The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms.
biogeography
diversity
marine ecology
metabarcoding
metadata
plankton
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
May 2021
May 2021
Historique:
revised:
09
12
2020
received:
21
09
2020
accepted:
05
01
2021
pubmed:
13
1
2021
medline:
20
8
2021
entrez:
12
1
2021
Statut:
ppublish
Résumé
The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA
Identifiants
pubmed: 33434383
doi: 10.1111/1755-0998.13322
doi:
Substances chimiques
RNA, Ribosomal, 18S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1347-1358Subventions
Organisme : French Government 'Investissements d'Avenir' programmes OCEANOMICS
ID : ANR-11-BTBR-0008
Organisme : FRANCE GENOMIQUE
ID : ANR-10-INBS-09-08
Organisme : Institut Français de Bioinformatique (IFB)
ID : ANR-11-INBS-0013
Organisme : MEMO LIFE
ID : ANR-10-LABX-54
Organisme : PSL* Research University
ID : ANR-11-IDEX-0001-02
Organisme : ANR SeqDigger
ID : ANR-19-CE45-0008
Informations de copyright
© 2021 John Wiley & Sons Ltd.
Références
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581-583. https://doi.org/10.1038/nmeth.3869
de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahe, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., … Velayoudon, D. (2015). Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science (New York, N.Y.), 348(6237), 1261605. https://doi.org/10.1126/science.1261605
Decelle, J., Carradec, Q., Pochon, X., Henry, N., Romac, S., Mahé, F., Dunthorn, M., Kourlaiev, A., Voolstra, C. R., Wincker, P., & de Vargas, C. (2018). Worldwide occurrence and activity of the reef-building coral symbiont symbiodinium in the open ocean. Current Biology: CB, 28(22), 3625-3633.e3. https://doi.org/10.1016/j.cub.2018.09.024
Dhariwal, A., Chong, J., Habib, S., King, I. L., Agellon, L. B., & Xia, J. (2017). MicrobiomeAnalyst : A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Research, 45(W1), W180-W188. https://doi.org/10.1093/nar/gkx295
Duarte, C. M. (2015). Seafaring in the 21St Century : The Malaspina 2010 circumnavigation expedition. Limnology and Oceanography Bulletin, 24(1), 11-14. https://doi.org/10.1002/lob.10008
Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008). The microbial engines that drive Earth’s biogeochemical cycles. Science (New York, N.Y.), 320(5879), 1034-1039. https://doi.org/10.1126/science.1153213
Fernández-Castro, B., Mouriño-Carballido, B., Benítez-Barrios, V. M., Chouciño, P., Fraile-Nuez, E., Graña, R., Piedeleu, M., & Rodríguez-Santana, A. (2014). Microstructure turbulence and diffusivity parameterization in the tropical and subtropical Atlantic, Pacific and Indian Oceans during the Malaspina 2010 expedition. Deep Sea Research Part I: Oceanographic Research Papers, 94, 15-30. https://doi.org/10.1016/j.dsr.2014.08.006
Field, C. B., Behrenfeld, M. J., Randerson, J. T., & Falkowski, P. (1998). Primary production of the biosphere: Integrating terrestrial and oceanic components. Science, 281(5374), 237-240. https://doi.org/10.1126/science.281.5374.237
Flegontova, O., Flegontov, P., Malviya, S., Audic, S., Wincker, P., de Vargas, C., Bowler, C., Lukeš, J., & Horák, A. (2016). Extreme diversity of diplonemid eukaryotes in the ocean. Current Biology, 26(22), 3060-3065. https://doi.org/10.1016/j.cub.2016.09.031
Geisen, S., Vaulot, D., Mahé, F., Lara, E., de Vargas, C., & Bass, D. (2019). A user guide to environmental protistology: Primers, metabarcoding, sequencing, and analyses. BioRxiv, 850610, https://doi.org/10.1101/850610
Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J. R., Coelho, L. P., Espinoza, J. C. I., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., … Gorsky, G. (2016). Plankton networks driving carbon export in the oligotrophic ocean. Nature, 532(7600), 465-470. https://doi.org/10.1038/nature16942
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., … Christen, R. (2013). The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(Database issue), D597-D604. https://doi.org/10.1093/nar/gks1160
Ibarbalz, F. M., Henry, N., Brandão, M. C., Martini, S., Busseni, G., Byrne, H., Coelho, L. P., Endo, H., Gasol, J. M., Gregory, A. C., Mahé, F., Rigonato, J., Royo-Llonch, M., Salazar, G., Sanz-Sáez, I., Scalco, E., Soviadan, D., Zayed, A. A., Zingone, A., … Wincker, P. (2019). Global trends in marine plankton diversity across kingdoms of life. Cell, 179(5), 1084-1097.e21. https://doi.org/10.1016/j.cell.2019.10.008
