A global ocean atlas of eukaryotic genes

Quentin Carradec, Eric Pelletier, Corinne Da Silva, Adriana Alberti, Yoann Seeleuthner, Romain Blanc-Mathieu, Gipsi Lima-Mendez, Fabio Rocha, Leila Tirichine, Karine Labadie, Amos Kirilovsky, Alexis Bertrand (+26 others)
2018 Nature Communications  
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
more » ... . 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. | www.nature.com/naturecommunications * * * Fig. 6 Ratios of differential gene abundance and relative expression of ferredoxin vs. flavodoxin in the five major photosynthetic groups. a Representation of the relative abundance (left) and expression (right) of the two genes identified in surface samples for Chlorophyta, Pelagophyceae, Haptophyceae (from 0.8 to 5 µm filters), Bacillariophyta and Dinophyceae (from the 5 to 20 µm filters). The circle colors, from red to blue, represent the relative expression of one gene compared to the other, with the color code given in the top diagram. The sum of the expression levels of the two genes affiliated to each taxonomic group is represented by the circle diameter as a percentage of the total expression of these genes. b Distribution of the relative abundance (left) or expression (right) of ferredoxin in low iron stations (<0.02 µmol m −3 , 15 stations, dark gray) or iron rich stations (>0.2 µmol m −3 , 31 stations, light gray) according to a model of iron concentration in the oceans (Supplementary Data 5). Significant differences of expression between low and rich iron stations are indicated with red stars (non-parametric wilcoxon rank-sum test, p < 10 -3 ) c Correlations between the relative metagenome (MetaG) abundance and metatranscriptome (MetaT) expression of ferredoxin in SRF and DCM samples, expressed as a percentage of the total value of ferredoxin + flavodoxin. Pearson correlation coefficients (r) and their statistical significance (p) are indicated in each graph. Ferredoxins and flavodoxins were identified using the Pfams PF00111 and PF00258, respectively NATURE COMMUNICATIONS |
doi:10.1038/s41467-017-02342-1 pmid:29371626 pmcid:PMC5785536 fatcat:32flzpeqwvf3dd54mgpavfvlfa