Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)
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- 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 taxonomicThe 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.…
Autor(en): | Christian Koetschan, Sandra Kittelmann, Jingli Lu, Djamila Al-Halbouni, Graeme N. Jarvis, Tobias Müller, Matthias Wolf, Peter H. Janssen |
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URN: | urn:nbn:de:bvb:20-opus-117058 |
Dokumentart: | Artikel / Aufsatz in einer Zeitschrift |
Institute der Universität: | Fakultät für Biologie / Theodor-Boveri-Institut für Biowissenschaften |
Sprache der Veröffentlichung: | Englisch |
Titel des übergeordneten Werkes / der Zeitschrift (Englisch): | PLOS ONE |
Erscheinungsjahr: | 2014 |
Band / Jahrgang: | 9 |
Heft / Ausgabe: | 3 |
Seitenangabe: | e91928 |
Originalveröffentlichung / Quelle: | PLoS ONE 9(3): e91928. doi:10.1371/journal.pone.0091928 |
DOI: | https://doi.org/10.1371/journal.pone.0091928 |
PubMed-ID: | https://pubmed.ncbi.nlm.nih.gov/24663345 |
Allgemeine fachliche Zuordnung (DDC-Klassifikation): | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Freie Schlagwort(e): | ITS2; RNA sequence; diversity; herbivores; phylogenetic trees; populations; profile distances; reconstruction; systematics; tool |
Datum der Freischaltung: | 14.08.2015 |
Lizenz (Deutsch): | CC BY: Creative-Commons-Lizenz: Namensnennung |