An Overview of the French eDNA Data Landscape: Focus on a national technical repository of reference genetic sequences

Abstract

Environmental DNA (eDNA) data enables biodiversity to be monitored at unprecedented resolution and scale. There is great potential in combining knowledge from traditional and innovative methods such as eDNA for biodiversity assessment. eDNA use cases are increasing in aquatic and marine environments, and studies on soils have been developed in recent years. PatriNat*1 (under the guardianship of the French Biodiversity Office (OFB), National Museum of Natural History (MNHN), National Center for Scientific Research (CNRS), and Research Institute for Development (IRD)) is a French data and expertise center working with environmental and research stakeholders to develop data exchanges at all levels. We discuss what eDNA data is (Fig. 1), the different types of data, and the importance of their storage and accessibility. As the amount of eDNA data increases, public agencies need to propose FAIR (Findable, Accessible, Interoperable, Reusable) tools and methods to facilitate their use and foster the development of relevant scientific expertise. We give an overview of the French eDNA data landscape and links with existing standards SINP*2 (National Heritage Inventory Information System), Darwin Core*3(Wieczorek et al. 2012) and workflows (Fig. 2). A priority of eDNA data is to have reliable reference bases and FAIR metadata. PatriNat's new tool will provide access to expertly validated genetic sequence data on species present in France, and is urgently needed for research but also knowledge, monitoring, public policies, and potential law enforcement purposes. We therefore present this technical database built in conjunction with, among other initiatives, DiSSCo*4, iBOL*5 and TaxRef*6 (Gargominy et al. 2022). It will manage 3 data types: Intrinsic sequence data (marker, sequencing methods, etc.). Sequence management (organization, identifiers, URLs, etc.). Voucher data Intrinsic sequence data (marker, sequencing methods, etc.). Sequence management (organization, identifiers, URLs, etc.). Voucher data It will use the nomenclature of Chakrabarty et al. (2013) as well as: The Global Genome Biodiversity Network (GGBN) standard*7 (Droege et al. 2016) The Minimum information about any sequence (MIxS) standard (Yilmaz et al. 2011) The Biological Collection Data (ABCD) standard*8 (Holetschek et al. 2012) The Collections Descriptions terms*9 (Woodburn et al. 2021) The Global Genome Biodiversity Network (GGBN) standard*7 (Droege et al. 2016) The Minimum information about any sequence (MIxS) standard (Yilmaz et al. 2011) The Biological Collection Data (ABCD) standard*8 (Holetschek et al. 2012) The Collections Descriptions terms*9 (Woodburn et al. 2021) The DwC DNA extension*10 can be used for sharing parts of its contents to the Global Biodiversity Information Facility, but referencing sequences associated with specimens/vouchers will require other standards.