A global ocean atlas of eukaryotic genes

By Q. Carradec, É. Pelletier, C. da Silva, A. Alberti, Yoann Seeleuthner, Romain Blanc-Mathieu, Gipsi Lima-Mendez, Fabio Rocha, L. Tirichine, K. Labadie and 28 more. 2018

329 citations recorded by the source corpus.

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry. Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles (2019, background): “Metagenomics can identify these genes in natural assemblages (Carradec et al. 2018), and reference genomes are then needed to assign the different versions of the same gene to a given eukaryotic species.”
Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale (2020, background): “Enhanced sequencing depth from newer next-generation, deep-sequencing platforms will also allow for the exploration of functional genes associated with environmental samples (Carradec et al., 2018), facilitating exciting new applications for connecting aspects of biostructure with measures of ecosys”