Hi, I am running orthofinder and Busco_phylogenomic on my species of interest (a generalist in the intertidal zone). My question is comparing the evolution between these species driving the adaptation to the intertidal region. Some species in the family have evolved to be terrestrial as well.
I am comparing it to a root species, 5 from the family and 2 from the genus. I was thinking of adding additional species. The problem is the published genome assemblies do not all have annotations, so I was aiming to run Busco_phylogenomics.
Does general phylogenists annotate other published assemblies and run orthofinder? What is the gold standard for phylogeny/how many species?
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written
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thrivenow •
1 answer
There are some pretty good ab initio annotation pipelines you can run quite quickly (depending on genome size and complexity), especially if you have access to a computing cluster and some GPUs (Helixer is GPU accelerated, for example).
You could also feasibly use a annotation liftover pipeline if you want to be especially quick, but you inherit all the misannotations and potentially missed genes from the source assembly. Not recommended, but better than nothing in a pinch.
The quality of the new genome is probably the biggest factor to consider in my opinion. If it's highly fragmented, the quality of annotations will likely be quite low.
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I would just use a BUSCO based phylogeny. This avoids having to annotate another genome and wondering if the annotation worked better or worse for different species etc and also comparing orthologs that might be more or less conserved and being concerned about how they group etc. Save yourself the trouble. For an outgroup, having at least a couple of varied outgroup genomes is ideal, sounds like you have enough although the those from different genera might be rather distant...
I guess the question here is what is OP trying to get out of this. If it's purely for building a phylogeny, then BUSCO_phylogenomic is fine. But if you want a deeper dive into comparative evolution, the BUSCO genes alone is a pretty boring dataset that likely won't cover any of the genes involved in interesting intertidal adaptations.
Absolutely. I forgot the initial line 'comparing the evolution between these species driving the adaptation to the intertidal region'.
So if these un-annotated genomes are not relevant for the comparison above then again, use just the BUSCOs for the full phylogeny. Otherwise if they are relevant for looking at genes driving this adaptation you will probably have to annotate them regardless for a proper comparison...but either way could still just use BUSCOs for the phylogeny.