Tara Pacific - A pan-ecosystemic approach to the -omics complexity of coral reef holobionts across the Pacific Ocean

There is a newer version of the record available.

Published October 13, 2022 | Version 3
Dataset Restricted

Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories

Creators

  • 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.zenodov2.txt - This document.

Voolstra_etal_23.zenodov2.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

 

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

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

Lan, D., et al. (2022) Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations (preprint) bioRxiv 10.1101/2022.07.17.500374

Lan, D (2021) The Variant Call Format - Dual Coordinates Extension (DVCF) Specification (preprint) doi:10.6084/m9.figshare.14685816

Lan, D., et al. (2021) Genozip: a universal extensible genomic data compressor Bioinformatics, 37, 2225–2230

Lan, D., et al. (2020) genozip: a fast and efficient compression tool for VCF files Bioinformatics, 36, 4091–4092

Notes

Special thanks to the Tara Ocean Foundation, the R/V Tara crew and the Tara Pacific Expedition Participants (https://doi.org/10.5281/zenodo.3777760). We are keen to thank the commitment of the following institutions for their financial and scientific support that made this unique Tara Pacific Expedition possible: CNRS, PSL, CSM, EPHE, Genoscope, CEA, Inserm, Université Côte d'Azur, ANR, agnès b., UNESCO-IOC, the Veolia Foundation, the Prince Albert II de Monaco Foundation, Région Bretagne, Billerudkorsnas, AmerisourceBergen Company, Lorient Agglomération, Oceans by Disney, L'Oréal, Biotherm, France Collectivités, Fonds Français pour l'Environnement Mondial (FFEM), Etienne Bourgois, and the Tara Ocean Foundation teams. Tara Pacific would not exist without the continuous support of the participating institutes. The authors also particularly thank Serge Planes, Denis Allemand, and the Tara Pacific consortium.

Files

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Additional details

Funding

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
Agence Nationale de la Recherche

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