-on activities, covering major steps of the genomic workflow. This journey included everything from sample collection and DNA extraction in the “wet lab” to the final stages of data processing and uploading to computational databases.

Above: Any biodiversity genomics workflow starts with sampling – the “tent-like” Malaise traps are one of the most classical methods for collecting insects in the field. Participants had a chance to learn more about this and other sampling techniques. 

Above: The production of high-quality reference genomes generally requires fresh biological samples and specialised techniques for the extraction of “high molecular weight DNA”.

This very productive workshop was just the start of the broader BGE Joint Network Training task. The valuable insights and lessons learned in Thessaloniki are now being summarised into a handbook. These guidelines will serve as a basis for similar workshops to be organised by other BGE partner institutions across Europe throughout 2024. 

Above: Real-time DNA sequencing allows for the fast identification of species in a sample through DNA barcoding.

BGE’s effort to connect expertise from the DNA barcode and full genome strands in joint actions is focused on priority areas in biodiversity research, training, and conservation where current challenges are recognised and there are clear needs for well-aligned developments that will accelerate future work.  Stay tuned while we continue our endeavour to demonstrate the benefits of working together! 

Images: BGE