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Transcribed Spacer Sequences (transcribed + spacer_sequence)

Distribution by Scientific Domains
Life Sciences100%

Kinds of Transcribed Spacer Sequences

  • internal transcribed spacer sequence
    		•

    Selected Abstracts

    THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCES

    JOURNAL OF PHYCOLOGY, Issue 2000
    S. Nemeth
    Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa, were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species. [source]

    Comparison of Small Subunit Ribosomal RNA Gene and Internal Transcribed Spacer Sequences Among Isolates of the Intranuclear Microsporidian Nucleospora salmonis

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2000
    STEPHANE J. GRESOVIAC
    ABSTRACT. Nucleospora salmonis is an intranuclear microsporidian associated with a proliferative disorder of the lymphoid cells of captive salmonid fish in the northwestern and northeastern regions of North America, in France, and in Chile. Newer diagnostic approaches have used the polymerase chain reaction (PCR) to detect the parasite in fish tissues. The target sequences for these assays lie in the small subunit ribosomal RNA (ssu rRNA) gene or internal transcribed spacer (ITS) as determined from N. salmonis from chinook salmon (Oncorhynchus tshawytscha) from the Pacific Northwest of North America. The lack of sequence data on parasites from diverse geographic origins and hosts led us to compare several isolates of N. salmonis. There was a high degree of similarity in the ssu rDNA sequences (> 98%) among all the isolates of N. salmonis examined, regardless of host or geographic origin. The greatest sequence differences were found between isolates from the Pacific regions of America. Isolates from Chile shared sequences with one or both geographic groups from North America. A similar distribution of sequence types was observed when ITS-1 sequences of selected isolates were analyzed. Sequence data from two N. salmonis -like isolates from marine non-salmonid fish showed one closely related and the second less closely related to N. salmonis isolates from salmonid fish. These results provide evidence for a homogeneous group of aquatic members of the genus Nucleospora found among salmonid fish (N. salmonis) that can be detected using diagnostic PCR assays with ssu rDNA target sequences. The presence of parasites related to N. salmonis among marine fish suggests a potentially broad host and geographic distribution of members of the family Enterocytozoonidae. [source]

    BIOCHEMICAL PHENOTYPES CORRESPONDING TO MOLECULAR PHYLOGENY OF THE RED ALGAE PLOCAMIUM (PLOCAMIALES, RHODOPHYTA): IMPLICATIONS OF INCONGRUENCE WITH THE CONVENTIONAL TAXONOMY,

    JOURNAL OF PHYCOLOGY, Issue 1 2006
    Tomomi Yano
    Among five species of the genus Plocamium Lamouroux distributed around Japan, P. cartilagineum (Linnaeus) Dixon, P. recurvatum Okamura and P. telfairiae (Hooker and Harvey) Harvey are often difficult to distinguish morphologically from each other. Our previous study demonstrated that P. recurvatum and P. telfairiae were divided into two groups, A and C, based on RUBISCO spacer sequence and that the specimens belonging to group C had acidic cell saps. In this study, we inferred evolutionary relationships of these Plocamium species from internal transcribed spacer sequence of the ribosomal RNA genes and obtained a similar topology to the RUBISCO spacer tree. Color of the dried specimens in the acidic group C was darker red than that in the non-acidic group A, although there was no difference in color in living thalli. The Br, concentration in the cell sap of the acidic group C was 20 times higher than that of the non-acidic group. We could not find any morphological differences to distinguish clearly between groups A and C despite exhaustive investigation of field-collected and cultured thalli in both P. recurvatum and P. telfairiae. These results suggest that the color of dried specimens and the composition of intracellular inorganic ions are significant criteria for interpreting phylogenetic relationships in Japanese Plocamium spp. [source]

    Yeast species composition differs between artisan bakery and spontaneous laboratory sourdoughs

