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Ribosomal DNA Sequences (ribosomal + dna_sequence)
Selected AbstractsA Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character OptimizationCLADISTICS, Issue 2 2000Gonzalo Giribet Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropod groups. Sequences of 139 taxa (23 outgroup and 116 ingroup taxa) representing all extant arthropod "classes" except Remipedia and Cephalocarida are analyzed using direct character optimization exploring six parameter sets. Parameter choice appears to be crucial to phylogenetic inference. The high level of sequence heterogeneity in the 18S rRNA gene (sequence length from 1350 to 2700 bp) makes placement of certain taxa with "unusual" sequences difficult and underscores the necessity of combining ribosomal gene data with other sources of information. Monophyly of Pycnogonida, Chelicerata, Chilopoda, Chilognatha, Malacostraca, Branchiopoda (excluding Daphnia), and Ectognatha are among the higher groups that are supported in most of the analyses. The positions of the Pauropoda, Symphyla, Protura, Collembola, Diplura, Onychophora, Tardigrada, and Daphnia are unstable throughout the parameter space examined. [source] Ribosomal DNA sequences indicate isolated populations of Ichthyophonus hoferi in geographic sympatry in the north-eastern Pacific OceanJOURNAL OF FISH DISEASES, Issue 10 2002C D Criscione Abstract Infections of Ichthyophonus hoferi, a cosmopolitan parasite of marine fish, have recently been reported in rockfish, Sebastes spp., from the north-eastern Pacific. Because I. hoferi also infects Pacific herring, Clupea pallasi Valenciennes, and salmonids in this region, we wanted to determine if Ichthyophonus parasites from rockfishes, Pacific herring and chinook salmon, Oncorhynchus tshawytscha (Walbaum), were the same. Small subunit ribosomal deoxyribonucleic acid sequence data revealed two haplotypes that were fixed among host species in geographic sympatry, one from rockfish and the other from both Pacific herring and salmon. These isolated populations of Ichthyophonus could be part of the same species that are ecologically separated because of host behaviours, or they could be distinct species that are host specific. Dietary patterns of the hosts indicate that ecological separation among hosts is possible, but the presence of distinct species may better explain the observed Ichthyophonus haplotype association with host species. [source] Fireflies with or without prespermatophores: Evolutionary origins and life-history consequencesENTOMOLOGICAL SCIENCE, Issue 1 2003Fumio Hayashi Abstract During mating, some male North American fireflies produce spermatophores from prespermatophores in their paired reproductive accessory glands. Other species of fireflies have neither prespermatophores nor spermatophores. To establish a pattern of spermatophore occurrence across firefly species, we examined the male internal reproductive system in 20 Japanese species belonging to 10 genera for the presence or absence of prespermatophores. Twelve species from seven genera produced prespermatophores, while eight species from three genera did not. Superimposed on a molecular phylogeny of Japanese fireflies based on mitochondrial 16S ribosomal DNA sequences, the basal group was prespermatophore producers. Prespermatophores appear to have been lost in two different lineages. Species without prespermatophores are characterized by degeneration of both the forewings and hindwings, and by body gigantism in females. [source] Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Xavier Mayali Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source] Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical GyreENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Vinh D. Pham Summary High-throughput identification of rRNA gene-containing clones in large insert metagenomic libraries is difficult, because of the high background of host ribosomal RNA (rRNA) and rRNA genes. To address this challenge, a membrane hybridization method was developed to identify all bacterial small subunit rRNA-containing fosmid clones of microbial community DNA from seven different depths in the North Pacific Subtropical Gyre. Out of 101,376 clones screened, 751 rDNA-containing clones were identified that grouped in ,60 different clades. Several rare sequences only remotely related to known groups were detected, including a Wolbachia -related sequence containing a putative intron or intervening sequence, as well as seven sequences from Order Myxococcales not previously detected in pelagic habitats. Stratified, depth-specific population structure was evident within both cultured and uncultured lineages. Conversely, some eurybathyal members of the genera Alcanivorax and Rhizobium shared identical small subunit ribosomal DNA sequences that were distributed from surface waters to the 4000 m depth. Comparison with similar analyses in Monterey Bay microbial communities revealed previously