Next-generation sequencing of environmental barcodes-DNA.
February 9th, 2019. Pierre-Edouard GUERIN
One of the most promising genetic techniques for improving biodiversity assessments is the metabarcoding of environmental DNA. I did a state of the Art of available methods and developed serveral workflows to process and manage metabarcoding data from the Monaco Marine Scientific Exploration.
Overview: the necessity to assess marine biodiversity
Marine environments, both coastal and offshore, are being severely impacted by traditional and emerging human activities. This is translated into habitat losses, pollution and overexploitation which treats marine biodiversity. It compromises the sustainability of marine ecosystems and services. As a response to the environmental degradation, initiatives aims to protect marine ecosystems. Development of reliable marine biodiversity assessment methods is necessary. One of the most promising genetic techniques for improving biodiversity assessments is the metabarcoding of environmental DNA.
What is Metabarcoding
Indeed, all organisms shed cells containing DNA in their environment, as intra or extra-cellular material for up to a few days. The amplification and high-throughput eDNA sequencing followed by bioinformatic analyses produces a list of sequences with the ultimate goal to assess species diversity in a given site.
Assess marine biodiversity all over the world with metabarcoding
eDNA samples were collected by Monaco Scientific Exploration Yersin in Guadeloupe, Lengguru, Malpelo Fakarava and Mediteranean sea. Sequencing were performed by SPYGEN company and I was in charge of the bioinformatics processing of sequencing data. I did a state of the Art of available methods and developed serveral workflows to process metabarcoding data in order to assess marine biodiversity all over the world. Source codes are available as git repositories on the Montpellier server dedicated to eDNA analysis.