The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
International audience 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 ava...
Published in: | Nucleic Acids Research |
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Main Authors: | , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2022
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Subjects: | |
Online Access: | https://hal.science/hal-03696136 https://hal.science/hal-03696136/document https://hal.science/hal-03696136/file/gkac420.pdf https://doi.org/10.1093/nar/gkac420 |
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openpolar |
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Open Polar |
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Université d'Évry-Val-d'Essonne: HAL |
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ftunivevry |
language |
English |
topic |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere |
spellingShingle |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere Vernette, Caroline Lecubin, Julien Sánchez, Pablo Tara Oceans Coordinators, (team) Sunagawa, Shinichi Delmont, Tom O. Acinas, Silvia, G Pelletier, Eric Hingamp, Pascal Lescot, Magali The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
topic_facet |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere |
description |
International audience 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/. |
author2 |
Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Institut Pythéas (OSU PYTHEAS) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Institute of Marine Sciences / Institut de Ciències del Mar Barcelona (ICM) Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC) Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology Zürich (ETH Zürich) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Centre National de la Recherche Scientifique (CNRS) French Government ‘Investissements d’Avenir’ programmes OCEANOMICS ANR-11-BTBR-0008 ANR-19-CE45-0008,SeqDigger,Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale(2019) ANR-21-ESRE-0038,AO-EMBRC,Augmented Observatories of the National Marine Biological Resource Centre (EMBRC-France)(2021) |
format |
Article in Journal/Newspaper |
author |
Vernette, Caroline Lecubin, Julien Sánchez, Pablo Tara Oceans Coordinators, (team) Sunagawa, Shinichi Delmont, Tom O. Acinas, Silvia, G Pelletier, Eric Hingamp, Pascal Lescot, Magali |
author_facet |
Vernette, Caroline Lecubin, Julien Sánchez, Pablo Tara Oceans Coordinators, (team) Sunagawa, Shinichi Delmont, Tom O. Acinas, Silvia, G Pelletier, Eric Hingamp, Pascal Lescot, Magali |
author_sort |
Vernette, Caroline |
title |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_short |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_full |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_fullStr |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_full_unstemmed |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_sort |
ocean gene atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://hal.science/hal-03696136 https://hal.science/hal-03696136/document https://hal.science/hal-03696136/file/gkac420.pdf https://doi.org/10.1093/nar/gkac420 |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/hal-03696136 Nucleic Acids Research, 2022, 11, ⟨10.1093/nar/gkac420⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkac420 info:eu-repo/semantics/altIdentifier/pmid/35687095 hal-03696136 https://hal.science/hal-03696136 https://hal.science/hal-03696136/document https://hal.science/hal-03696136/file/gkac420.pdf doi:10.1093/nar/gkac420 PUBMED: 35687095 |
op_rights |
http://creativecommons.org/licenses/by-nc-sa/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1093/nar/gkac420 |
container_title |
Nucleic Acids Research |
container_volume |
50 |
container_issue |
W1 |
container_start_page |
W516 |
op_container_end_page |
W526 |
_version_ |
1799475642806304768 |
spelling |
ftunivevry:oai:HAL:hal-03696136v1 2024-05-19T07:36:31+00:00 The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes Vernette, Caroline Lecubin, Julien Sánchez, Pablo Tara Oceans Coordinators, (team) Sunagawa, Shinichi Delmont, Tom O. Acinas, Silvia, G Pelletier, Eric Hingamp, Pascal Lescot, Magali Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Institut Pythéas (OSU PYTHEAS) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Institute of Marine Sciences / Institut de Ciències del Mar Barcelona (ICM) Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC) Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology Zürich (ETH Zürich) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Centre National de la Recherche Scientifique (CNRS) French Government ‘Investissements d’Avenir’ programmes OCEANOMICS ANR-11-BTBR-0008 ANR-19-CE45-0008,SeqDigger,Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale(2019) ANR-21-ESRE-0038,AO-EMBRC,Augmented Observatories of the National Marine Biological Resource Centre (EMBRC-France)(2021) 2022-06-10 https://hal.science/hal-03696136 https://hal.science/hal-03696136/document https://hal.science/hal-03696136/file/gkac420.pdf https://doi.org/10.1093/nar/gkac420 en eng HAL CCSD Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkac420 info:eu-repo/semantics/altIdentifier/pmid/35687095 hal-03696136 https://hal.science/hal-03696136 https://hal.science/hal-03696136/document https://hal.science/hal-03696136/file/gkac420.pdf doi:10.1093/nar/gkac420 PUBMED: 35687095 http://creativecommons.org/licenses/by-nc-sa/ info:eu-repo/semantics/OpenAccess ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/hal-03696136 Nucleic Acids Research, 2022, 11, ⟨10.1093/nar/gkac420⟩ [SDE.BE]Environmental Sciences/Biodiversity and Ecology [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDU.OCEAN]Sciences of the Universe [physics]/Ocean Atmosphere info:eu-repo/semantics/article Journal articles 2022 ftunivevry https://doi.org/10.1093/nar/gkac420 2024-04-28T23:57:16Z International audience 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/. Article in Journal/Newspaper Arctic Université d'Évry-Val-d'Essonne: HAL Nucleic Acids Research 50 W1 W516 W526 |