recognized, as well as some distinctive, depth-stratified partitioning that distinguished coastal from open ocean bacterioplankton populations. While some bias was evident in fosmid clone recovery in a few particular lineages, the overall phylogenetic group recovery and distributions were consistent with previous studies, as well as with direct shotgun sequence data from the same source DNA. [source] Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspenENVIRONMENTAL MICROBIOLOGY, Issue 4 2008Celine Lesaulnier Summary The effects of elevated atmospheric CO2 (560 p.p.m.) and subsequent plant responses on the soil microbial community composition associated with trembling aspen was assessed through the classification of 6996 complete ribosomal DNA sequences amplified from the Rhinelander WI free-air CO2 and O3 enrichment (FACE) experiments microbial community metagenome. This in-depth comparative analysis provides an unprecedented, detailed and deep branching profile of population changes incurred as a response to this environmental perturbation. Total bacterial and eukaryotic abundance does not change; however, an increase in heterotrophic decomposers and ectomycorrhizal fungi is observed. Nitrate reducers of the domain bacteria and archaea, of the phylum Crenarchaea, potentially implicated in ammonium oxidation, significantly decreased with elevated CO2. These changes in soil biota are evidence for altered interactions between trembling aspen and the microorganisms in its surrounding soil, and support the theory that greater plant detritus production under elevated CO2 significantly alters soil microbial community composition. [source] Phylogeographic variation among isolates of the Sirococcus conigenus P groupFOREST PATHOLOGY, Issue 1 2007H. Konrad Summary In this study the phylogeographic variation among isolates of the Sirococcus conigenus P group and the phylogenetic relationships of S. conigenus with Sirococcus clavigignenti-juglandacearum and other species previously placed in the genus Sirococcus were investigated. A collection of 33 isolates originating from Picea, Pinus and Larix in Europe, North America and Bhutan were characterized by sequence analyses of the internal transcribed spacer (ITS) region (including ITS1, 5.8S ribosomal DNA, ITS2) of the nuclear rDNA and a portion of the , -tubulin gene. In phylogenetic analyses most isolates from pine, spruce and larch formed a distinct clade, representing the P group of S. conigenus, which was separated from the T group of this pathogen. Four isolates from Picea in Europe and Canada formed a third clade within S. conigenus and these isolates are referred to as the S group. The P group consisted of five distinct ITS haplotypes, which partly differed in their optimum growth temperature and their growth rates at 25°C on malt extract agar. Nested clade analysis resolved the five haplotypes into three distinct clades and revealed significant genetic/geographic associations for some of the haplotypes. Parsimony analysis of the small subunit (18S) ribosomal DNA sequences confirmed the phylogenetic affinities between S. conigenus and S. clavigignenti-juglandacearum. In contrast, Godronia cassandrae and Hormococcus conorum, which formerly had been placed in the genus Sirococcus, were found to be only distantly related to S. conigenus and S. clavigignenti-juglandacearum. [source] Isolation of flagellated bacteria implicated in Crohn's diseaseINFLAMMATORY BOWEL DISEASES, Issue 10 2007L. Wayne Duck BS Abstract Background: Serologic expression cloning has identified flagellins of the intestinal microbiota as immunodominant antigens in experimental colitis in mice and in individuals with Crohn's disease (CD). The present study was done to identify the microbial source of such flagellins. Methods: Using a variety of isolation and culture approaches, a number of previously unknown flagellated bacteria were isolated. Based on 16S ribosomal DNA sequences, these bacteria fall into the family Lachnospiraceae of the phylum Firmicutes. Results: Serum IgG from patients with CD and from mice with colitis reacted to the flagellins of these bacteria, and only their flagellins, whereas serum IgG from controls did not. The sequence of these flagellins demonstrate conserved amino- and carboxy-terminal domains that cluster phylogenetically and have a predicted 3D structure similar to Salmonella fliC, including an intact TLR5 binding site. The flagellin of 1 of these bacteria was likely O -glycosylated. Conclusions: The conserved immune response in both mouse and human to these previously unknown flagellins of the microbiota indicate that they play an important role in host,microbe interactions in the intestine. (Inflamm Bowel Dis 2007) [source] Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular dataINVERTEBRATE BIOLOGY, Issue 3 2007Patrick M. Erwin Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina. The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity. [source] Viable ultramicrocells