Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling.

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Molecular Phylogenetics and Evolution

• Publication date

  2013-04-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/j.ympev.2013.01.018PMID 23403224
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• R: A language and environment for statistical computing.

  2014cited by this paper
• New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities.

  2012cited by this paper
• MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

  2011cited by this paper
• Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology

  2011cited by this paper
• UCHIME improves sensitivity and speed of chimera detection

  2011cited by this paper
• Discovery of novel intermediate forms redefines the fungal tree of life

  2011influential reference
• Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

  2011cited by this paper
• Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota).

  2010cited by this paper
• TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

  2010cited by this paper
• Structure and resilience of fungal communities in Alaskan boreal forest soils

  2010cited by this paper
• The environmental clade LKM11 and Rozella form the deepest branching clade of fungi.

  2010cited by this paper
• High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: incomplete concerted evolution and the origin of pseudogenes.

  2010cited by this paper
• Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium.

  2009influential reference
• The ITS2 Database III—sequences and structures for phylogeny

  2009cited by this paper
• An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.

  2009cited by this paper
• Consensus Structure Prediction for RNA Alignments

  2009cited by this paper
• Mesquite: a modular system for evolutionary analysis. Version 2.6

  2009cited by this paper
• The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.

  2009influential reference
• Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA

  2009cited by this paper
• Random number generation for DNA-based security circuitry

  2008cited by this paper
• Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus.

  2008influential reference
• Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life.

  2008cited by this paper
• Fine-Scale Phylogeographic Congruence Despite Demographic Incongruence in Two Low-Mobility Saproxylic Springtails

  2008cited by this paper
• Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

  2008cited by this paper
• BMC Bioinformatics BioMed Central Methodology article RNAalifold: improved consensus structure prediction for RNA

  2008cited by this paper
• The Vienna RNA Websuite

  2008cited by this paper
• Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

  2008cited by this paper
• Domain II Hairpin Structure in ITS1 Sequences as an Aid in Differentiating Recently Evolved Animal and Plant Pathogenic Fungi

  2008cited by this paper
• 5.8S motifs for the identification of pseudogenic ITS regions

  2008cited by this paper
• Soil Fungal Communities Underneath Willow Canopies on a Primary Successional Glacier Forefront: rDNA Sequence Results Can Be Affected by Primer Selection and Chimeric Data

  2007influential reference
• Enhancements and modifications of primer design program Primer3

  2007cited by this paper
• Pan-eukaryote ITS2 homologies revealed by RNA secondary structure

  2007influential reference
• Distinguishing gorilla mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases.

  2007cited by this paper
• TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction.

  2007cited by this paper
• The protistan origins of animals and fungi.

  2006cited by this paper
• Reconstructing the early evolution of Fungi using a six-gene phylogeny

  2006cited by this paper
• Phylogeny of the Zygomycota based on nuclear ribosomal sequence data.

  2006cited by this paper
• RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

  2006cited by this paper
• Non-concerted ITS evolution in Mammillaria (Cactaceae).

  2006influential reference
• Unusual compact rDNA gene arrangements within some members of the Ascomycota: evidence for molecular co-evolution between ITS1 and ITS2.

  2005influential reference
• A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota.

  2005influential reference
• PCR-generated artefact from 16S rRNA gene-specific primers.

  2005cited by this paper
• Assessment of Ribosomal Large-Subunit D1-D2, Internal Transcribed Spacer 1, and Internal Transcribed Spacer 2 Regions as Targets for Molecular Identification of Medically Important Aspergillus Species

  2005cited by this paper
• Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics.

  2005cited by this paper
• Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.

  2005cited by this paper
• Which side of the tree is more basal?

  2004cited by this paper
• Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

  2004cited by this paper
• NUMTs in sequenced eukaryotic genomes.

  2004cited by this paper
• On the unreliability of published DNA sequences.

  2003cited by this paper
• Seasonal Dynamics of Previously Unknown Fungal Lineages in Tundra Soils

  2003cited by this paper
• Pseudogenes: are they "junk" or functional DNA?

  2003cited by this paper
• MrBayes 3: Bayesian phylogenetic inference under mixed models

  2003influential reference
• Vienna RNA secondary structure server

  2003cited by this paper
• Contamination and chimerism are perpetuating the legend of the snake-eating cow with twisted horns (Pseudonovibos spiralis). A case study of the pitfalls of ancient DNA.

