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Quentin Carradec

Coral holobionte species identification onboard Tara with MinION sequencing of multiple barcodes.

About Quentin Carradec

Quentin Carradec received his PhD in genetics and molecular biology from Pierre and Marie Curie University in Paris in 2014. He currently works on environmental genomics at Genoscope Institute, France in Patrick Wincker’s research group. His research focuses on the diversity and activity of marine planktonic species with the analysis of metagenomic and metatranscriptomic sequencing data in the framework of Tara expedition projects. He recently joined the Tara Pacific project to study resistance and adaptation of coral holobionte to environmental change.

Abstract

Molecular identification of species has long been possible via marker gene sequencing but requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in isolated places. Recent advances in sequencing technologies now permit rapid in situ sequencing, but development of specific protocol pipelines from DNA extraction to bio-informatic analyses is still required for efficient sample processing. Here, we chose a combination of 3 marker genes in order to identify 85 different coral colonies and their holobionte onboard the research vessel Tara. We developed specific protocols for DNA extraction and multi-PCR amplifications in order to process a large number of samples in a restricted space and time. We used Oxford Nanopore Technologies to sequence amplicons on a MinION device and developed bioinformatics pipelines to analyze nanopore reads on a simple laptop, obtaining results in less than 36 hours. Protocols and tools used in this work may be applicable at a larger scale for rapid environmental diagnosis of complex samples in the context of climate change.

Quentin Carradec

Quentin Carradec

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