title: Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).
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.
authors.affiliation: AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
authors.forename: Christian
authors.initials: C
authors.lastname: Koetschan
authors.affiliation: AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
authors.forename: Sandra
authors.initials: S
authors.lastname: Kittelmann
authors.affiliation: AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
authors.forename: Jingli
authors.initials: J
authors.lastname: Lu
authors.affiliation: ViaLactia Biosciences Ltd., Newmarket, Auckland, New Zealand.
authors.forename: Djamila
authors.initials: D
authors.lastname: Al-Halbouni
authors.affiliation: New Zealand Trade and Enterprise, Wellington, New Zealand.
authors.forename: Graeme N
authors.initials: GN
authors.lastname: Jarvis
authors.affiliation: University of Würzburg, Department of Bioinformatics, Biocenter, Würzburg, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.affiliation: University of Würzburg, Department of Bioinformatics, Biocenter, Würzburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Wolf
authors.affiliation: AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Janssen
mesh_terms: D000693:Anaerobiosis; D001483:Base Sequence; D021903:DNA, Ribosomal Spacer / Q000737:chemistry* / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D008390:Markov Chains; D055136:Neocallimastigomycota / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010802:Phylogeny
chemical_list: D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers