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