SNIC
SUPR
SNIC SUPR
DNA metabrcoding for environmental monitoring
Dnr:

SNIC 2017/7-291

Type:

SNAC Small

Principal Investigator:

Rodrigo Esparza-Salas

Affiliation:

Naturhistoriska riksmuseet

Start Date:

2017-12-07

End Date:

2019-07-01

Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Webpage:

Allocation

Abstract

This is a long-term research and development project for the development of laboratory and data-analytical protocols for the use of NGS tools in environmental monitoring. Even though DNA metabarcoding has been gaining populatiry in recent years, there is a constant need for the development of protocols specific to non-model organisms. In addition to the development of new DNA-barcoding markers we modify existing protocols for the optimal use of resources and propose analytical pipelines for the eventual use in environmental monitoring as a routine. The data is generated by next generation sequencing using Illumina platforms (HiSeq/MiSeq). During 2018-2019 we continue to test protocols for the study of marine vertebrates and microplankton, and will develop new methods for the study of land arthropods and various endangered freshwater organisms This project has a substantial bioinformatic component, for which the use of cluster-computing resources is essential. We will use existing pipelines and adapt them to specific needs, aiming to develop in-house methods to be provided to researchers in different institutions, to facilitate the routine use of NGS in environmental monitoring. This project is carried out in close collaboration with the Swedish museum of Natural History (NRM), Stockholms University and the Swedish University of Agricultural Sciences (SLU).