Dealing with Taxonomic Inconsistencies in Reference Trees of Functional Gene for pplacer

[Zhu Agathe]

Hi Eric and all,

I am currently using pplacer to place amplicon sequences targeted by a universal nifH primer set onto a reference phylogenetic tree. Since the nifH gene is highly diverse in taxonomy and prone to horizontal gene transfer across different taxa, the reference tree I constructed - using the nifHdada2 database as reference - shows intermixed taxa and genus-level clusters that do not fully align with the expected taxonomy.

I am wondering whether such phylogenetic "mixing" in nifH trees could potentially affect the accuracy or reliability of the placements made by pplacer. If so, are there any recommendations you could offer to improve either the phylogenetic tree construction or the downstream placement results?

 I would greatly appreciate any insights or suggestions. Please let me know if you would like me to provide more detailed information.

[Erick Matsen]

Hello Zhu--

Are you just doing placement, or are you also doing taxonomic classification? 

If it's the former, and the HGTs are on the gene level rather than gene fragment level, you can place sequences and it will be correct phylogenetically. OTOH it may not be helpful for your particular goals.

My only suggestions are to make sure that you are dealing with a sequence alignment that doesn't contain breakpoints. 

Erick

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