Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems
Supplementary Table 1. List of Tara Oceans samples sequenced with a metabarcoding (18S V9) approach and with a metagenomic approach, including identifiers for sequencing reads deposited in the DDBJ/ENA/GenBank Short Read Archives (SRA). [This Table is identical in version 2.] Supplementary Table 2....
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/311644 |
| Acceso en línea: | http://hdl.handle.net/10261/311644 |
| Access Level: | acceso abierto |
| Palabra clave: | Plankton biogeography Metagenomics Metabarcoding Microbial oceanography Biogeography and phylogeography Genomics Marine biology Microbial ecology Biological oceanography |
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| dc.title.none.fl_str_mv |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| title |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| spellingShingle |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems Richter, Daniel J. Plankton biogeography Metagenomics Metabarcoding Microbial oceanography Biogeography and phylogeography Genomics Marine biology Microbial ecology Biological oceanography |
| title_short |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| title_full |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| title_fullStr |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| title_full_unstemmed |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| title_sort |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems |
| dc.creator.none.fl_str_mv |
Richter, Daniel J. Watteaux, Romain Vannier, Thomas Leconte, Jade Frémont, Paul Reygondeau, Gabriel Maillet, Nicolas Henry, Nicolas Benoit, Gaëtan da Silva, Ophélie Delmont, Tom O. Fernández-Guerra, Antonio Suweis, Samir Narci, Romain Berney, Cedric Eveillard, Damien Gavory, Frederick Guidi, Lionel Labadie, Karine Mahieu, Eric Poulain, Julie Romac, Sarah Roux, Simon Dimier, Céline Kandels‐Lewis, Stefanie Picheral, Marc Searson, Sarah Oceans, Tara Pesant, Stéphane Aury, Jean‐Marc Brum, Jennifer R. Lemaitre, Claire Pelletier, Eric Bork, Peer Sunagawa, Shinichi Lombard, Fabien Karp-Boss, Lee Bowler, Chris Sullivan, Matthew B. Karsenti, Eric Mariadassou, Mahendra Probert, Ian Peterlongo, Pierre Wincker, Patrick Vargas, Colomban de Ribera d’Alcalà, Maurizio Iudicone, Daniele Jaillon, Olivier Tara Oceans Coordinators |
| author |
Richter, Daniel J. |
| author_facet |
Richter, Daniel J. Watteaux, Romain Vannier, Thomas Leconte, Jade Frémont, Paul Reygondeau, Gabriel Maillet, Nicolas Henry, Nicolas Benoit, Gaëtan da Silva, Ophélie Delmont, Tom O. Fernández-Guerra, Antonio Suweis, Samir Narci, Romain Berney, Cedric Eveillard, Damien Gavory, Frederick Guidi, Lionel Labadie, Karine Mahieu, Eric Poulain, Julie Romac, Sarah Roux, Simon Dimier, Céline Kandels‐Lewis, Stefanie Picheral, Marc Searson, Sarah Oceans, Tara Pesant, Stéphane Aury, Jean‐Marc Brum, Jennifer R. Lemaitre, Claire Pelletier, Eric Bork, Peer Sunagawa, Shinichi Lombard, Fabien Karp-Boss, Lee Bowler, Chris Sullivan, Matthew B. Karsenti, Eric Mariadassou, Mahendra Probert, Ian Peterlongo, Pierre Wincker, Patrick Vargas, Colomban de Ribera d’Alcalà, Maurizio Iudicone, Daniele Jaillon, Olivier Tara Oceans Coordinators |
| author_role |
author |
| author2 |
Watteaux, Romain Vannier, Thomas Leconte, Jade Frémont, Paul Reygondeau, Gabriel Maillet, Nicolas Henry, Nicolas Benoit, Gaëtan da Silva, Ophélie Delmont, Tom O. Fernández-Guerra, Antonio Suweis, Samir Narci, Romain Berney, Cedric Eveillard, Damien Gavory, Frederick Guidi, Lionel Labadie, Karine Mahieu, Eric Poulain, Julie Romac, Sarah Roux, Simon Dimier, Céline Kandels‐Lewis, Stefanie Picheral, Marc Searson, Sarah Oceans, Tara Pesant, Stéphane Aury, Jean‐Marc Brum, Jennifer R. Lemaitre, Claire Pelletier, Eric Bork, Peer Sunagawa, Shinichi Lombard, Fabien Karp-Boss, Lee Bowler, Chris Sullivan, Matthew B. Karsenti, Eric Mariadassou, Mahendra Probert, Ian Peterlongo, Pierre Wincker, Patrick Vargas, Colomban de Ribera d’Alcalà, Maurizio Iudicone, Daniele Jaillon, Olivier Tara Oceans Coordinators |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
Plankton biogeography Metagenomics Metabarcoding Microbial oceanography Biogeography and phylogeography Genomics Marine biology Microbial ecology Biological oceanography |
| topic |
Plankton biogeography Metagenomics Metabarcoding Microbial oceanography Biogeography and phylogeography Genomics Marine biology Microbial ecology Biological oceanography |
| description |
