ArticleNucleic acids research2022
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 93 citations in OpenAlex.
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- Regulation of DMSP organosulfur cycling in ubiquitous Roseobacter marine bacteria.The EMBO journal · 2026Article
- Structural and functional insights into Uly1040, an ulvan lyase from polysaccharide lyase family 40.Applied and environmental microbiology · 2026Article
- Fructan utilization by members of marine Gammaproteobacteria involves SusC/D-like proteins.The ISME journal · 2026Article
- Phylogenetic support of pebS as a phage-exclusive auxiliary metabolic gene.FEMS microbiology letters · 2026Article
- Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.Nucleic acids research · 2026Article
- The Ratio of Silicon to Chitin in Diatom Cell Walls Influences Their Resilience to Environmental Stress.Research (Washington, D.C.) · 2026Article
- Metagenomics of the MAST-3 stramenopile,Microbial genomics · 2025Article
- Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.Nature communications · 2025Article
- Methionine synthesis and glycine betaine demethylation are intricately intertwined in cosmopolitan marine bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Widespread Presence of SPX and Its Potential Role as a Phosphorus Nutrient Regulator in Dinoflagellates.Microorganisms · 2025Article
- A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans.bioRxiv : the preprint server for biology · 2025Article
- Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea.Nature microbiology · 2025Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.