Phylogenetic placement on a ghost-tree

[vmikk]

Dear Jennifer and ghost-tree team, Is it possible to perform a phylogenetic placement of sequences on a ghost-tree (e.g., with pplacer, EPA, SEPP or others)? Or it is impossible in principle, because of a hybrid nature of this tree?

With best regards, Vladimir

[JTFouquier]

Hi @vmikk, sorry for the delay.

I'm a bit confused by your question because ghost-tree was designed to build a phylogenetic tree using sequence data/phylogenetic information from a marker gene that provides high taxonomic resolution. I'm also not familiar with these specific methods and neither were some of my colleagues. Can you please expand/clarify your question?

I'm not sure if you found the paper first or the tool, so here is the paper if you have not seen it. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0153-6

Thank you!

[vmikk]

Hello Jennifer! Thank you for the reply.

Sorry, I should clarify my question. The next step after obtaining of DNA sequences is the identification of species to which they belong. There are different approaches for identification – the most common are the similarity-based search (e.g. BLAST) or a Bayesian classification (e.g., RDP). However there is another approach that allows inferring the position of (short) reads on an existing phylogenetic tree – so called ‘phylogenetic placement’.

In brief, it is possible to find the placement of sequences of interest on a reference phylogenetic tree given that one have the sequences that were used to build this tree. This method does not assign names to query sequences, but instead it returns an assignment of the query sequences to edges of a phylogenetic tree.

If I understand it correctly, to perform phylogenetic placement one will need to specify the model of sequence evolution, which will be problematic for a hybrid tree. So the question was about the possibility of usage of the ghost-tree in such applications.

More about phylogenetic placement:

• Matsen et al. BMC Bioinformatics 2010 11:538 DOI: 10.1186/1471-2105-11-538
• Zhang et al. Bioinformatics 2013 29:22 DOI: 10.1093/bioinformatics/btt499

[vmikk]

It seems that the problem is even more complicated.

Assume that one sequenced the SSU and wish to place it on a foundation tree from ghost-tree. It will be problematic because the sequences from SILVA (that were used to build the foundation tree) were gap- and entropy filtered and hence they are not directly comparable with the query sequences.

By the way, here and here are short tutorials for phylogenetic placement for the 16S rRNA gene by Jeff Bowman. I hope that one day this approach will be easy accessible for fungi.

[JTFouquier]

Hi @vmikk, I'll likely get to this on Sunday. I've been super busy getting ready for my wedding and honeymoon (1 week away), so I am sorry for the delay.

[vmikk]

Hello Jennifer! Actually I thought that if we have phylogenetic tree with fine resolution (ghost-tree) and DNA sequences from SILVA & UNITE we will be able to identify shorter query sequences and place them on this tree. But now I see that this is out of the scope of ghost-tree and will require quite different approach.

Wishing you the very best on your wedding day and I hope you'll have a fantastic honeymoon! With best regards, Vladimir

[JTFouquier]

Thanks for putting so much thought into this and for the well wishes! I plan to do more development on this project in a few months after things calm down. I'll also be moving out of state, so I apologize if I am out of touch for a few months. Thank you! -Jennifer

[JTFouquier]

@vmikk... I'm closing this now. Did you need anything else with this issue? Thanks!