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Tara Oceans: more news on plankton

A team from the Genomics Metabolics laboratory (Genoscope / CEA-Jacob) has developed a bioinformatics analysis method for environmental genomics data and applied it to those of plankton resulting from the Tara Oceans expeditions. The method reconstructs transcriptomes of eukaryotes from environmental sequencing data, thus enabling access to the genetic organization of these organisms, even those that have not yet been described, to study their functional potential. Also, with the method, interspecies associations can be identified across samples taken in different oceanic provinces. The novel approach is a door to the environmental context and biological functions of numerous species of ecological interest. The team's work was published in Genome Research.

Published on 26 June 2020

Over the past few years, environmental genomics has been developing as a way to access the global genetic content of the organisms present in a given ecosystem. To date, the large-scale use of the metagenomic and metatranscriptomic data obtained from environmental genomics has been gene-centric. Thus, it does not currently provide information on the biology of an environment's organisms or communities. The gene-centric focus also makes it difficult to identify large, complex genomes, like those of eukaryotic organisms.

However, the Genomic Analysis of Eukaryotes team of the Genomics Metabolics Laboratory (Genoscope) recently developed a method for crossing metagenomic and metatranscriptomic data to reconstruct eukaryote transcriptomes. Their approach involves grouping gene transcripts that have similar variations in abundancy across a collection of samples. The groups thus gathered, called Metagenomic-based transcriptomes (MGTs) enable the identification of organisms or their associations.

The team deployed their method on a collection of 37 million genes identified in 365 samples harvested as part of the Tara Oceans expeditions. The transcripts were grouped into several hundred MGTs, some of which corresponded to known organisms.

Notably, the team's analyses revealed the formerly unknown role of several eukaryote organisms, particularly in the Chloropicon genus, in the biosynthesis and catabolism of dimethylsulfoniopropionate, a key compound in the sulfur cycle, which in turn plays a role in ocean/atmosphere/climate interactions. Other MGTs corresponded to associations of organisms, including a symbiotic relationship between a nitrogen-fixing cyanobacteria and a single-cell alga, for which no genomics data were previously available.  

The grouping of transcripts into MGTs provides a unique resource for studies on the eukaryotic planktonic organisms and communities of the open ocean. 

The approach published by the Genomic Analysis of Eukaryotes team could provide access to the biological functions of numerous species of ecological interest, including many that are waiting to be discovered.

To learn more about the Tara Oceans project

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