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OfflineRenegadeMycologist
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Delimitation of gene loci for phylogenetic analysis
    #27622729 - 01/17/22 04:51 PM (2 years, 3 months ago)

I'm trying to construct phylogram of the whole Psilocybe genus and one thing I noticed is that I'm often getting distorted phylogeny. After some manual curation of the sequence alignment like deleting sequences where let's say there is only partial ITS data, tree starts making sense.
However, after chosing only complete ITS region sequences, and trimming all the garbage parts, I still get somewhat unsatisfactory phylogram.

My guess is that due to a use of a different primers 5.8S gene is overall badly represented, and this is inflicting damage to a tree replication algorithm.

So how should I detect start and end motifs for ITS1 and ITS2, so I can omit 5.8S - which in my current understanding is what is causing problems here ?

I also want to know this for one more reason, so I can perform multi gene phylogenetic analysis when I acquire enough bet and tef1 sequences.


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:mushroom2:  l e a r n i n g  t h i n g s :mushroom2:

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OfflinePhDCube
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Re: Delimitation of gene loci for phylogenetic analysis [Re: RenegadeMycologist]
    #27641686 - 02/02/22 12:01 AM (2 years, 3 months ago)

Hi Renegade Mycologist,
Wao! What you are doing is super interesting.

Give a few days and I'll try to get more informed and trying to help you, for the start and end motifs of the ITS.

In any case, sometime ITSs has been reported to be variegated also within species and arebnot always suitable to taxonomy studies.
I'm not expert in taxonomy but I made my thesis is trascriptomic analysis in Olive tree.
Maybe could be usefull to use other gene sequence for you phylogenetic tree?

PhDCube

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OfflinePhDCube
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Re: Delimitation of gene loci for phylogenetic analysis [Re: PhDCube]
    #27641688 - 02/02/22 12:02 AM (2 years, 3 months ago)

By tht way where did you get the sequences, are they available on NCBI website or BLAST?

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OfflineAlan RockefellerM
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Re: Delimitation of gene loci for phylogenetic analysis [Re: RenegadeMycologist]
    #27644185 - 02/03/22 04:01 PM (2 years, 3 months ago)



A typical ITS sequence contains the start of the 18s (SSU) which is where the forward primer binds, then ITS1, followed by 5.8S, ITS2 and the beginning of LSU, where the reverse primer binds.    You will pretty much always have 5.8s since it's in the middle - unless a sequence is unusually short.

I don't think that 5.8s is causing the problem - it's pretty much always left in when doing analysis.

You can use ITSx to split the sequence into the different genes, and run the tree with each gene separately if you like.

What are the problems with the tree - how is it distorted?  Can you share your alignment?

Regarding the multigene analysis, run it with each gene first, and if the tree comes out the same way for each gene you can safely concatenate the data.

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