Large Subunit Ribosomal RNA Sequences Research Articles

Megx.net: integrated database resource for marine ecological genomics.

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.

Phylogenetic analysis of two putative Nosema isolates from Cruciferous Lepidopteran pests in Taiwan

In this study, a new microsporidian, PX2, was isolated from the diamondback moth, Plutella xylostella, and then compared with another isolate (PX1), and with Nosema spodopterae and N. bombycis. Sequence data showed that the rRNA gene organizations of PX1 and PX2 exhibited a typical Nosema-specific organization: 5′-LSUrRNA (large subunit ribosomal RNA)-ITS (internal transcribed spacer)-SSUrRNA-IGS (intergenic spacer)-5S-3′. Phylogenetic analysis (maximum likelihood, neighbor joining, maximum parsimony, and Bayesian analysis) of the LSUrRNA and SSUrRNA gene sequences, and the sequences of the alpha-tubulin, beta-tubulin, and RPB1 (DNA dependent RNA polymerase II largest subunit) genes found that PX1 was closer to N. bombycis and N. spodopterae than to PX2. Comparison of the identities of the rRNA domains and of the other three genes showed a high divergence in the sequences of the rRNA spacer regions (ITS and IGS). This is consistent with the hypothesis that PX2, if not PX1, might represent a new Nosema species.

First complete large subunit ribosomal RNA sequence and secondary structure for a parasitic nematode: phylogenetic and diagnostic implications

The complete sequence and secondary structure of the large subunit of nuclear ribosomal RNA(LSUrRNA) were determined for the parasitic nematode Labiostrongylus bipapillosus (order Strongylida). Its LSU rRNA sequence was shorter (by 18 bp) than that of the free-living nematode, Caenorhabditis elegans (order Rhabditida), the only other species within the Nematoda for which a complete LSU rRNA sequence has been determined. Interspecific differences in sequence were greater in the 12 D domains compared with the core segments, with the secondary structure being maintained by partial or complete compensatory base pair changes. The magnitude of interspecific sequence difference in each D domain (except for D6 and D12) was similar, suggesting that several domains contain informative genetic markers for phylogenetic studies of the phylum Nematoda at different taxonomic levels. The LSU rRNA may also provide species-specific markers for the identification of some bursate nematodes of veterinary and medical importance.

The European Large Subunit Ribosomal RNA Database.

The European Large Subunit Ribosomal RNA Database compiles all complete or nearly complete large subunit ribosomal RNA sequences available from public sequence databases. These are provided in aligned format and the secondary structure, as derived by comparative sequence analysis, is included. Additional information about the sequences such as literature references and taxonomic information is also included. The database is available from our WWW server at http://rrna.uia.ac.be/lsu/.

Phylogenetic relationships of ophiostomatoid fungi associated with Protea infructescences in South Africa

Five ophiostomatoid taxa have been found associated with the infructescences of Protea species, an ancient group of flowering plants endemic to South Africa. Two of these fungi are characterized by their unusual Knoxdavesia anamorphs and have been placed in Gondwanamyces. The three remaining species have Sporothrix anamorphs and have accordingly been accommodated in Ophiostoma. The phylogenetic relationships between the fungi associated with Protea spp. and other ophiostomatoid fungi in Ceratocystis and Ophiostoma are unknown. Large subunit ribosomal RNA sequence data was obtained for the fungi associated with Protea infructescences as well as for the type species of Ceratocystis and Ophiostoma. Both groups of ophiostomatoid fungi were phylogenetically distinct from either Ceratocystis or Ophiostoma, despite sharing morphological and physiological characters with these genera. The species of Ophiostoma associated with Protea infructescences group within the Ophiostomatales while species of Gondwanamyces group within the Microascales. Furthermore, the Ophiostoma spp. from Protea should reside in a separate genus and are a fascinating example of convergent evolution towards insect dispersal. Ceratocystis sensu lato includes Ceratocystis sensu stricto, Ceratocystiopsis and Ophiostoma. Species of Ceratocystis are very dierent from species of Ceratocystiopsis and Ophiostoma based on morphological, physiological and molecular data

Fine structure of the flagellar apparatus and morphological details of Gymnodinium nolleri sp. nov. (Dinophyceae), an unarmored dinoflagellate producing a microreticulate cyst

