ITS Non phylogentically-informative marker gene Inquiry

[Patrick]

Dear all,

As refer to tutorial below, http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/Fungal-ITS-analysis.ipynb

Am I right that ITS is Non phylogentically-informative marker gene while 16S/18S are phylogentically-informative marker gene?

That explain why the ITS tutorial did not built a phylogenetic tree for ITS sequence but we need to build a phylogenetic tree for 16S/18S sequence?

Thanks for any advice.

best regards

Patrick

UM Student

[Colin Brislawn]

Hello Patrick,

This is a great question. In theory, all genes are 'phylogentically-informative' because their encoding shows their genetic history. However, in practice, some genes are more useful than others. 16S is especially useful for amplicons, because it contains highly conserved regions interspaced with more variable regions. ITS is less useful because it contains large regions which don't align well, so using it to reconstruct phylogeny is hard / impossible. 

That explain why the ITS tutorial did not built a phylogenetic tree for ITS sequence

Yes. The trees you can build are not reliable. 

When you build a .tre file, you can calculate UniFrac distances. However, you can still calculate other beta diversity things, like Bray-Curtis Dissimilarities without the tree.

I hope that helps,

Colin

 

[Patrick]

Dear Colin,

Many thanks for your explanation regarding phylogentically-informative among 16S, 18S and ITS in practical.

Really thanks for your knowledge sharing.

I learn a lot from you :)

Thanks.

best regards

Patrick

[Colin Brislawn]

I'm glad to help. Keep in touch,

Colin

[Patrick]

Dear Colin,

Sure.

I will let you know if I have any inquiry regarding Qiime to analyse 16S and ITS data.

Thanks.

best regards

Patrick