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LSU rDNA (lsu + rdna)

Distribution by Scientific Domains
Life Sciences100%

Terms modified by LSU rDNA

  • lsu rdna sequence
    		•

    Selected Abstracts

    Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples

    ENVIRONMENTAL MICROBIOLOGY, Issue 12 2009
    William Marande
    Summary The recent introduction of molecular techniques in eukaryotic microbial diversity studies, in particular those based in the amplification and sequencing of small-subunit ribosomal DNA (SSU rDNA), has revealed the existence of an unexpected variety of new phylotypes. The taxonomic ascription of the organisms bearing those sequences is generally deduced from phylogenetic analysis. Unfortunately, the SSU rDNA sequence alone has often not enough phylogenetic information to resolve the phylogeny of fast-evolving or very divergent sequences, leading to their misclassification. To address this problem, we tried to increase the phylogenetic signal by amplifying the complete eukaryotic rDNA cluster [i.e. the SSU rDNA, the internal transcribed spacers, the 5.8S rDNA and the large-subunit (LSU) rDNA] from environmental samples, and sequencing the SSU and LSU rDNA part of the clones. Using marine planktonic samples, we showed that surveys based on either SSU or SSU + LSU rDNA retrieved comparable diversity patterns. In addition, phylogenetic trees based on the concatenated SSU + LSU rDNA sequences showed better resolution, yielding good support for major eukaryotic groups such as the Opisthokonta, Rhizaria and Excavata. Finally, highly divergent SSU rDNA sequences, whose phylogenetic position was impossible to determine with the SSU rDNA data alone, could be placed correctly with the SSU + LSU rDNA approach. These results suggest that this method can be useful, in particular for the analysis of eukaryotic microbial communities rich in phylotypes of difficult phylogenetic ascription. [source]

    Ticks have R2 retrotransposons but not the consensus transposon target site of other arthropods

    INSECT MOLECULAR BIOLOGY, Issue 5 2005
    J. Bunikis
    Abstract Some copies of the large subunit rRNA genes (LSU rDNA) of most arthropods studied to date are inactivated by R-element retrotransposons at a specific target region that is highly conserved in sequence across all kingdoms of organisms. Here we report finding R2 elements in low copy numbers in the LSU rDNA of hard and soft ticks. Although the elements were inserted at the same LSU rDNA location as in insects, there were substitutions in the consensus R2 endonuclease cleavage site in the ticks and some other parasitiform mites. The substituted region comprises a critical contact point with small subunit rRNA, but in vitro structure probing analysis revealed novel, presumably stabilizing base-pairing. [source]

    ULTRASTRUCTURE AND LSU rDNA,BASED REVISION OF PERIDINIUM GROUP PALATINUM (DINOPHYCEAE) WITH THE DESCRIPTION OF PALATINUS GEN.

    JOURNAL OF PHYCOLOGY, Issue 5 2009

    The name Peridinium palatinum Lauterborn currently designates a freshwater peridinioid with 13 epithecal and six cingular plates, and no apical pore complex. Freshwater dinoflagellate floras classify it in Peridinium group palatinum together with P. pseudolaeve M. Lefèvre. General ultrastructure, flagellar apparatus, and pusular components of P. palatinum were examined by serial section TEM and compared to P. cinctum (O. F. Müll.) Ehrenb. and Peridiniopsis borgei Lemmerm., respectively, types of Peridinium and Peridiniopsis. Partial LSU rDNA sequences from P. palatinum, P. pseudolaeve and several peridinioids, woloszynskioids, gymnodinioids, and other dinoflagellates were used for a phylogenetic analysis. General morphology and tabulation of taxa in group palatinum were characterized by SEM. Differences in plate numbers, affecting both the epitheca and the cingulum, combine with differences in plate ornamentation and a suite of internal cell features to suggest a generic-level distinction between Peridinium group palatinum and typical Peridinium. The branching pattern of the phylogenetic tree is compatible with this conclusion, although with low support from bootstrap values and posterior probabilities, as are sequence divergences estimated between species in group palatinum, and typical Peridinium and Peridiniopsis. Palatinus nov. gen. is proposed with the new combinations Palatinus apiculatus nov. comb. (type species; syn. Peridinium palatinum), P. apiculatus var. laevis nov. comb., and P. pseudolaevis nov. comb. Distinctive characters for Palatinus include a smooth or slightly granulate, but not areolate, plate surface, a large central pyrenoid penetrated by cytoplasmic channels and radiating into chloroplast lobes, and the presence of a peduncle-homologous microtubular strand. Palatinus cells exit the theca through the antapical-postcingular area. [source]

    ON THE IDENTITY OF KARLODINIUM VENEFICUM AND DESCRIPTION OF KARLODINIUM ARMIGER SP.