Supplementary Table 1. List of Tara Oceans samples sequenced with a metabarcoding (18S V9) approach and with a metagenomic approach, including identifiers for sequencing reads deposited in the DDBJ/ENA/GenBank Short Read Archives (SRA). [This Table is identical in version 2.] Supplementary Table 2. Table of environmental parameters for each sample. [This Table is identical in version 2.] Supplementary Table 3. Matrix of metagenomic dissimilarity for the 0-0.22 μm size fraction. [This Table is identical in version 2.] Supplementary Table 4. Matrix of metagenomic dissimilarity for the 0.22-1.6/3 μm size fraction. [This Table is identical in version 2.] Supplementary Table 5. Matrix of metagenomic dissimilarity for the 0.8-5 μm size fraction. [This Table is identical in version 2.] Supplementary Table 6. Matrix of metagenomic dissimilarity for the 5-20 μm size fraction. [This Table is identical in version 2.] Supplementary Table 7. Matrix of metagenomic dissimilarity for the 20-180 μm size fraction. [This Table is identical in version 2.] Supplementary Table 8. Matrix of metagenomic dissimilarity for the 180-2000 μm size fraction. [This Table is identical in version 2.] Supplementary Table 9. Matrix of OTU dissimilarity for the 0-0.22 μm size fraction. [This Table is identical in version 2.] Supplementary Table 10. Matrix of OTU dissimilarity for the 0.22-1.6/3 μm size fraction. [This Table is identical in version 2.] Supplementary Table 11. Matrix of OTU dissimilarity for the 0.8-5 μm size fraction. [This Table is identical in version 2.] Supplementary Table 12. Matrix of OTU dissimilarity for the 5-20 μm size fraction. [This Table is identical in version 2.] Supplementary Table 13. Matrix of OTU dissimilarity for the 20-180 μm size fraction. [This Table is identical in version 2.] Supplementary Table 14. Matrix of OTU dissimilarity for the 180-2000 μm size fraction. [This Table is identical in version 2.] Supplementary Table 15. Matrix of minimum travel time, in years. [This Table is identical in version 2.] Supplementary Table 16. Matrix of minimum geographic distance (without traversing land), in kilometers. [This Table is identical in version 2.] Supplementary Table 17. Matrix of imaging-based dissimilarity. [This Table is identical in version 2.] Supplementary Table 18. Matrix of metagenome-assembled genome (MAG)-based dissimilarity for the 20-180 μm size fraction. [The filename of this Table was modified from version 2. The contents of the Table are identical.] Supplementary Table 19. The cophenetic correlation coefficient for different methods of clustering metagenomic dissimilarity. [This Table is identical in version 2.] Supplementary Table 20. Baker's Gamma index comparing clustering results within size fractions. [This Table is identical in version 2.] Supplementary Table 21. Rand Index for K-means and spectral clustering, and multivariate ANOVA calculated by the adonis function. [This Table is identical in version 2.] Dataset 1. Reference database (in FASTA format) used to perform taxonomic assignment of metabarcodes. The header line of each reference V9 rDNA barcode (with a > sign) contains a unique identifier derived from GenBank accession number, followed by the taxonomic path associated to the reference barcode. [This Dataset is identical in version 2.] Dataset 2. V9 rDNA abundance at the metabarcode level. md5sum = unique identifier; totab = total abundance across all samples; cid = identifier of the OTU to which the barcode belongs (see Dataset 3); pid = best percentage identity to a barcode in Dataset 1; refs = identifier(s) of the best matching barcode(s) in Dataset 1; lineage = taxononmic lineage of the best match in Dataset 1; taxogroup = high-level taxonomic grouping of the best match in Dataset 1; sequence = V9 rDNA sequence; TV9_XXX = barcode abundance by sample (see Supplementary Table 1 for sample identifiers). [This Dataset is identical in version 2.] Dataset 3. V9 rDNA abundance at the OTU (operational taxonomic unit) level. cid = identifier of the OTU; md5sum = unique identifier of the most abundant barcode in the OTU; pid, refs, lineage, taxogroup, sequence = defined as in Dataset 2; rtotab = total abundance of the most abundant barcode in the OTU; ctotab = total abundance of all barcodes in the OTU; TV9_XXX = abundance by sample of all barcodes in the OTU (see Supplementary Table 1 for sample identifiers). [This Dataset is identical in version 2.] Dataset 4. Relative abundances of metagenome-assembled genomes (MAGs) in metagenomic samples from the 20-180 μm size fraction. [This Dataset is new in version 3.] |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2021 2023 2023 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/dataset http://purl.org/coar/resource_type/c_ddb1 |
