Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)
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{"title"=>"Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota)", "type"=>"journal", "authors"=>[{"first_name"=>"Christian", "last_name"=>"Koetschan", "scopus_author_id"=>"35345210000"}, {"first_name"=>"Sandra", "last_name"=>"Kittelmann", "scopus_author_id"=>"23397427600"}, {"first_name"=>"Jingli", "last_name"=>"Lu", "scopus_author_id"=>"56146577000"}, {"first_name"=>"Djamila", "last_name"=>"Al-Halbouni", "scopus_author_id"=>"14055492900"}, {"first_name"=>"Graeme N.", "last_name"=>"Jarvis", "scopus_author_id"=>"56147022400"}, {"first_name"=>"Tobias", "last_name"=>"Müller", "scopus_author_id"=>"55252939100"}, {"first_name"=>"Matthias", "last_name"=>"Wolf", "scopus_author_id"=>"7402497634"}, {"first_name"=>"Peter H.", "last_name"=>"Janssen", "scopus_author_id"=>"7201762494"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84899757626", "pmid"=>"24663345", "pui"=>"373006655", "issn"=>"19326203", "scopus"=>"2-s2.0-84899757626", "doi"=>"10.1371/journal.pone.0091928"}, "id"=>"8a51edbb-4185-3582-ac31-340fbed1b50d", "abstract"=>"The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments.", "link"=>"http://www.mendeley.com/research/internal-transcribed-spacer-1-secondary-structure-analysis-reveals-common-core-throughout-anaerobic", "reader_count"=>24, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>6, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>6, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>14, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Czech Republic"=>1, "United States"=>1, "Brazil"=>1, "United Kingdom"=>1, "Chile"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1433159"], "description"=>"<p>(<b>A</b>) The secondary structure of the ITS1 region of JF423742 (selected as an example) illustrates the common core shape observed in all analysed neocallimastigomycete sequences. It folds into a three helix conformation, with two short helices (I and III) and a longer one in between (II). Additionally, four very conserved sequence motifs are highlighted in the structure. (<b>B</b>) The black bar shows a nucleotide string of rDNA. On the left is the terminus of the 18S rRNA gene, with its 18S HMM. Together with the 5.8S HMM motif on the right, both enable an exact delineation of the ITS1 region.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "motifs"], "article_id"=>972620, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_secondary_structure_sequence_motifs_and_sequence_annotation_/972620", "title"=>"Visualization of secondary structure, sequence motifs and sequence annotation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433168"], "description"=>"<p>Number and per cent of anaerobic fungal ITS1 secondary structures that folded into a total of 2 to 9 different helices using energy minimization by UNAFold 3.8.1.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "structures", "anaerobic", "fungal", "its1"], "article_id"=>972629, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.t001", "stats"=>{"downloads"=>3, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Secondary_structures_of_anaerobic_fungal_ITS1_sequences_/972629", "title"=>"Secondary structures of anaerobic fungal ITS1 sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433167"], "description"=>"<p>The “Start” and “Stop” region marked in the Table represent the nucleotides before the first and after the third helix, respectively. “Inter 1” and “Inter 2” represent interhelical regions between first and second and second and third helix, respectively.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "elements", "neocallimastigomycete", "its1", "regions"], "article_id"=>972628, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.t002", "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AT_content_of_different_structural_elements_from_neocallimastigomycete_ITS1_regions_in_per_cent_/972628", "title"=>"AT content of different structural elements from neocallimastigomycete ITS1 regions in per cent.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433164"], "description"=>"<p>(<b>A</b>) Parts of the consensus secondary ITS1 structure of GQ850303 and JF423532 from helix II. Marked in yellow are compensatory base changes between the two sequences. (<b>B</b>) Partial consensus secondary ITS1 structure of JF423714 and JX184822. CBCs occurring in helix I are highlighted in yellow.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "visualization", "neocallimastigomycete", "its1"], "article_id"=>972625, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.g003", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CBC_visualization_of_neocallimastigomycete_ITS1_regions_/972625", "title"=>"CBC visualization of neocallimastigomycete ITS1 regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433162"], "description"=>"<p>ITS1 secondary structures from (<b>A</b>) EU414759, (<b>B</b>) HQ832485 and (<b>C</b>) JF423612. The illustrated structures did not fold into the typical three helix conformation when folded initially with UNAFold (upper images). By breaking the sequences into three parts based on the known location of sequence motifs, each part could be folded individually. The concatenated helices (bottom images) result in the typical three-helix common core structure predicted by the direct folding of the majority of all annotated sequences.