Karsenti, E., Acinas, S. G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.-M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., … Tara Oceans Consortium. (2011). A holistic approach to marine eco-systems biology. PLoS Biology, 9(10), e1001177. https://doi.org/10.1371/journal.pbio.1001177
Kopf, A., Bicak, M., Kottmann, R., Schnetzer, J., Kostadinov, I., Lehmann, K., Fernandez-Guerra, A., Jeanthon, C., Rahav, E., Ullrich, M., Wichels, A., Gerdts, G., Polymenakou, P., Kotoulas, G., Siam, R., Abdallah, R. Z., Sonnenschein, E. C., Cariou, T., O’Gara, F., … Glöckner, F. O. (2015). The ocean sampling day consortium. GigaScience, 4, 27. https://doi.org/10.1186/s13742-015-0066-5
Logares, R., Deutschmann, I. M., Junger, P. C., Giner, C. R., Krabberød, A. K., Schmidt, T. S. B., Rubinat-Ripoll, L., Mestre, M., Salazar, G., Ruiz-González, C., Sebastián, M., de Vargas, C., Acinas, S. G., Duarte, C. M., Gasol, J. M., & Massana, R. (2020). Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome, 8(1), 55. https://doi.org/10.1186/s40168-020-00827-8
Logares, R., Sunagawa, S., Salazar, G., Cornejo-Castillo, F. M., Ferrera, I., Sarmento, H., Hingamp, P., Ogata, H., de Vargas, C., Lima-Mendez, G., Raes, J., Poulain, J., Jaillon, O., Wincker, P., Kandels-Lewis, S., Karsenti, E., Bork, P., & Acinas, S. G. (2014). Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology, 16(9), 2659-2671. https://doi.org/10.1111/1462-2920.12250
Lopes dos Santos, A., Gourvil, P., Tragin, M., Noël, M.-H., Decelle, J., Romac, S., & Vaulot, D. (2017). Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. The ISME Journal, 11(2), 512-528. https://doi.org/10.1038/ismej.2016.120
Mahé, F., Rognes, T., Quince, C., de Vargas, C., & Dunthorn, M. (2014). Swarm: Robust and fast clustering method for amplicon-based studies. PeerJ, 2, e593. https://doi.org/10.7717/peerj.593
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1), 10-12. https://doi.org/10.14806/ej.17.1.200
Oksanen, J., Blanchet, F. G., & Friendly, M. (2019). Vegan.pdf. Package « Vegan ». Retrieved from https://cran.ism.ac.jp/web/packages/vegan/vegan.pdf
Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12(1), 385. https://doi.org/10.1186/1471-2105-12-385
Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., Dimier, C., & Searson, S. (2015). Open science resources for the discovery and analysis of Tara Oceans data. Scientific Data, (2), 150023. https://doi.org/10.1038/sdata.2015.23
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590-D596. https://doi.org/10.1093/nar/gks1219
Richter, D. J., Watteaux, R., Vannier, T., Leconte, J., Frémont, P., Reygondeau, G., Maillet, N., Henry, N., Benoit, G., Fernàndez-Guerra, A., Suweis, S., Narci, R., Berney, C., Eveillard, D., Gavory, F., Guidi, L., Labadie, K., Mahieu, E., Poulain, J., … Coordinators, T. O. (2019). Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. BioRxiv, 867739, https://doi.org/10.1101/867739
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584. https://doi.org/10.7717/peerj.2584
Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J. M., Remington, K., Beeson, K., Tran, B., Smith, H., Baden-Tillson, H., Stewart, C., Thorpe, J., Freeman, J., Andrews-Pfannkoch, C., Venter, J. E., … Venter, J. C. (2007). The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biology, 5(3), e77. https://doi.org/10.1371/journal.pbio.0050077
Salazar, G., Cornejo-Castillo, F. M., Borrull, E., Díez-Vives, C., Lara, E., Vaqué, D., Arrieta, J. M., Duarte, C. M., Gasol, J. M., & Acinas, S. G. (2015). Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Molecular Ecology, 24(22), 5692-5706. https://doi.org/10.1111/mec.13419
Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.-J., Cuenca, M., Field, C. M., Coelho, L. P., Cruaud, C., Engelen, S., Gregory, A. C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A. A., … Wincker, P. (2019). Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell, 179(5), 1068-1083.e21. https://doi.org/10.1016/j.cell.2019.10.014
Tangherlini, M., Miralto, M., Colantuono, C., Sangiovanni, M., Dell’ Anno, A., Corinaldesi, C., Danovaro, R., & Chiusano, M. L. (2018). GLOSSary: The GLobal Ocean 16S subunit web accessible resource. BMC Bioinformatics, 19(Suppl 15), 443. https://doi.org/10.1186/s12859-018-2423-8
Villar, E., Vannier, T., Vernette, C., Lescot, M., Cuenca, M., Alexandre, A., Bachelerie, P., Rosnet, T., Pelletier, E., Sunagawa, S., & Hingamp, P. (2018). The Ocean Gene Atlas: Exploring the biogeography of plankton genes online. Nucleic Acids Research, 46(W1), W289-W295. https://doi.org/10.1093/nar/gky376