DNA data validation workshop

Goals
To connect the taxonomic experts, who are collecting specimens voluntarily for DNA-barcoding programmes at Naturalis Biodiversity Center, and to share knowledge on biodiversity genomics which can be enriching in their taxonomic work.

Content
In this interactive workshop, we discussed how DNA barcoding works, how it is carried out, and how DNA barcodes can help with taxonomic research. After a brief explanation of how DNA barcodes are extracted from specimens, we looked at a number of important (online) tools and databases in which you can get started with the analysis once you have DNA data in your hands. The workshop was set up in such a way that in principle everyone could participate.

09.30 Walk-in with coffee
10.00 Start workshop
12.00 Lunch
12.45 Continued workshop with more complex analyses
16.30 End

Topics
How are DNA barcodes generated in the context of Project ARISE and other activities at Naturalis (e.g. BGE)? What are the targets for DNA analysis in plants and animals? What do generated DNA sequences (fasta files) look like and how can you edit these files? Checking the translatability of the generated DNA sequences into proteins. Comparing individual and batches of DNA sequences with entries in the largest global public databases (Genbank and BoldSystems). Interpreting one or more and different Nanopore generated DNA sequences from one specimen. Comparing one or more DNA sequences of specimens of the same species and of similar species (Clustal Omega analysis). How do you validate DNA sequences that do not yet have homologous entries in the databases? How do you assess DNA sequences that correspond to incorrect entries in the databases? How do you validate DNA sequences of species groups with little difference in the DNA targets? How do you validate DNA data of species that are included in global databases under different scientific names? What are Clades and how can the CO1 sequences of specimens from multiple Clades be validated? Interpreting literature references and geographical data for entries in global databases How do you apply literature references for the validations, consulted databases and online software? How do you create a phylogenetic tree with the DNA data of multiple species and how should you read it based on the DNA data?

Feedback summary
A total of 9 participants provided feedback on the workshop. Here’s an overview of their responses:

• Clarity of Workshop Content: 100% of respondents felt that the content of the workshop was clearly communicated beforehand.
  
• Difficulty Level: 89% found the difficulty level to be appropriate, while 11% considered it somewhat challenging.
• Pace of the Workshop: 100% of respondents were satisfied with the pace of both the workshop and the exercises.
• Workshop Facilities: 100% agreed that the facilities met their expectations.
• Key Takeaways: Participants shared a range of insights they gained from the workshop, including:
  “Start using the tools yourself.”
  “Clustering and translating to check an open reading frame was a real eye-opener.”
  “The genetic code of invertebrates and mitochondria differs.”
  “Don’t assume the computer knows everything, stay critical.”
  “I gained more knowledge about the possibilities.”
  “Applying the workshop to my own study materials.”
  “I now better understand and can evaluate the results from Arise.”
  “It’s quite manageable if you know how to navigate the various tools.”
  “Species identification via DNA barcoding doesn’t always provide a definitive answer.”
• Suggestions for Improvement: A few participants offered suggestions for future workshops:
  “Perhaps include more about sequencing techniques.”
  “Fewer exercises might allow more time to focus on different aspects of the challenges.”
  “Clearer information on the Barcoding NL days’ program. Last time I ended up in a workshop that wasn’t relevant for me due to unclear descriptions.”
  “Less exercises and more time to work through them.”
• Additional Comments: Participants had several additional remarks:
  “The instructors were very good.”
  “It would be great to receive sample data earlier.”
  “I’m very happy with what I’ve learned; it’s immediately applicable and highly useful. Many thanks for the organization and compliments on its setup. Unfortunately, I had to leave early but would have loved to learn more about creating phylogenetic trees. I’ll certainly complete the exercises I missed at home. If there’s ever a follow-up workshop, I’d love to attend.”
  “It was so well-organized, with a delicious lunch and clear explanations. I really appreciate how taxonomists are being supported in this way, and I’m excited to work with my own samples.”
  “Could we get Peter van Bragt’s email address? At the end, it was mentioned that we can reach out to him with questions.”

Header: Participants during the workshop. Photo by: Naturalis Biodiversity Center