I would like to generate phylogenetic distance metrics for groups of ITS2 sequences from different geographical locations. Obviously it is not possible to make an 'all fungi' phylogeny with ITS2 like you can with 16S for bacteria - so what I would like to know is what is the accepted minimum resolution for reasonably accurate phylogenetic reconstructions?
I am not sure why it is obviously not possible to build some type of all fungi phylogeny from the internal transcribed spacer region. A 2012 paper in PANS explored this topic and it looks reasonable to me.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List.
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6241-6. doi: 10.1073/pnas.1117018109. Epub 2012 Mar 27.
PMID: 22454494
No single gene or gene region is going to be best for all evolutionary questions about any organism, but these types of "barcoding" and classification/taxonomy/phylogeny projects require that the same genomic region be sequenced from thousands of different isolates/samples so one region that is useful needs to be chosen.
w.pnas.org/content/109/16/6241.long
I do not know how will it work with fungi (ITS2 create different problems problems within different groups of organisms). But there are examples of phylogenies on the base of ITS2 and its secondary structure for algae, e.g.
Mark A. Buchheim, Alexander Keller, Christian Koetschan, Frank Förster, Benjamin Merget, Matthias Wolf (2011):
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: Towards an automated reconstruction of the green algal tree of life
Plos One 6(2):e16931
More about tools and related publication you could find here.
http://its2.bioapps.biozentrum.uni-wuerzburg.de/
Paul,
I agree wit Brian, despite the all benefitial properties of IST2 and wide use of this region for plant phylgenetic/barcoding, it will be just a taxonomy of IST2 sequence, not taxonomy of the studied fungi.
Paul,
A general answer would be "at most genus/subfamily level", although in some genera you can't align the ITS region across the full genus (and still have a meaningful alignment).
Related reading: https://www.researchgate.net/publication/255483379_Towards_a_unified_paradigm_for_sequence-based_identification_of_Fungi
Article Towards a unified paradigm for sequence-based identification of Fungi
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