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PLoS One. 2014 Mar 24;9(3):e91928. doi: 10.1371/journal.pone.0091928. eCollection 2014.

Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).

Author information

1
AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
2
ViaLactia Biosciences Ltd., Newmarket, Auckland, New Zealand.
3
New Zealand Trade and Enterprise, Wellington, New Zealand.
4
University of Würzburg, Department of Bioinformatics, Biocenter, Würzburg, Germany.

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.

PMID:
24663345
PMCID:
PMC3963862
DOI:
10.1371/journal.pone.0091928
[Indexed for MEDLINE]
Free PMC Article

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