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  • 1
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    Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean (2022)
    Elsevier
    In:  EPIC3Cell Genomics, Elsevier, 2(5), pp. 100123-100123, ISSN: 2666-979X
    Details
    Publication Date: 2024-04-03
    Description: Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
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    PAPER (OA)
  • 2
    Electronic Resource
    Electronic Resource
    Evolution of homeobox genes: Q50 Paired-like genes founded the Paired class (1999)
    Springer
    Development genes and evolution 209 (1999), S. 186-197 
    Details
    ISSN: 1432-041X
    Keywords: Key words Cnidaria ; Paired class ; Paired-like ; Homeobox gene ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The genes belonging to the Paired class exert primary developmental functions. They are characterized by six invariant amino acid residues in the homeodomain, while the residue at position 50 can be a serine, glutamine or lysine as in the Pax-type, Q50 Paired-like or the K50 Paired-like homeodomains respectively. Genes in this class emerged early in animal evolution: three distinct Pax genes and two Q50 Paired-like genes have recently been characterised from cnidarians. Phylogenetic molecular reconstructions taking into account homeodomain and paired-domain sequences provide some new perspectives on the evolution of the Paired-class genes. Analysis of 146 Paired-class homeodomains from a wide range of metazoan taxa allowed us to identify 18 families among the three sub-classes from which the aristaless family displays the least diverged position. Both Pax-type and K50 families branch within the Q50 Paired-like sequences implying that these are the most ancestral. Consequently, most Pax genes arose from a Paired-like ancestor, via fusion of a Paired-like homebox gene with a gene encoding only a paired domain; the Cnidaria appear to contain genes representing the ’before’ and ’after’ fusion events.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050243
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    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 285-294 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Planktonic foraminifera — Molecular phylogenetics — Rates of substitution — Ribosomal DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10−9 substitutions/site/year in the Globigerinidae to less than 1.0 × 10−9 substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006232
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    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Evolution all at sea (2000)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 405 (2000), S. 23-24 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Planktonic organisms evolve in continuous motion. Drifting passively in oceanic currents, their distributions seem to be limited mostly by changes in the temperature, nutrients and structure of the water masses in which they live. Or are they? The long distances separating species in the Arctic ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35011162
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    Paper (German National Licenses)
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  • 5
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    Total V9 rDNA information organized at the metabarcode level for the Tara Oceans Expedition (2009-2012) (2017)
    PANGAEA
    Details
    Publication Date: 2023-03-08
    Description: The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields:md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode belongs; and taxogroup = high-taxonomic level assignation of this barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. For example, the collodarian/Brandtodinium symbiosis is annotated: Chloroplast, "no"; Symbiont (small), "no"; Symbiont (host), "photo", for the collodarian host; and: Chloroplast, "yes"; Symbiont (small), "mutualist"; Symbiont (host), "no", for the dinoflagellate microalgal endosymbiont.chloroplast = "yes", "no" or "NA"; symbiont.small = "parasite", "commensal", "mutualist", "no" or "NA"; symbiont.host = "photo", "photo_falc", "photo_klep", "Nfix", no or NA; benef = "Nfix", "no" or "NA"; trophism = Metazoa , heterotroph , NA , photosymbiosis , phototroph according to the previous fields.
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 710.6 MBytes
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    DATA PANGAEA
  • 6
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    Svalbard 2010 mesocosm experiment: Protistan diversity (2010)
    PANGAEA
    In:  Station Biologique de Roscoff
    Details
    Publication Date: 2023-07-11
    Description: Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,…) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above.
