Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi NeocallimastigomycotaReport as inadecuate




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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 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.



Author: Christian Koetschan, Sandra Kittelmann , Jingli Lu, Djamila Al-Halbouni, Graeme N. Jarvis, Tobias Müller, Matthias Wolf, Peter H

Source: http://plos.srce.hr/



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