in drinking waterJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009F.S. Silbaq Abstract Aims:, To examine the diversity of cultivable 0·2 micron filtrate biofilm forming bacteria from drinking water systems. Methods and Results:, Potable chlorinated drinking water hosts phylogenetically diverse ultramicrocells (UMC) (0·2 and 0·1 ,m filterable). UMC (starved or dwarf bacteria) were isolated by cultivation on minimal medium from a flow system wall model with polyvinyl chloride (PVC) pipes. All cultivated cells (25 different isolates) did not maintain their ultra-size after passages on rich media. Cultured UMC were identified by their 16S ribosomal DNA sequences. The results showed that they were closely related to uncultured and cultured members of the Proteobacteria, Actinobacteria and Firmicutes. The isolates of phylum Actinobacteria included representatives of a diverse set of Actinobacterial families: Micrococcaceae, Microbacteriaceae, Dermabacteraceae, Nocardiaceae and Nocardioidaceae. Conclusions:, This study is the first to show an abundance of cultivable UMC of various phyla in drinking water system, including a high frequency of bacteria known to be involved in opportunistic infections, such as Stenotrophomonas maltophilia, Microbacterium sp., Pandoraea sp. and Afipia strains. Significance and Impact of the Study:, Chlorinated tap water filtrate (0·2 and 0·1 ,m) still harbours opportunistic micro-organisms that can pose some health threat. [source] Phylogeny of the subgenus Culicoides and related species in Italy, inferred from internal transcribed spacer 2 ribosomal DNA sequencesMEDICAL AND VETERINARY ENTOMOLOGY, Issue 2 2006L. M. Gomulski Abstract., Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) include vectors for the economically important animal diseases, bluetongue (BT) and African horse sickness (AHS). In the Mediterranean Basin, these diseases are transmitted by four species of Culicoides: the first three belong in the subgenus Avaritia Fox and are Culicoides imicola Kieffer, Culicoides obsoletus (Meigen) and Culicoides scoticus Downes and Kettle; the fourth is Culicoides pulicaris (Linnaeus) in the subgenus Culicoides Latreille. In the Palaearctic Region, this subgenus (usually referred to as the C. pulicaris group) now includes a loose miscellany of some 50 taxa. The lack of clarity surrounding its taxonomy stimulated the present morphological and molecular study of 11 species collected in Italy. Phylogenetic analysis of nuclear ribosomal DNA internal transcribed spacer 2 (ITS2) sequence variation demonstrated a high degree of divergence. These results, combined with those from a parallel morphological study, disclosed: (1) that some previously described taxa should be resurrected from synonymy; (2) that there are new species to be described; (3) that the subgenus Culicoides (as currently employed) is a polyphyletic assemblage of four lineages , the subgenus Culicoides sensu stricto, the subgenus Silvicola Mirzaeva and Isaev, the subgenus Hoffmania Fox and the hitherto unrecognized Fagineus species complex. Each is discussed briefly (but not defined) and its constituent Palaearctic taxa listed. Strong congruence between morphological and molecular data holds promise for resolving many of the difficult taxonomic issues plaguing the accurate identification of vector Culicoides around the world. [source] The Phylogeny of the Families Lecanoraceae and Bacidiaceae (Lichenized Ascomycota) Inferred from Nuclear SSU rDNA SequencesPLANT BIOLOGY, Issue 3 2000S. Ekman Abstract: The phylogeny of the families Lecanoraceae and Bacidiaceae (Lecanorales, Ascomycota) was investigated using 29 nuclear small subunit ribosomal DNA sequences, 9 of which were newly determined. The data set contained 368 variable characters, 234 of which were parsimony-informative. Phylogenetic estimations were performed with maximum parsimony and maximum likelihood optimality criteria. In the most parsimonious and most likely reconstructions, the Bacidiaceae sensu Hafellner 1988 forms a monophyletic group and the Lecanoraceae sensu Hafellner a paraphyletic group. The genera Tephromela and Scoliciosporum appear to belong outside these families. However, the hypothesis that the Lecanoraceae sensu Hafellner is monophyletic cannot be rejected, as indicated by a Kishino-Hasegawa test. Three hypotheses were rejected by Kishino-Hasegawa tests, viz. (1) that the Lecanoraceae and Bacidiaceae together form a monophyletic group; (2) that both the Lecanoraceae (incl. Scoliciosporum) and Bacidiaceae (incl. Tephromela) are monophyletic; and (3) that the ascus apex anatomy reflects phylogeny. The suborder Lecanorineae is paraphyletic unless the Stereocaulaceae and Cladoniaceae are included. One or both of the Bacidia and Lecanora types of ascus have probably evolved at least twice. [source] Development of species-specific primers for the ectoparasitic nematode species Xiphinema brevicolle, X. diffusum, X. elongatum, X. ifacolum and X. longicaudatum (Nematoda: Longidoridae) based on ribosomal DNA sequencesANNALS OF APPLIED BIOLOGY, Issue 3 2005CLAUDIO M G OLIVEIRA Summary The objective of this study was to develop single-step PCR species-specific primers that reliably discriminate four economically important Xiphinema species (X. brevicolle, X. elongatum, X. ifacolum and X. longicaudatum) and X. diffusum that is taxonomically very similar to X. brevicolle. Each species-specific reverse primer was located in the ITS-1 rDNA region and was used in combination with a universal forward primer located in the 18S rDNA gene. Primer reliability was confirmed by screening seven and 11 populations, respectively of X. diffusum and X. elongatum. Potential species-specific primers were also identified for X. brevicolle, X. longicaudatum and X. ifacolum, however too few populations of these species were available to thoroughly assess their reliability. For all species-specific primers, specificity was demonstrated by the absence of cross-reactions with 14 non-target Xiphinema species. Multiplex PCR was effective and reproducible for two (X. longicaudatum and X. ifacolum) or three (X. brevicolle, X. diffusum and X. elongatum) of the target nematode species, thus improving the applicability of the diagnostic primers. [source] Influence of different substrates on the evolution of morphology and life-history traits of azooxanthellate solitary corals (Scleractinia: Flabellidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010YUKI TOKUDA Sessile organisms are influenced considerably by their substrate conditions, and their adaptive strategies are key to understanding their morphologic evolution and traits of life history. The family Flabellidae (Cnidaria: Scleractinia) is composed of the representative azooxanthellate solitary corals that live on both soft and hard substrates using various adaptive strategies. We reconstructed the phylogenetic tree and ancestral character states of this family from the mitochondrial 16S and nuclear 28S ribosomal DNA sequences of ten flabellids aiming to infer the evolution of their adaptive strategies. The Javania lineage branched off first and adapted to hard substrates by using a tectura-reinforced base. The extant free-living flabellids, including Flabellum and Truncatoflabellum, invaded soft substrates and acquired the flabellate corallum morphology of their common ancestor, followed by a remarkable radiation with the exploitation of adaptive strategies, such as external soft tissue [e.g. Flabellum (Ulocyathus)], thecal edge spine, and transverse division (e.g. Placotrochus and Truncatoflabellum). Subsequently, the free-living ancestors of two genera (Rhizotrochus and Monomyces) invaded hard substrates independently by exploiting distinct attachment apparatuses such as tube-like and massive rootlets, respectively. In conclusion, flabellids developed various morphology and life-history traits according to the differences in substrate conditions during the course of their evolution. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 184,192. [source] New chromosome reports in the subtribes Diocleinae and Glycininae (Phaseoleae: Papilionoideae: Fabaceae)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2008SHIRLEY M. ESPERT The base chromosome number of x = 11 is the most probable in all the subtribes included in tribe Phaseoleae, although some aneuploid reduction is evident in Collaea and Galactia (Diocleinae) and chromosome duplications are seen in Amphicarpaea, Cologania and Glycine (Glycininae). The aims of this study were to improve the cytological knowledge of some species of Collaea and Galactia and to examine the anomalous counts reported for Calopogonium (Glycininae) and verify its taxonomic position. In addition, a molecular phylogeny was constructed using nuclear ribosomal DNA sequences (internal transcribed spacer region), and the chromosome number was optimized on the topology. In this work, the chromosome counts for Galactia lindenii, Galactia decumbens and Collaea cipoensis (all 2n = 20), and Calopogonium sericeum (2n = 22) are reported for the first time. The new reports for Galactia and Collaea species are in agreement with the chromosome number proposed for subtribe Diocleinae. The study rejects the concept of a cytologically anomalous Calopogonium and, based on the phylogenetic analysis, corroborates the position of this genus within subtribe Glycininae. The ancestral basic chromosome number of x = 11 proposed for Phaseoleae is in agreement with the evolutionary pathway of chromosome numbers analysed in this work. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 336,341. [source] Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysisCLADISTICS, Issue 2 2008Michael J. Bayly Pseudogenes from the 18S,5.8S,26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent "deep" ribosomal DNA paralogues that pre-date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses. © The Willi Hennig Society 2007. [source] | ||||||||||||||||||||||