    FEMS YEAST RESEARCH, Issue 4 2010
    Gino Vrancken
    Abstract Sourdough fermentations are characterized by the combined activity of lactic acid bacteria and yeasts. An investigation of the microbial composition of 21 artisan sourdoughs from 11 different Belgian bakeries yielded 127 yeast isolates. Also, 12 spontaneous 10-day laboratory sourdough fermentations with daily backslopping were performed with rye, wheat, and spelt flour, resulting in the isolation of 217 yeast colonies. The isolates were grouped according to PCR-fingerprints obtained with the primer M13. Representative isolates of each M13 fingerprint group were identified using the D1/D2 region of the large subunit rRNA gene, internal transcribed spacer sequences, and partial actin gene sequences, leading to the detection of six species. The dominant species in the bakery sourdoughs were Saccharomyces cerevisiae and Wickerhamomyces anomalus (formerly Pichia anomala), while the dominant species in the laboratory sourdough fermentations were W. anomalus and Candida glabrata. The presence of S. cerevisiae in the bakery sourdoughs might be due to contamination of the bakery environment with commercial bakers yeast, while the yeasts in the laboratory sourdoughs, which were carried out under aseptic conditions with flour as the only nonsterile component, could only have come from the flour used. [source]

    Yeast diversity of Ghanaian cocoa bean heap fermentations

    FEMS YEAST RESEARCH, Issue 5 2009
    Heide-Marie Daniel
    Abstract The fermentation of the Theobroma cacao beans, involving yeasts, lactic acid bacteria, and acetic acid bacteria, has a major influence on the quality of the resulting cocoa. An assessment of the microbial community of cocoa bean heap fermentations in Ghana resulted in 91 yeast isolates. These were grouped by PCR-fingerprinting with the primer M13. Representative isolates were identified using the D1/D2 region of the large subunit rRNA gene, internal transcribed spacer sequences and partial actin gene sequences leading to the detection of 15 species. Properties of importance for cocoa bean fermentation, namely sucrose, glucose, and citrate assimilation capacity, pH-, ethanol-, and heat-tolerance, were examined for selected isolates. Pichia kudriavzevii (Issatchenkia orientalis), Saccharomyces cerevisiae, and Hanseniaspora opuntiae formed the major components of the yeast community. Hanseniaspora opuntiae was identified conclusively for the first time from cocoa fermentations. Among the less frequently encountered species, Candida carpophila, Candida orthopsilosis, Kodamaea ohmeri, Meyerozyma (Pichia) caribbica, Pichia manshurica, Saccharomycodes ludwigii, and Yamadazyma (Pichia) mexicana were not yet documented from this substrate. Hanseniaspora opuntiae was preferably growing during the earlier phase of fermentation, reflecting its tolerance to low pH and its citrate-negative phenotype, while no specific temporal distribution was recognized for P. kudriavzevii and S. cerevisiae. [source]

    Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences

    MOLECULAR ECOLOGY, Issue 3 2004
    M. C. Le Goff-Vitry
    Abstract The azooxanthellate scleractinian coral Lophelia pertusa has a near-cosmopolitan distribution, with a main depth distribution between 200 and 1000 m. In the northeast Atlantic it is the main framework-building species, forming deep-sea reefs in the bathyal zone on the continental margin, offshore banks and in Scandinavian fjords. Recent studies have shown that deep-sea reefs are associated with a highly diverse fauna. Such deep-sea communities are subject to increasing impact from deep-water fisheries, against a background of poor knowledge concerning these ecosystems, including the biology and population structure of L. pertusa. To resolve the population structure and to assess the dispersal potential of this deep-sea coral, specific microsatellites markers and ribosomal internal transcribed spacer (ITS) sequences ITS1 and ITS2 were used to investigate 10 different sampling sites, distributed along the European margin and in Scandinavian fjords. Both microsatellite and gene sequence data showed that L. pertusa should not be considered as one panmictic population in the northeast Atlantic but instead forms distinct, offshore and fjord populations. Results also suggest that, if some gene flow is occurring along the continental slope, the recruitment of sexually produced larvae is likely to be strongly local. The microsatellites showed significant levels of inbreeding and revealed that the level of genetic diversity and the contribution of asexual reproduction to the maintenance of the subpopulations were highly variable from site to site. These results are of major importance in the generation of a sustainable management strategy for these diversity-rich deep-sea ecosystems. [source]