A recap of the BGE workshop at the Berlin Center for Genomics in Biodiversity Research

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