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Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

Please always quote using this URN: urn:nbn:de:bvb:20-opus-117058
  • 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.show moreshow less

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Metadaten
Author: Christian Koetschan, Sandra Kittelmann, Jingli Lu, Djamila Al-Halbouni, Graeme N. Jarvis, Tobias Müller, Matthias Wolf, Peter H. Janssen
URN:urn:nbn:de:bvb:20-opus-117058
Document Type:Journal article
Faculties:Fakultät für Biologie / Theodor-Boveri-Institut für Biowissenschaften
Language:English
Parent Title (English):PLOS ONE
Year of Completion:2014
Volume:9
Issue:3
Pagenumber:e91928
Source:PLoS ONE 9(3): e91928. doi:10.1371/journal.pone.0091928
DOI:https://doi.org/10.1371/journal.pone.0091928
Pubmed Id:http://www.ncbi.nlm.nih.gov/pubmed?term=24663345
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Tag:ITS2; RNA sequence; diversity; herbivores; phylogenetic trees; populations; profile distances; reconstruction; systematics; tool
Release Date:2015/08/14
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung