Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition

Sánchez Fernández, Pablo; Coutinho, Felipe Hernandes; Sebastián, Marta; Pernice, Massimo; Rodríguez-Martínez, Raquel; Salazar, Guillem; Cornejo-Castillo, Francisco M.; Pesant, Stéphane; López Alforja, Xabier; López-García, Ester-María; Agustí, Susana; Gojobori, Takashi; Logares, Ramiro; Sala, M. Montserrat; Vaqué, Dolors; Massana, Ramon; Duarte, Carlos M.; Acinas, Silvia G.; Gasol, Josep M.

Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/345338

COMPARTIR / EXPORTAR:

SHARE CORE BASE	Comparte tu historia de Acceso Abierto
Visualizar otros formatos: MARC \| Dublin Core \| RDF \| ORE \| MODS \| METS \| DIDL \| DATACITE
Refman EndNote Bibtex RefWorks Excel CSV PDF DataCite Send via email

Título:	Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition
Autor:	Sánchez Fernández, Pablo CSIC ORCID ; Coutinho, Felipe Hernandes CSIC ORCID; Sebastián, Marta CSIC ORCID; Pernice, Massimo CSIC ORCID ; Rodríguez-Martínez, Raquel CSIC ORCID; Salazar, Guillem CSIC ORCID; Cornejo-Castillo, Francisco M. CSIC ORCID; Pesant, Stéphane; López Alforja, Xabier; López-García, Ester-María; Agustí, Susana CSIC ORCID; Gojobori, Takashi; Logares, Ramiro CSIC ORCID ; Sala, M. Montserrat CSIC ORCID ; Vaqué, Dolors CSIC ORCID ; Massana, Ramon CSIC ORCID ; Duarte, Carlos M. CSIC ORCID; Acinas, Silvia G. CSIC ORCID ; Gasol, Josep M. CSIC ORCID
Fecha de publicación:	feb-2024
Editor:	Nature Publishing Group
Citación:	Scientific Data 11: 154 (2024)
Resumen:	The Ocean microbiome has a crucial role in Earth’s biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2–3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome
Descripción:	12 pages, 6 figures, supplementary information https://doi.org/10.1038/s41597-024-02974-1.-- Data Records: All sequencing products described here, as well as the primary metagenome assemblies, can be found under BioProject accession number PRJEB52452 hosted by the European Nucleotide Archive28. ENA accession numbers for each metagenome sequencing run and for each megahit assembly are provided in Supplementary Tables 1, 4 respectively. File 1: 17,425,759 non-redundant coding DNA sequences (gene catalog) can be found in MP-GeneDB-VP.fasta.gz23. File 2: Prokka annotation for each CDS from the gene catalog, plus annotations for PFAM, KEGG-KO, CAZy and lowest common ancestor taxonomy can be found in file MP-GeneDB-VP-annotation-enhanced.tsv.gz23. File 3: 16S rRNA mTAG-based OTU table of the 76 metagenomes can be found in file mp-mtags.otu.tsv23. File 4: Counts of reads from each metagenome mapping to the gene catalog can be found in file MP-GeneDB-VP-raw-counts.tbl.gz23. File 5: Counts of reads from each metagenome mapping to the gene catalog normalized by gene length can be found in file MP-GeneDB-VP-length-norm-counts.tbl.gz23. File 6: Counts of reads from each metagenome mapping to the gene catalog annotated to COGs, normalized by gene length and 10 universal single copy COGs can be found in file MP-GeneDB-VP-length-norm-scgNorm-counts-cog.tbl.gz23. File 7: Counts of reads from each metagenome mapping to the gene catalog annotated to KEGG KOs, normalized by gene length and 10 universal single copy KOs can be found in file MP-GeneDB-VP-length-norm-scgNorm-counts-ko.tbl.gz23. File 8. Counts of reads from each metagenome mapping to the gene catalog normalized by gene length and aggregated per COG can be found in file MP-GeneDB-VP-length-norm-cog.tbl.gz23. File 9. Counts of reads from each metagenome mapping to the gene catalog normalized by gene length and aggregated per KO can be found in file MP-GeneDB-VP-length-norm-ko.tbl.gz23. File 10. Counts of reads from each metagenome mapping to the gene catalog normalized by gene length and aggregated per PFAM can be found in file MP-GeneDB-VP-length-norm-pfam.tbl.gz23. File 11. Counts of reads from each metagenome mapping to the gene catalog normalized by gene length and aggregated per CAZy can be found in file MP-GeneDB-VP-length-norm-cazy.tbl.gz23. File 12: fasta sequences for the 2,672 MAGs with estimated genome completeness above 50% and contamination below 5% can be found at file Malaspina-VP-MAGs.tar.gz23. File 13. Functional annotation of each MAG can be found in file Malaspina-VP-MAGs_CDS-annotation.tsv.gz23. File 14. Amino acid sequences of predicted genes in the MAGs sequences can be found in file Malaspina-VP-MAGs_CDS.faa.gz23. File 15: Nucleotide sequences of predicted genes in the MAGs sequences can be found in file Malaspina-VP-MAGs_CDS.fna.gz23. File 16: Viral genomic sequences can be found in file Malaspina_Profiles_Viruses_Genomic_Sequences.fasta.gz23. File 17: Descriptive information on the viral genomic sequences can be found in file Malaspina_Profiles_Viruses_Genomic_Info.tsv23. File 18: Virus-derived coding DNA sequences can be found in file Malaspina_Profiles_Viruses_CDS_Sequences.fna.gz23. File 19: Information of the annotation of the protein encoding genes predicted in the viral genomic sequences can be found in file Malaspina_Profiles_Viruses_PEG_Annotation_Info.tsv23. Underway and meteorological data measured on board R/V Hesperides for all 7 legs of the Malaspina Expedition 2010 on board R/V Hespérides are available from the Marine Technology Unit (UTM, CSIC).-- Code availability: All the software used to process the data set presented here is publicly available and distributed by their developers. All versions have been specified in the main text, along with the options used when departing from defaults. Custom scripts used in intermediate or summarizing steps are available at https://gitlab.com/malaspina-public/picoplankton-vertical-profiles. Code for bin decontamination step can be found at https://github.com/felipehcoutinho/QueroBins
Versión del editor:	https://doi.org/10.1038/s41597-024-02974-1
URI:	http://hdl.handle.net/10261/345338
DOI:	10.1038/s41597-024-02974-1
E-ISSN:	2052-4463
Aparece en las colecciones:	(ICM) Artículos