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Conference Abstract
GAPeDNA: Assessing and mapping global species gaps in genetic databases for metabarcoding studies
expand article infoVirginie Marques‡, Tristan Milhau§, Camille Albouy|, Tony Dejean§, Stéphanie Manel‡, David Mouillot, Jean-Baptiste Juhel#
‡ CEFE, Montpellier, France
§ SPYGEN, Le Bourget du Lac, France
| IFREMER, Nantes, France
¶ Université de Montpellier, Montpellier, France
# TAAF, La Réunion, France
Corresponding author: Virginie Marques (virginie.marques01@gmail.com)
Received: 23 Feb 2021 | Published: 04 Mar 2021
© 2021 Virginie Marques, Tristan Milhau, Camille Albouy, Tony Dejean, Stéphanie Manel, David Mouillot, Jean-Baptiste Juhel
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.
Citation: Marques V, Milhau T, Albouy C, Dejean T, Manel S, Mouillot D, Juhel J-B (2021) GAPeDNA: Assessing and mapping global species gaps in genetic databases for metabarcoding studies. ARPHA Conference Abstracts 4: e64884. https://doi.org/10.3897/aca.4.e64884
 Open Access

Abstract

Environmental DNA metabarcoding has recently emerged as a non-invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. One of the major limitations currently impairing the large-scale application of DNA-based inventories, such as eDNA or bulk-sample analysis is the lack of species sequences available in public genetic databases. These gaps are still largely unknown spatially and taxonomically for most regions of the world, which can hinder targeted future sequencing efforts. We propose GAPeDNA, a user-friendly web-interface (Fig. 1) that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an initial application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of DNA-based inventories at larger scale. It is flexible and can be expanded to other taxa and primers upon data availability. Using our global fish case study, we show that gaps increase toward the tropics where species diversity and the number of threatened species were the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non-sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non-sequenced threatened species. As an open-acces, updatable and flexible tool, GAPeDNA can be used to evaluate the completeness of sequence reference libraries of various markers and for any taxonomic group.

Figure 1.  

Screenshot of the GAPeDNA web-application, developped with R shiny

Keywords

genetic markers, shiny, marine and freshwater fish, threatened species, IUCN, non-indigenous species, environmental DNA, reference database

Presenting author

Virginie Marques

Presented at

1st DNAQUA International Conference (March 9-11, 2021)

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