    Keywords: BIOACID; Biological Impacts of Ocean Acidification; Class; EPOCA; European Project on Ocean Acidification; Experimental treatment; Experiment day; Family; Fraction; Fraction of sample; Kingdom; Number of sequences; Order; Phylum; Sample ID; Sequence abundance
    Type: Dataset
    Format: text/tab-separated-values, 93578 data points
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    DATA PANGAEA
  • 7
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    List of size fractionated eukaryotic plankton community samples and associated metadata (Database W1) (2015)
    PANGAEA
    In:  Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, G; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael E; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600
    Details
    Publication Date: 2024-01-06
    Description: The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 51.7 kBytes
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    DATA PANGAEA
  • 8
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    Total V9 rDNA information organized at the metabarcode level (Database W4) (2015)
    PANGAEA
    In:  Supplement to: De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Jean-Claude; Logares, Ramiro; Lara, Enrique; Berney, Cédric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sébastien; Aury, Jean-Marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Horák, Aleš; Jaillon, Olivier; Lima-Mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Zingone, Adriana; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Acinas, Silvia G; Gorsky, G; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Sieracki, Michael E; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Wincker, Patrick; Karsenti, Eric (2015): First Tara Oceans V9 rDNA metabarcoding dataset. zenodo, https://doi.org/10.5281/zenodo.15600
    Details
    Publication Date: 2024-01-06
    Description: The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields: md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode belongs; and taxogroup = high-taxonomic level assignation of this barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. For example, the collodarian/Brandtodinium symbiosis is annotated: Chloroplast, "no"; Symbiont (small), "no"; Symbiont (host), "photo", for the collodarian host; and: Chloroplast, "yes"; Symbiont (small), "mutualist"; Symbiont (host), "no", for the dinoflagellate microalgal endosymbiont.chloroplast = "yes", "no" or "NA"; symbiont.small = "parasite", "commensal", "mutualist", "no" or "NA"; symbiont.host = "photo", "photo_falc", "photo_klep", "Nfix", no or NA; benef = "Nfix", "no" or "NA"; trophism = Metazoa , heterotroph , NA , photosymbiosis , phototroph according to the previous fields.
    Keywords: Fondation Tara Expeditions; FondTara; Tara_Oceans_2009-2013; Tara Oceans Expedition
    Type: Dataset
    Format: application/zip, 252.1 MBytes
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    DATA PANGAEA
  • 9
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    Temperature and salinity data collected using thermosalinograph [TSG] during the Tara Pacific Expedition 2016-2018 (2022)
    PANGAEA
    Details
    Publication Date: 2024-01-06
    Description: The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from the thermosalinograph [TSG] instrument acquiring continuously during the full course of the campaign. Surface seawater was pumped continuously through a hull inlet located 1.5 m under the waterline using a membrane pump (10 LPM; Shurflo), circulated through a vortex debubbler, a flow meter, and distributed to a number of flow-through instruments. A thermosalinograph [TSG] (SeaBird Electronics SBE45/SBE38), measured temperature, conductivity, and thus salinity. Salinity measurements where intercalibrated against unfiltered seawater samples [SAL] taken every week from the surface ocean, and corrected for any observed bias. Moreover, temperature and salinity measurements were validated against Argo floats data collocated with Tara.
    Keywords: CTD, Sea-Bird, SBE45/SBE38; DATE/TIME; Fondation Tara Expeditions; FondTara; LATITUDE; LONGITUDE; Pacific Ocean; Salinity; SV Tara; TARA_2016-2018; Tara_Pacific; TARA_PACIFIC_2016-2018; Tara Pacific Expedition; Temperature; Temperature, water; UMS; Underway, multiple sensors
    Type: Dataset
    Format: text/tab-separated-values, 1770033 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 10
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    Aerosol concentration and size distribution (0.25-32µm) measured with an optical particle counter at a 30min granularity during the Tara Pacific Expedition 2016-2018 (2022)
    PANGAEA
    Details
    Publication Date: 2024-01-06
    Description: The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) instrument acquiring continuously during the full course of the campaign. Aerosols pumped through one of the ([MAST-PUMP]) inlets were channeled through a conductive tubing of 1.9 cm inner diameter to four parallel 47mm filter holders installed in the rear hold using a vacuum pump (Diaphragm pumpME16 NT, VACUUBRAND BmbH & Co KG, Wertheim, Germany) at a minimum flow rate of 30 lpm (20lpm prior to may 2016). Air was conducted to an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) measuring and counting particles in the size range 0.25 - 32 µm as a 30 minutes average, both the particle concentration (nb cm-3) together with its normalized size distribution (dN/dlogDp (nb cm-3 log(nm)-1) i.e., the concentration divided by the log of the width of the bin).
    Keywords: aerosol; DATE/TIME; Fondation Tara Expeditions; FondTara; LATITUDE; Log-normal particle size distribution; LONGITUDE; Optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) measuring and counting particles in 30 minutes average; Pacific Ocean; Particle concentration, standard deviation; Particle number, total; size distribution; SV Tara; TARA_2016-2018; Tara_Pacific; TARA_PACIFIC_2016-2018; Tara Pacific Expedition; UMS; Underway, multiple sensors
    Type: Dataset
    Format: text/tab-separated-values, 1851846 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
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