    JOURNAL OF PHYCOLOGY, Issue 1 2006
    AND PIGMENT COMPOSITION, BASED ON LIGHT AND ELECTRON MICROSCOPY, NOV. (DINOPHYCEAE), NUCLEAR-ENCODED LSU RDNA
    An undescribed species of the dinoflagellate genus Karlodinium J. Larsen (viz. K. armiger sp. nov.) is described from Alfacs Bay (Spain), using light and electron microscopy, pigment composition, and partial large subunit (LSU) rDNA sequence. The new species differs from the type species of Karlodinium (K. micrum (Leadbeater et Dodge) J. Larsen) by lacking rows of amphiesmal plugs, a feature presently considered to be a characteristic of Karlodinium. In K. armiger, an outer membrane is underlain by a complex system of cisternae and vacuoles. The pigment profile of K. armiger revealed the presence of chlorophylls a and c, with fucoxanthin as the major carotenoid. Phylogenetic analysis confirmed K. armiger to be related to other species of Karlodinium; thus forming a monophyletic genus, which, in the LSU tree, occupies a sister group position to Takayama de Salas, Bolch, Botes et Hallegraeff. The culture used by Ballantine to describe Gymnodinium veneficum Ballantine (Plymouth 103) was examined by light and electron microscopy and by partial LSU rDNA. Ultrastructurally, it proved identical to K. micrum (cultures Plymouth 207 and K. Tangen KT-77D, the latter also known as K-0522), and in LSU sequence, differed in only 0.3% of 1438 bp. We consider the two taxa to belong to the same species. This necessitates a change of name for the most widely found species, K. micrum, to K. veneficum. The three genera Karlodinium, Takayama, and Karenia constitute a separate evolutionary lineage, for which the new family Kareniaceae fam. nov. is suggested. [source]

    PHYLOGENY OF THE EUGLENOPHYTES INFERRED FROM SSU AND LSU rDNA

    JOURNAL OF PHYCOLOGY, Issue 2001
    Article first published online: 24 SEP 200
    Zimmermann, S. & Triemer, R. E. Department of Life Sciences, Rutgers University, Piscataway, NJ 08854 USA The phylogeny of the Euglenophytes has previously been examined using the SSU rDNA. Results from these analyses indicated that the phototrophic genera are not monophyletic. To test this hypothesis, a second gene was sequenced, the LSU rDNA. The taxa used in this study were selected from clades represented in the SSU analyses so that comparisons could be made between gene phylogenies and a combined dataset could be created. Conserved areas of the aligned sequences for both the LSU and SSU were used to generate parsimony, maximum likelihood, and distance trees. Topology of the SSU and LSU trees was similar. The SSU and LSU data consistently generated the same four highly supported terminal clades and varied only in the placement of Euglena stellata and Euglena viridis. The internal nodes of the SSU trees were weakly supported, whereas the LSU provided higher support for these nodes. A combined LSU and SSU dataset was then created. Analysis of the combined dataset yielded trees with identical topologies to those found in the individual datasets and demonstrated strong support for the four terminal clades. These results show that phylogeny of the Euglenophytes as inferred previously from SSU data is confirmed by the LSU data and that the LSU rDNA gene may be useful in elucidating relationships among the major clades. [source]

    Phylogenetic study of benthic, spine-bearing prorocentroids, including Prorocentrum fukuyoi sp. nov.

    PHYCOLOGICAL RESEARCH, Issue 2 2007
    Shauna Murray
    SUMMARY Species of prorocentroid dinoflagellates are common in marine benthic sediment and epibenthic habitats, as well as in planktonic habitats. Marine planktonic prorocentroids typically possess a small spine in the apical region. In this study, we describe a new, potentially widely distributed benthic species of Prorocentrum, P. fukuyoi sp. nov., from tidal sand habitats in several sites in Australia and from central Japan. This species was found to possess an apical spine or flange and was sister species to P. emarginatum. We analyzed the phylogeny of the group including this new species, based on large subunit (LSU) rDNA sequences. The genus contained a high level of divergence in LSU rDNA, in some cases among sister taxa. P. fukuyoi and P. emarginatum were found to be most closely related to a clade of generally planktonic taxa. Several morphological features may constitute more informative synapomorphies than habitat in distinguishing clades of prorocentroid species. [source]

    Informative Characteristics of 12 Divergent Domains in Complete Large Subunit rDNA Sequences from the Harmful Dinoflagellate Genus, Alexandrium (Dinophyceae)