| format |
dataset |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/311644 |
| url |
http://hdl.handle.net/10261/311644 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Richter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; Frémont, Paul; Reygondeau, Gabriel; Maillet, Nicolas; Henry, Nicolas; Benoit, Gaëtan; da Silva, Ophélie; Delmont, Tom O.; Fernández-Guerra, Antonio; Suweis, Samir; Narci, Romain; Berney, Cedric; Eveillard, Damien; Gavory, Frederick; Guidi, Lionel; Labadie, Karine; Mahieu, Eric; Poulain, Julie; Romac, Sarah; Roux, Simon; Dimier, Céline; Kandels‐Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Oceans, Tara; Pesant, Stéphane; Aury, Jean‐Marc; Brum, Jennifer R.; Lemaitre, Claire; Pelletier, Eric; Bork, Peer; Sunagawa, Shinichi; Lombard, Fabien; Karp-Boss, Lee; Bowler, Chris; Sullivan, Matthew B.; Karsenti, Eric; Mariadassou, Mahendra; Probert, Ian; Peterlongo, Pierre; Wincker, Patrick; Vargas, Colomban de; Ribera d’Alcalà, Maurizio; Iudicone, Daniele; Jaillon, Olivier; Tara Oceans Coordinators. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. https://doi.org/10.7554/eLife.78129 . http://hdl.handle.net/10261/304394 https://doi.org/10.6084/m9.figshare.11303177.v3 Sí |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Figshare |
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Figshare |
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reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
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Consejo Superior de Investigaciones Científicas (CSIC) |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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1869412326566789120 |
| spelling |
Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systemsRichter, Daniel J.Watteaux, RomainVannier, ThomasLeconte, JadeFrémont, PaulReygondeau, GabrielMaillet, NicolasHenry, NicolasBenoit, Gaëtanda Silva, OphélieDelmont, Tom O.Fernández-Guerra, AntonioSuweis, SamirNarci, RomainBerney, CedricEveillard, DamienGavory, FrederickGuidi, LionelLabadie, KarineMahieu, EricPoulain, JulieRomac, SarahRoux, SimonDimier, CélineKandels‐Lewis, StefaniePicheral, MarcSearson, SarahOceans, TaraPesant, StéphaneAury, Jean‐MarcBrum, Jennifer R.Lemaitre, ClairePelletier, EricBork, PeerSunagawa, ShinichiLombard, FabienKarp-Boss, LeeBowler, ChrisSullivan, Matthew B.Karsenti, EricMariadassou, MahendraProbert, IanPeterlongo, PierreWincker, PatrickVargas, Colomban deRibera d’Alcalà, MaurizioIudicone, DanieleJaillon, OlivierTara Oceans CoordinatorsPlankton biogeographyMetagenomicsMetabarcodingMicrobial oceanographyBiogeography and phylogeographyGenomicsMarine biologyMicrobial ecologyBiological oceanographySupplementary Table 1. List of Tara Oceans samples sequenced with a metabarcoding (18S V9) approach and with a metagenomic approach, including identifiers for sequencing reads deposited in the DDBJ/ENA/GenBank Short Read Archives (SRA). [This Table is identical in version 2.] Supplementary Table 2. Table of environmental parameters for each sample. [This Table is identical in version 2.] Supplementary Table 3. Matrix of metagenomic dissimilarity for the 0-0.22 μm size fraction. [This Table is identical in version 2.] Supplementary Table 4. Matrix of metagenomic dissimilarity for the 0.22-1.6/3 μm size fraction. [This Table is identical in version 2.] Supplementary Table 5. Matrix of metagenomic dissimilarity for the 0.8-5 μm size fraction. [This Table is identical in version 2.] Supplementary Table 6. Matrix of metagenomic dissimilarity for the 5-20 μm size fraction. [This Table is identical in version 2.] Supplementary Table 7. Matrix of metagenomic dissimilarity for the 20-180 μm size fraction. [This Table is identical in version 2.] Supplementary Table 8. Matrix of metagenomic dissimilarity for the 180-2000 μm size fraction. [This Table is identical in version 2.] Supplementary Table 9. Matrix of OTU dissimilarity for the 0-0.22 μm size fraction. [This Table is identical in version 2.] Supplementary Table 10. Matrix of OTU dissimilarity for the 0.22-1.6/3 μm size fraction. [This Table is identical in version 2.] Supplementary Table 11. Matrix of OTU dissimilarity for the 0.8-5 μm size fraction. [This Table is identical in version 