A naked dinoflagellate producing microreticulate cysts is described as Gymnodinium nolleri sp. nov. It was previously misidentified as Gymnodinium catenatum based on strong morphological similarity with this species in both the cyst and motile stages. Gymnodinium nolleri differs from G. catenatum primarily in the size of the cyst and the vegetative stage, G. nolleri being smaller, although there is overlap, particularly in the size of the vegetative cell. The cyst of G. nolleri is 28–38 μm in diameter, whereas G. catenatum measures 38–59 μm. The vegetative cell of G. nolleri on average is 26 × 33 μm and G. catenatum is 36 × 45 μm. The motile stage of G. nolleri never forms long chains, whereas such chains are common in G. catenatum. The cyst of G. nolleri has fewer rows of polygons in the paracingulum than G. catenatum, and the polygons on the cyst are generally slightly smaller, although they appear larger due to the smaller size of the cyst. These differences and earlier described differences at the molecular level (large subunit ribosomal RNA sequence, isozyme profile, lack of paralytic shellfish poisoning (PSP) toxins in G. nolleri) justify describing G. nolleri as a new species. The fine structure of the flagellar apparatus of G. nolleri is included in the description. It shows features common to most dinoflagellates studied so far and has many similarities with the flagellar apparatus of ‘Gymnodinium sp.' of Roberts (1986) and G. catenatum, e.g. a nuclear fibrous connective, longitudinal microtubular root–longitudinal basal body connectives, and a longitudinal microtubular root–ventral ridge connective.

Database on the structure of large ribosomal subunit RNA.

The rRNA WWW Server at URL http://rrna.uia.ac.be/ now provides a database of 496 large subunit ribosomal RNA sequences. All these sequences are aligned, incorporate secondary structure information, and can be obtained in a number of formats. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available and searchable. If necessary, the data on the server can also be obtained by anonymous ftp.

Complete large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale, and phylogenetic analysis.

The large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale were determined. These sequences were combined with small subunit ribosomal RNA sequences in order to carry out a phylogenetic analysis based on neighbor-joining, maximum parsimony, and maximum likelihood methods. Our results indicate that heterokont fungi and heterokont algae each are monophyletic, and confirm that they together form a monophyletic group called "stramenopiles." Within the heterokont algae, the eustigmatophyte Nannochloropsis salina either clusters with the chrysophyte Ochromonas danica or forms a sister group to a cluster comprising the phaeophyte Scytosiphon lomentaria and the xanthophyte Tribonema aequale. The alveolates were identified as the closest relatives of the stramenopiles, but the exact order of divergence between the eukaryotic crown taxa could not be established with confidence.

The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides.

Based on biochemical and ultrastructural data, hyphochytriomycetes are believed to share an ancestor with oomycetes and heterokont algae. In order to study the phylogeny of the hyphochytriomycetes, we determined both the small- and large-subunit ribosomal RNA sequence of Hyphochytrium catenoides. Phylogenetic trees were constructed using the neighbor-joining and maximum-parsimony method and include representatives of Chlorobionta, Fungi, Metazoa, Alveolata, and all known Heterokonta. Our main conclusion is that the hyphochytriomycetes form a monophyletic group with the oomycetes and heterokont algae and that they are probably the closest relatives of the oomycetes. However, the order of divergence between the various heterokont algal phyla and the oomycete-hyphochytriomycete cluster remains uncertain.

Theileria: Improved Species Discrimination Using Oligonucleotides Derived from Large Subunit Ribosomal RNA Sequences

Partial nucleotide sequences of large subunit ribosomal RNA (LSU rRNA) coding genes of Theileria parva and T. taurotragi were determined. Alignment of the T. parva and T. taurotragi sequences revealed species-specific regions within the LSU rRNA genes. A major species-variable region, located between the first and second conserved secondary structure domains of LSU rRNA, was identified. The sequence of the major species-variable region was determined for T. annulata, T. buffeli, and an unclassified Theileria species isolated from buffalo. Species-specific oligonucleotides complementary to LSU rRNA sequences were designed for five species of Theileria. The oligonucleotide probes discriminated between Theileria species when hybridized to amplified parasite LSU rRNA genes or directly to parasite rRNA. Three species-specific oligonucleotides derived from nonoverlapping sequences were developed for each of T. parva and T. taurotragi. A simplified procedure was developed in which T. parva- and T. taurotragi-specific oligonucleotides were used to discriminate the two species under nonstringent hybridization and washing conditions. Use of the nonstringent conditions also increased the sensitivity of target detection. Comparison of Theileria species-specific oligonucleotides derived from large subunit and small subunit rRNA genes demonstrated that, for closely related species, probes derived from LSU rRNA sequences had improved specificity.