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2007
    JANG-SEU KI
    ABSTRACT. The genus Alexandrium includes organisms of interest, both for the study of dinoflagellate evolution and for their impacts as toxic algae affecting human health and fisheries. Only partial large subunit (LSU) rDNA sequences of Alexandrium and other dinoflagellates are available, although they contain much genetic information. Here, we report complete LSU rDNA sequences from 11 strains of Alexandrium, including Alexandrium affine, Alexandrium catenella, Alexandrium fundyense, Alexandrium minutum, and Alexandrium tamarense, and discuss their segmented domains and structure. Putative LSU rRNA coding regions were recorded to be around 3,400bp long. Their GC content (about 43.7%) is among the lowest when compared with other organisms. Furthermore, no AT-rich regions were found in Alexandrium LSU rDNA, although a low GC content was recorded within the LSU rDNA. No intron-like sequences were found. The secondary structure of the LSU rDNA and parsimony analyses showed that most variation in LSU rDNA is found in the divergent (D) domains with the D2 region being the most informative. This high D domain variability can allow members of the diverse Alexandrium genus to be categorized at the species level. In addition, phylogenetic analysis of the alveolate group using the complete LSU sequences strongly supported previous findings that the dinoflagellates and apicomplexans form a clade. [source]

    A Marine Dinoflagellate, Amphidinium eilatiensis n. sp., from the Benthos of a Mariculture Sedimentation Pond in Eilat, Israel

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2003
    JOHN J. LEE
    ABSTRACT. A species of Amphidinium bloomed in a mariculture sedimentation pond that was used to grow bivalves near the Gulf of Eilat, Israel. Its overall length averaged 13 ,m, the hypocone was 11 ,m, and its width was 8,m. It has a ventral ridge. The sulcus begins at the longitudinal flagellar pore and does not project forward in the apex toward the transverse flagellar pore and left margin of the cingulum. The sulcus is a very shallow groove that projects variably about a third of the body length toward the antapex. The cingulum is a deep groove as it circles the cell from the left ventral side to the dorsal side and then becomes very shallow on the right ventral side as it arches posterior toward the longitudinal flagellar pore. Using a modified method for studying dinoflagellate chromosomes in the SEM, we observed 31 chromosomes. The plastid is dorsal and peripheral with 6 ventrally projecting peripheral digital lobes that wrap around the sides of the ventral and posterior nucleus. Amphidinium eilatiensis n. sp. is morphologically closest to Amphidinium carterae and Amphidinium rhynchocephalum, but it does not have the obvious thecal plates or polygonal units described for the former species. Instead, it has a series of spicules, bumps, and ridges on its surface. It differs from A. rhynchocephalum by two morphological characters: surface morphology and gross plastid architecture. The amplified fragments of the rDNA from A. eilatiensis n. sp. isolated from 2 separate sedimentation ponds in Eilat include the 3,-end of the SSU rDNA (about 100 nt), the whole ITS region (ITS1 + 5. 8S + ITS2) and the 5,-end of the LSU rDNA (about 900 nts). The total length of the sequences ranged from 1,460 nt. (A. eilatiensis isolate #1) to 1,461 nts. (A. eilatiensis isolate #2). The latter sequences are identical, the difference in length being due to three insertions. Amphidinium eilatiensis is genetically more closely related to A. carterae than to A. klebsii, with respectively 2. 36% and 6. 93% of sequence divergence. [source]

    Molecular phylogeny of the Sphaerophorus globosus species complex

    CLADISTICS, Issue 3 2003
    Filip Högnabba
    The Sphaerophorus globosus complex (Lecanorales, lichenized Ascomycota) shows a large morphological variation, and three relatively distinct morphotypes can be distinguished in parts of the distribution area. Here, we utilize a multigene-based maximum-parsimony approach (nITS+ LSU rDNA, mtSSU rDNA, ,-tubulin, and actin) to investigate whether these morphotypes constitute distinct species. The results show that there are at least two well-supported monophyletic groups that we interpret as phylogenetic species within the S. globosus complex. These species do not completely correspond to the predefined morphotypes. One group, an apparently undescribed species, contains noncoralloid specimens from the North American Pacific Northwest. The other group, S. globosus, consists of two well-supported monophyletic groups: one contains coralloid epiphytic specimens from the North American Pacific Northwest that are morphologically indistinguishable from epiphytic specimens from Europe and are presently interpreted as belonging to the same species and the other is morphologically variable and contains terrestrial specimens from Europe, North America, and southernmost South America and coralloid epiphytic and epilithic specimens from Europe. The results suggest that the population in southernmost South America originated by long-distance dispersal from arctic populations in the Northern Hemisphere. [source]