Deliverable 4.2 (D4.2): Protocol for building and organising reference collections of DNA sequences, EnvMetaGen project (Grant Agreement No 668981).

The overall goal of ERA Chair/EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasingly being used for biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics and ecosystem functional analysis. In this context, the work plan of EnvMetaGen includes one work package dedicated to the Deployment of an eDNA Lab (WP4), which involves the training of InBIO researchers and technicians for implementing best practice protocols for the analysis of eDNA (Task 4.2). These protocols are essential for key application areas and to the development of research projects in association with business partners and other stakeholders, and thus to the strengthening of InBIO triple-helix initiatives (InBIO-Industry-Government; WP5). This report provides an overview of the current state of the art for the development of best practice for building DNA reference collections of voucher specimens identified by specialised taxonomists, and how these practices are being implemented at InBIO. Building and organising reference collections of DNA sequences is an essential component of this task because eDNA studies require that DNA sequences recovered from the environment are compared to reference collections, which thus need to be developed following consistent and repeatable procedures. Such reference collections are likely to become a tool with significant relevance to the InBIO-Industry-Government triple-helix activities (WP5) by promoting the development of partnerships in all key areas: Monitoring of freshwater eDNA for species detection; Assessing natural pest control using faecal metagenomics; and Next-generation biomonitoring using DNA metabarcoding. Protocols described herein were developed in close connection and due to the accomplishment of the other WPs in the project, including: i) the recruitment of the ERA Chair team (WP2), ii) secondments researcher exchanges through collaborations with international networks (WP3), iii) the enhancement of the computational infrastructure at InBIO (WP4) and iv) participation and organization in workshops and conferences (WP6). Future directions in the improvement to enlarge the reference collection of DNA sequences of InBIO are identified. Together, Deliverables D4.2-D4.5 (this document; Egeter et al., 2018; Galhardo et al., 2018; Paupério et al., 2018) form a detailed account of the successful deployment of a fully functional eDNA lab under the EnvMetaGen project, and provide a valuable resource for eDNA practitioners in all spheres of the triple-helix model.