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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | W516-W526 |
| Journal | Nucleic acids research |
| Volume | 50 |
| Issue number | W1 |
| DOIs | |
| State | Published - Jun 10 2022 |
| Externally published | Yes |
Bibliographical note
KAUST Repository Item: Exported on 2022-09-14Acknowledgements: The web server is hosted by the OSU Pythéas cluster with the help of Cyrille Blanpain and SIP members. Adrien Malgoyre from SIP is thanked for the development of the OSU Pythéas gitlab. We are grateful to the Institut Français de Bioinformatique for providing help and computing resources. Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of Tara Oceans consortium members. We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research, and the French Government ‘Investissements d'Avenir’ programmes, FRANCE GENOMIQUE, MEMO LIFE and PSL* Research University. We also thank the support and commitment of agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST. The global sampling effort was enabled by countless scientists and crew who sampled aboard the Tara from 2009–2013, and we thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. We are also grateful to the countries who graciously granted sampling permissions. The authors declare that all data reported herein are fully and freely available from the date of publication, with no restrictions, and that all of the analyses, publications, and ownership of data are free from legal entanglement or restriction by the various nations whose waters were sampled by the Tara Oceans expedition.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.
ASJC Scopus subject areas
- Genetics