  2003cited by this paper
• Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.

  2003cited by this paper
• Secondary structure prediction for aligned RNA sequences.

  2002cited by this paper
• Molecular diversity and phylogenetic affinities of symbiotic root-associated ascomycetes of the Helotiales in burnt and metal polluted habitats.

  2002cited by this paper
• Using secondary structure to identify ribosomal numts: cautionary examples from the human genome.

  2002influential reference
• A new fungal phylum, the Glomeromycota: phylogeny and evolution * * Dedicated to Manfred Kluge (Tech

  2001cited by this paper
• Molecular Phylogenetics and Evolution

  2001cited by this paper
• Multiplex PCR Using Internal Transcribed Spacer 1 and 2 Regions for Rapid Detection and Identification of Yeast Strains

  2001cited by this paper
• Polymorphic Internal Transcribed Spacer Region 1 DNA Sequences Identify Medically Important Yeasts

  2001cited by this paper
• Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale

  2001cited by this paper
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.

  2000cited by this paper
• Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

  2000cited by this paper
• EMBOSS: the European Molecular Biology Open Software Suite.

  2000cited by this paper
• A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes.

  2000cited by this paper
• Community structure of ectomycorrhizal fungi in a Pinus muricata forest: minimal overlap between the mature forest and resistant propagule communities

  1999cited by this paper
• Structural equivalence in the transcribed spacers of pre-rRNA transcripts in Schizosaccharomyces pombe.

  1999cited by this paper
• Construction of a variability map for eukaryotic large subunit ribosomal RNA.

  1999cited by this paper
• Database on the structure of large subunit ribosomal RNA

  1999cited by this paper
• A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution

  1998cited by this paper
• MODELTEST: testing the model of DNA substitution

  1998influential reference
• Conserved core structure in the internal transcribed spacer 1 of the Schizosaccharomyces pombe precursor ribosomal RNA.

  1998cited by this paper
• The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants

  1997cited by this paper
• Mitochondrial DNA: molecular fossils in the nucleus.

  1996cited by this paper
• Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins.

  1993cited by this paper
• ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts

  1993cited by this paper
• Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences.

  1992cited by this paper
• GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes

  1990cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• A universal model for the secondary structure of 5.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent.

  1984cited by this paper
• Chinese Academy of Sciences, Beijing, People’s Republic of China.

  year unknowncited by this paper
• Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm

  year unknowncited by this paper

• Ceratobasidium oryzicola, a new fungal species causing sheath blight on rice in Brazil

  2025cites this paper
• Development of a recombinase-aided amplification coupled with lateral flow dipstick assay for tobacco Corynespora leaf spot disease detection

  2025cites this paper
• Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples

  2021cites this paper
• High-throughput sequencing view on the magnitude of global fungal diversity

  2021cites this paper
• Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

  2021cites this paper
• High-throughput sequencing view on the magnitude of global fungal diversity

  2021cites this paper
• Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference

  2019cites this paper
• Secondary structure prediction of ITS rRNA region and molecular phylogeny: an integrated approach for the precise speciation of Muscodor species

  2018cites this paper
• Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

  2018cites this paper
• Pathogenicity and rDNA-ITS sequence analysis of the Corynespora cassiicola isolates from rubber plantations in Indonesia

  2017influential citation
• Sequence-based classification and identification of Fungi

  2016cites this paper
• The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

  2016cites this paper
• The Soil Fungi

  2015cites this paper
• A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

  2015cites this paper
• Surveying the biodiversity of the Cryptomycota using a targeted PCR approach

  2015cites this paper
• Clone Libraries of Ribosomal RNA Gene Sequences for Characterization of Microbial Communities

  2015cites this paper
• Nuclear rDNA pseudogenes in Chagas disease vectors: evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North, Central and northern South America.

  2014cites this paper
• Habitat preferences, distribution, and temporal persistence of a novel fungal taxon in Alaskan boreal forest soils

  2014cites this paper
• A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

  2014cites this paper
• RESEARCH ARTICLE INTERNAL TRANSCRIBED SPACER (ITS), ITS 2 BASED IDENTIFICATION OF ENDOPHYTIC FUNGI FROM MILLINGTONIAHORTENSISAND TABEBUIASP

  2014cites this paper
• Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region

  2014cites this paper