Analysing fungal ITS data - questions about the pipeline - phylogenetic analysis

[Nicholas_Bokulich]

Hi @Cat ,

@Cat

whilst not often seen, the ITS1 region does produce a reasonable tree and is used frequently in published analyses including gold standard taxonomy papers from eg CBS.

This is sort of true — ITS alignments are sometimes used for examining phylogeny of closely related fungal species. Thus, fungal taxonomy papers (which are generally concerned with parsing closely related species/groups) will sometimes use this for comparison of isolated strains.

@Cat

I would argue that a taxonomy paper is a far cry from a mycobiome study

Indeed it is. In a mycobiome study you are almost inevitably comparing fungi from highly divergent groups. ITS will not generate a reliable alignment/phylogeny for such divergent groups.

As a non-coding region, it is highly variable, which is a two-edged sword: on the one hand, this means that it can be used to differentiate even many closely related species (taxonomically and phylogenetically) but on the other hand the mutation rate is so high that it loses the "molecular clock" aspects of conserved genes (such as rRNA genes) that are used for molecular phylogeny of highly divergent groups.

This looks like a relevant paper on the topic:
https://www.sciencedirect.com/science/article/pii/S1055790302003664?via%3Dihub

I hope that helps!