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "structures", "its1"], "article_id"=>972623, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.g002", "stats"=>{"downloads"=>3, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Secondary_structures_of_the_ITS1_region_from_three_different_sequence_types_/972623", "title"=>"Secondary structures of the ITS1 region from three different sequence types.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433169", "https://ndownloader.figshare.com/files/1433170", "https://ndownloader.figshare.com/files/1433171", "https://ndownloader.figshare.com/files/1433172", "https://ndownloader.figshare.com/files/1433173"], "description"=>"<div><p>The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments.</p></div>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "transcribed", "spacer", "reveals", "anaerobic"], "article_id"=>972630, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0091928.s001", "https://dx.doi.org/10.1371/journal.pone.0091928.s002", "https://dx.doi.org/10.1371/journal.pone.0091928.s003", "https://dx.doi.org/10.1371/journal.pone.0091928.s004", "https://dx.doi.org/10.1371/journal.pone.0091928.s005"], "stats"=>{"downloads"=>8, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Internal_Transcribed_Spacer_1_Secondary_Structure_Analysis_Reveals_a_Common_Core_throughout_the_Anaerobic_Fungi_Neocallimastigomycota_/972630", "title"=>"Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433166"], "description"=>"<p>Sequences could either be folded into the three-helix core structure using both direct folding and helix-wise folding (direct and helix-wise folding) or only by helix-wise folding (helix-wise folding only). All 575 sequence-structure combinations were used for phylogenetic tree inference.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "sequence-structure", "combinations", "included", "phylogenetic", "ordered", "taxonomic"], "article_id"=>972627, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.t003", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_sequence_structure_combinations_included_in_phylogenetic_tree_reconstruction_ordered_by_taxonomic_group_/972627", "title"=>"Number of sequence-structure combinations included in phylogenetic tree reconstruction, ordered by taxonomic group.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-24 03:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1433165"], "description"=>"<p>Profile Neighbor Joining tree calculated using sequence and structure data from 1120 (575 unique) complete neocallimastigomycete ITS1 sequences with 1000 bootstrap replicates in 29 iterations. Open circles indicate bootstrap values in a range of 50 to 90, closed circles indicate a bootstrap value above 90, and the scale bar indicates the distance. The tree contains the six known genera <i>Anaeromyces</i>, <i>Caecomyces</i>, <i>Cyllamyces</i>, <i>Neocallimastix</i>, <i>Orpinomyces</i> and <i>Piromyces</i>. and the unclassified sequences GQ850325, AF170206 and AF170205. Other monophyletic groups are highlighted and named according to Kittelmann <i>et al.. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091928#pone.0091928-Kittelmann1\" target=\"_blank\">[10]</a>. A total of ten sequences did not cluster into any of the defined groups and were named according to their accession numbers only (JF423517, JF423484, JF423882, GU055516, JX184570, JF423626, JF423625, GQ850325, AF170205, and AF170206). Sequences, accession numbers and taxonomic classifications (including definitions of subclusters of the genera <i>Cyllamyces</i>, <i>Orpinomyces</i> and <i>Piromyces</i>) are available from the taxonomy file (File S2). Subcluster Orpinomyces 3 is not represented in this tree due to the lack of full-length ITS1 sequences for this group. A comparison of bootstrap values from this study to the sequence–only analysis of Kittelmann <i>et al.. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091928#pone.0091928-Kittelmann1\" target=\"_blank\">[10]</a> is given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091928#pone.0091928.s005\" target=\"_blank\">Table S1</a>. YE505  =  <i>Anaeromyces mucronatus</i> YE505.</p>", "links"=>[], "tags"=>["Biochemistry", "rna", "RNA structure", "Nucleic acids", "Computational biology", "Evolutionary biology", "Evolutionary systematics", "Molecular systematics", "phylogenetics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "Sequence databases", "Macromolecular structure analysis", "Mycology", "organisms", "fungi", "joining", "neocallimastigomycete", "its1"], "article_id"=>972626, "categories"=>["Biological Sciences"], "users"=>["Christian Koetschan", "Sandra Kittelmann", "Jingli Lu", "Djamila Al-Halbouni", "Graeme N. Jarvis", "Tobias Müller", "Matthias Wolf", "Peter H. Janssen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091928.g004", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Profile_Neighbor_Joining_tree_of_neocallimastigomycete_ITS1_sequences_/972626", "title"=>"Profile Neighbor Joining tree of neocallimastigomycete ITS1 sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:44:53"}

PMC Usage Stats | Further Information

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Relative Metric

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