Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories
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Voolstra, Christian R1
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Hume, Benjamin C C1
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Armstrong, Eric2
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Mitushasi, Guinther3
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Porro, Barbara4
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Oury, Nicolas5
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Agostini, Sylvain3
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Boissin, Emilie6
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Poulain, Julie7
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Carradec, Quentin7
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Paz-García, David A8
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Zoccola, Didier9
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Magalon, Hélène5
- Moulin, Clémentine10
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Bourdin, Guillaume11
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Iwankow, Guillaume6
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Romac, Sarah12
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Banaigs, Bernard6
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Boss, Emmanuel13
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Bowler, Chris14
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de Vargas, Colomban12
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Douville, Eric15
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Flores, Michel16
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Furla, Paola17
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Galand, Pierre E18
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Gilson, Eric19
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Lombard, Fabien20
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Pesant, Stéphane21
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Reynaud, Stéphanie9
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Sullivan, Matthew B22
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Sunagawa, Shinichi23
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Thomas, Olivier24
- Troublé, Romain10
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Vega Thurber, Rebecca25
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Wincker, Patrick7
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Planes, Serge6
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Allemand, Denis9
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Forcioli, Didier17
- 1. Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- 2. PSL Research University, EPHE, CNRS, Université de Perpignan, Perpignan, France
- 3. Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
- 4. Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France; Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France; LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco; French National Institute for Agriculture, Food, and Environment (INRAE), France
- 5. UMR 250/9220 ENTROPIE UR-IRD-CNRS-Ifremer-UNC, Laboratoire d'Excellence CORAIL, Université de la Réunion, St Denis de la Réunion, France
- 6. PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
- 7. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- 8. CONACyT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR). Laboratorio de Necton y Ecología de Arrecifes. La Paz, Baja California Sur, 23096, México
- 9. Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco
- 10. Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012 Paris, France
- 11. School of Marine Sciences, University of Maine, Orono, 04469, Maine, USA; Laboratoire d'Océanographie de Villefranche, UMR 7093, Sorbonne Université, CNRS, 06230 Villefranche sur mer, France
- 12. Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000 Paris, France
- 13. School of Marine Sciences, University of Maine, Orono, 04469, Maine, USA
- 14. Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000 Paris, France
- 15. Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
- 16. Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100 Rehovot, Israel
- 17. Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France; Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France; LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco
- 18. Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, UMR 8222, LECOB, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
- 19. Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France; Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France; LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco; Department of Medical Genetics, CHU Nice, France
- 20. Laboratoire d'Océanographie de Villefranche, UMR 7093, Sorbonne Université, CNRS, 06230 Villefranche sur mer, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000 Paris, France; Institut Universitaire de France, 75231 Paris, France
- 21. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- 22. Department of Microbiology and Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
- 23. Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
- 24. Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway, Ireland
- 25. Department of Microbiology, Oregon State University, Corvallis, OR, United States
Description
The following files are contained in this repository:
README.Hume_et_al_2022.zenodov4.txt - This document.
scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.
acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.
TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis.
Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).
Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.
Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.
Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.
Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.
Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.
Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).
Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.
Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.
Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.
Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.
Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.
PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.
PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.
Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.
Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.
Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.
mtORF Phylogeny
TP-Johnston_mtORF-Pocillo.fa = all sequences
TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment
TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick
Hellberg genotype network Porites
TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded
TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded
TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,
TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,
TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format
Gradient Forest Analysis
Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island
Por_abund.csv - Porites SSH Occurrences per Site er Island
mean_depth_por.csv - per site per island mean depth among Porites colonies
mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies
Notes
Files
acknowledgements_local_authorities.Hume_et_al_2022.zenodov3.pdf
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Additional details
Funding
- Agence Nationale de la Recherche
- CORALGENE - Genomic complexity of the coral holobiont across the Pacific ANR-17-CE02-0020
- Agence Nationale de la Recherche
- UCA JEDI - Idex UCA JEDI ANR-15-IDEX-0001
- Agence Nationale de la Recherche
- SIGNALIFE - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie ANR-11-LABX-0028
References
- Lan, D., et al. (2022) Genozip 14 - advances in compression of BAM and CRAM files (preprint) bioRxiv, doi:10.1101/2022.09.12.507582
- Planes, et al., (2019) The Tara Pacific expedition—A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean, PLOS Biology, doi:https://doi.org/10.1371/journal.pbio.3000483