Constructing a fungal ITS phylogeny tree

[David Toole]

Hello,

I've been working with fungal ITS data in QIIME to ultimately get an otu table (otu_table_mc2_w_tax.biom) and a phylogenetic tree (rep_set.tre). So far, I've been able to get the otu table through assign_taxonomy.py followed by biom add-metadata, but in order to run align_seqs.py with pynast method, I would need a fungal ITS template (since the default is set to greengenes for 16S data). I am using the Unite database and the directory that I've downloaded it to has .fasta files and .txt files, but I'm not sure if it's maybe possible to create a template file from these.  Does anybody know how I can either create or find a template file or should I go about this using de novo picking instead?

Thanks for any and all help,

David

[Sophie]

Hi David,

Have you seen this post?  Tony's post here may also be helpful.  You'll have to suppress the alignment/tree building step.  If this doesn't help, please let us know.

Thanks,

Sophie

[Andrew Krohn]

For what it's worth, I usually go through the exercise of doing alignments and building trees of my ITS data, although I know they aren't great quality (neither do the templated 16S alignments that I have generated - always use the gg tree for downstream analyses), but the output is still quite reasonable given everything else.  Even for bacteria I prefer bray curtis as it seems to be the most sensitive to differences among treatments.

Anyway, I just run mafft for my alignment, filter the alignment (-e 0.1), then build phylogeny with fasttree.  I spent a month or two trying to get something I could actually use given my own data, and eventually just gave up.  Hibbet et al is probably the most current paper on fungal phylogeny, and mentions the taxonomy resources available via genbank and a few other sources.  The page here (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4751&session=1RQm4JH7uol2JyDU40v9ne1x_8Pfm2op8ZGuYoTkiZv7EZSeASEWSH9xxicMaum5z8tPTthJpng80Ja9pIbQRLuDV4IP4ApFLUpCelbTl9tVdzn5JvZFlg8casSDx8JQxyPI0HA&opsess=1lI4x4N4cLxsLouOvppnq8ZJeT8G9jg0-a8h-_dSN1UbN0EnQA8z0_C4FZCQVbP7HOj7TGJKW7BNEgzbIfgUJVqh9LYazCW1WlkUK7gqAQBczGefQqq37rtNwQ0sq6srqvYHMit) may help you to find a useful tree to get started, and then try to restrict your individual tree building efforts to certain groups.  Then it may be a cut and paste affair of newick-formatted trees in a text editor to graft your fine scale phylogenies onto the master phylogeny.  This is the advice I have been given, but luckily I found I don't need this right now.  Let us all know if you find a publicly available tree that you like and trust for fungi.

[Sophie]

Thanks for letting us know about your work.  We'll definitely let you all know if we find a good solution.

Sophie

[David Toole]

Thanks Sophie: I did see the first post, but the second one was very helpful with adjusting the default parameters to get a better OTU table. Even though I don't have a tree yet, I feel much more comfortable with this OTU table than the previous one I had made.

And Andrew: Thanks for the input, I will definitely check out that page tonight or tomorrow and post back with any useful progress/results on getting a suitable tree...or if I get stuck somewhere. That will probably happen too.

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