2.] Supplementary Table 12. Matrix of OTU dissimilarity for the 5-20 μm size fraction. [This Table is identical in version 2.] Supplementary Table 13. Matrix of OTU dissimilarity for the 20-180 μm size fraction. [This Table is identical in version 2.] Supplementary Table 14. Matrix of OTU dissimilarity for the 180-2000 μm size fraction. [This Table is identical in version 2.] Supplementary Table 15. Matrix of minimum travel time, in years. [This Table is identical in version 2.] Supplementary Table 16. Matrix of minimum geographic distance (without traversing land), in kilometers. [This Table is identical in version 2.] Supplementary Table 17. Matrix of imaging-based dissimilarity. [This Table is identical in version 2.] Supplementary Table 18. Matrix of metagenome-assembled genome (MAG)-based dissimilarity for the 20-180 μm size fraction. [The filename of this Table was modified from version 2. The contents of the Table are identical.] Supplementary Table 19. The cophenetic correlation coefficient for different methods of clustering metagenomic dissimilarity. [This Table is identical in version 2.] Supplementary Table 20. Baker's Gamma index comparing clustering results within size fractions. [This Table is identical in version 2.] Supplementary Table 21. Rand Index for K-means and spectral clustering, and multivariate ANOVA calculated by the adonis function. [This Table is identical in version 2.] Dataset 1. Reference database (in FASTA format) used to perform taxonomic assignment of metabarcodes. The header line of each reference V9 rDNA barcode (with a > sign) contains a unique identifier derived from GenBank accession number, followed by the taxonomic path associated to the reference barcode. [This Dataset is identical in version 2.] Dataset 2. V9 rDNA abundance at the metabarcode level. md5sum = unique identifier; totab = total abundance across all samples; cid = identifier of the OTU to which the barcode belongs (see Dataset 3); pid = best percentage identity to a barcode in Dataset 1; refs = identifier(s) of the best matching barcode(s) in Dataset 1; lineage = taxononmic lineage of the best match in Dataset 1; taxogroup = high-level taxonomic grouping of the best match in Dataset 1; sequence = V9 rDNA sequence; TV9_XXX = barcode abundance by sample (see Supplementary Table 1 for sample identifiers). [This Dataset is identical in version 2.] Dataset 3. V9 rDNA abundance at the OTU (operational taxonomic unit) level. cid = identifier of the OTU; md5sum = unique identifier of the most abundant barcode in the OTU; pid, refs, lineage, taxogroup, sequence = defined as in Dataset 2; rtotab = total abundance of the most abundant barcode in the OTU; ctotab = total abundance of all barcodes in the OTU; TV9_XXX = abundance by sample of all barcodes in the OTU (see Supplementary Table 1 for sample identifiers). [This Dataset is identical in version 2.] Dataset 4. Relative abundances of metagenome-assembled genomes (MAGs) in metagenomic samples from the 20-180 μm size fraction. [This Dataset is new in version 3.]Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.Peer reviewedFigshareConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232021info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1http://hdl.handle.net/10261/311644reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésRichter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; Frémont, Paul; Reygondeau, Gabriel; Maillet, Nicolas; Henry, Nicolas; Benoit, Gaëtan; da Silva, Ophélie; Delmont, Tom O.; Fernández-Guerra, Antonio; Suweis, Samir; Narci, Romain; Berney, Cedric; Eveillard, Damien; Gavory, Frederick; Guidi, Lionel; Labadie, Karine; Mahieu, Eric; Poulain, Julie; Romac, Sarah; Roux, Simon; Dimier, Céline; Kandels‐Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Oceans, Tara; Pesant, Stéphane; Aury, Jean‐Marc; Brum, Jennifer R.; Lemaitre, Claire; Pelletier, Eric; Bork, Peer; Sunagawa, Shinichi; Lombard, Fabien; Karp-Boss, Lee; Bowler, Chris; Sullivan, Matthew B.; Karsenti, Eric; Mariadassou, Mahendra; Probert, Ian; Peterlongo, Pierre; Wincker, Patrick; Vargas, Colomban de; Ribera d’Alcalà, Maurizio; Iudicone, Daniele; Jaillon, Olivier; Tara Oceans Coordinators. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. https://doi.org/10.7554/eLife.78129 . http://hdl.handle.net/10261/304394https://doi.org/10.6084/m9.figshare.11303177.v3Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3116442026-05-22T06:33:51Z |
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15,811543 |