Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Abstract

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Fig. 1

Overview of genomic analysis strategies applied on Tara Pacific samples.

Fig. 2

Metagenomic library protocol guideline. The choice of the protocol is depending on the amount of the extracted DNA.

Fig. 3

Metatranscriptomic library protocol guideline. The choice of the protocol is depending on the amount of the extracted RNA (Dual-T for Dual transcriptomic and MetaT for metatranscriptomic).

Fig. 4

Assignment of the Metabarcoding samples against the negative controls database. Samples and negative controls (NC) sequences are clustered separately. NC clusters are assigned against SILVA databases. An OTU table is generated for each NC and a database from the NC clusters is generated. The sample clusters are assigned against these databases. OTU tables are generated and statistics are generated and visible through the NGL-BI web interface.

Fig. 5

NGL (Next Generation Laboratory Information Management System) complete scheme. NGL is composed of different specialized parts: NGL-P for project management, NGL-S for instrument management, NGL-SQ for experiments management, NGL-BI for bioinformatic pipelines management and NGL-SUB for sequencing files submission.