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  • 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  (1)
  • Ciliates  (1)
  • Evolution  (1)
Document type
Keywords
Publisher
Years
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Development genes and evolution 209 (1999), S. 186-197 
    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
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  • 2
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    PANGAEA
    In:  Station Biologique de Roscoff
    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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  • 3
    Publication Date: 2022-05-26
    Description: Author Posting. © Inter-Research, 2009. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 57 (2009): 279-310, doi:10.3354/ame01340.
    Description: Acquisition of phototrophy is widely distributed in the eukaryotic tree of life and can involve algal endosymbiosis or plastid retention from green or red origins. Species with acquired phototrophy are important components of diversity in aquatic ecosystems, but there are major differences in host and algal taxa involved and in niches of protists with acquired phototrophy in marine and freshwater ecosystems. Organisms that carry out acquired phototrophy are usually mixotrophs, but the degree to which they depend on phototrophy is variable. Evidence suggests that ‘excess carbon’ provided by acquired phototrophy has been important in supporting major evolutionary innovations that are crucial to the current ecological roles of these protists in aquatic ecosystems. Acquired phototrophy occurs primarily among radiolaria, foraminifera, ciliates and dinoflagellates, but is most ecologically important among the first three. Acquired phototrophy in foraminifera and radiolaria is crucial to their contributions to carbonate, silicate, strontium, and carbon flux in subtropical and tropical oceans. Planktonic ciliates with algal kleptoplastids are important in marine and fresh waters, whereas ciliates with green algal endosymbionts are mostly important in freshwaters. The phototrophic ciliate Myrionecta rubra can be a major primary producer in coastal ecosystems. Our knowledge of how acquired phototrophy influences trophic dynamics and biogeochemical cycles is rudimentary; we need to go beyond traditional concepts of ‘plant’ and ‘animal’ functions to progress in our understanding of aquatic microbial ecology. This is a rich area for exploration using a combination of classical and molecular techniques, laboratory and field research, and physiological and ecosystem modeling.
    Description: F.N. and C.dV were supported by a SAD grant SYMFORAD from the Région Bretagne (France) and the BioMarKs project funded by the European ERA-net program BiodivERsA.
    Keywords: Mixotrophy ; Radiolaria ; Foraminifera ; Ciliates ; Dinoflagellates ; Kleptoplastidy ; Karyoklepty ; Endosymbiosis ; Myrionecta rubra
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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