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Supplemental data for 76 marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and sub-tropical oceans

ABSTRACT: Supplemental data for 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 μm) collected in 11 stations along the Malaspina Expedition circumnavigation (http://www.expedicionmalaspina.es) that cover vertical profiles sampled at 7 depths, from the surface to 4,000 m deep (or the sea floor in shallower waters), published in Sánchez, P., Coutinho, F.H., Sebastián, M. et al. Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition. Sci Data 11, 154 (2024). https://doi.org/10.1038/s41597-024-02974-1 This repository includes i) 17.4 million non-redundant gene compendium with their corresponding annotations (M-GeneDB-VP), clustered at 95% sequence similarity. ii) the functional profile tables of the genes of the catalog. iii) taxonomic profiles based on 16S mTAGs analysis at the OTU level. iv) The fasta sequences of 2,672 medium and high-quality Metagenome-Assembled Genomes (MAGs) of bacteria and archaea (Malaspina-VP-MAGs) corresponding to microorganisms from 22 bacterial and 5 archaeal phyla reconstructed from the individual assembly of each of the 76 metagenomes. v) Functional annotation of the MAGs, plus amino acid and nucleotide sequences of the predicted genes. vi) A total of 101,219 viral genomic sequences of at least one Kbp identified in the assembled contigs and 3,105 unique viral sequences identified as prophages within the MAGs sequences. vii) Functional annotation of the viral sequences.

ORGANISM(S): marine metagenome

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PROVIDER: S-BSST1059 | biostudies-other |

SECONDARY ACCESSION(S): PRJEB52452

REPOSITORIES: biostudies-other

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Project description:The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Project description:RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans.IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.

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Supplemental data for 76 marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and sub-tropical oceans

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