The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

• Published in: Nucleic Acids Research
• Main Authors: Vernette, Caroline, Lecubin, Julien, Sanchez, Pablo, Tara Oceans Coordinators, Sunagawa, Shinichi, Delmont, Tom O, Acinas, Silvia G, Pelletier, Eric, Hingamp, Pascal, Lescot, Magali
• Other Authors: Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110 , Marseille , France, Research Federation for the study of Global Ocean systems ecology and evolution , FR2022/ Tara Oceans-GOSEE, Paris , France, SIP , OSU PYTHEAS, Marseille , France, Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM) , CSIC, Barcelona , Spain, Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics , ETH Zurich, Zurich , Switzerland, Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob , CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91057 Evry , France
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Oxford University Press (OUP) 2022
• Subjects: Arctic
• Online Access: http://hdl.handle.net/10754/680011; https://doi.org/10.1093/nar/gkac420

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. 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 ...