The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas

Biodiversity Information Science and Standards 7: e110488 doi: 10.3897/biss.7.110488 Conference Abstract The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas Maria Prager‡, Daniel Lundin§, Fredrik Ronquist|, Anders F. Andersson¶ ‡ Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University & Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden § Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden | Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden ¶ Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden Corresponding author: Maria Prager (), Anders F. Andersson (anders.andersson@scil ifelab.se) Received: 03 Aug 2023 | Published: 07 Aug 2023 Citation: Prager M, Lundin D, Ronquist F, Andersson AF (2023) The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas. Biodiversity Information Science and Standards 7: e110488. https://doi.org/10.3897/biss.7.110488 Abstract The Living Atlas platform functions as the national hub for integration of biodiversity data with environmental and contextual information in many countries, but it has had limited functionality for species occurrence data derived from DNA sequences. Meanwhile, molecular methods for species observation, such as metabarcoding of environmental DNA, are becoming increasingly important for documenting the diversity of life. To incorporate this rapidly growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface for DNA sequence-derived observations in the Living Atlas. We identified three key features that would enhance the utility of the atlas platform for species occurrence data derived from metabarcoding: 1) storage of the processed barcode sequences (ASVs) underlying such occurrences, along with the ability to locate them using sequence alignment search; 2) the option to search for data based on sequencing details, such as target genes and primers; and 3) the possibility to update the taxonomic annotation of observed ASVs as reference databases evolve. © Prager M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 2 Prager M et al In this presentation, we demonstrate how these features have been implemented in the ASV portal, which now operates as a module within the Swedish Biodiversity Data Infrastructure (SBDI). We provide a brief overview of the underlying architecture and its integration with the Living Atlas and Global Biodiversity Information Facility (GBIF) platforms, showcase the online functionality, and conclude by discussing challenges and future development plans. Keywords biodiversity informatics, species occurrence, Darwin Core standard, amplicon sequencing, metabarcoding, eDNA, BLAST Presenting author Maria Prager Presented at TDWG 2023 Acknowledgements We thank Martin Norling, Andreas Kusalananda Kähäri and Pontus Freyhult at the National Bioinformatics Infrastructure Sweden (NBIS) for advice and coding contributions, as well as SBDI colleagues Manash Shah, Anna Rosling and Jeanette Tångrot for useful feedback. Grant title Swedish Research Council: 2019-00242 Conflicts of interest The authors have declared that no competing interests exist.  (...truncated)