search for intron conservancy across species

Question

[Buffo]

I'm working with a non-model organism, and I would like to test the conservancy of the new introns I found (or orthologs genes). Do you know any tool and/or database to do that? I've tried many databases, such as OrthoDB, OMA, IAOD, and IntronDB (is not working), but I have nothing so far, most of those databases are precomputed for model organisms (mainly), and I can't compare them with my new sequences. Any recommendations would be much appreciated

EDIT:

• I'm working with a parasite (non-model parasite).
• I found 100 genes containing one intron, and I validated the intron already.
• I'm trying to find whether or not the introns (including the gene) are conserved in other species.

[cmdcolin]

just for context, you are looking for a particular splice isoform being conserved, correct? not necessarily that the actual sequence inside the intron is conserved (that is a somewhat different issue)

[LauferVA]

irrespective the same procedures would apply, right colin? what do you think?

[Buffo]

thanks, I edited my question

Answer 1

[Pei]

1. Is your organism vertebrate? If so, is it included in UCSF multi ways alignment? (> 100 species)

2. Maybe you could consider start with identifying ortholog coding gene, then do some sequence comparison of the intron?

HTH.

[Buffo]

No, is not a vertebrate, it's a parasite.

1. Maybe you could consider start with identifying ortholog coding gene, then do some sequence comparison of the intron?

That's what I'm asking, databases to find orthologs where I can use my sequences as input. But thanks.

[Pei]

Quite interesting.

Recent publication from Günzl lab may be helpful.

https://today.uconn.edu/2019/05/making-in-roads-with-parasite-introns/

[Buffo]

Is not helpful but it's very interesting!. I used to work with T. cruzi and I didn't find any spliceosomal introns, only trans-splicing. Their genomes are very fragmented, so I wouldn't say they don't exist though.

Answer 2

[LauferVA]

Buffo , in some ways i think that i must be missing something - the process of calculating conservation scores does not, so far as i am aware, change dependent upon functional annotations (such as, for instance, "is exonic"), unless you are specifically attempting just such an analysis but I did not get the sense taht you are.

As such, I'd guess that the procedure does not vary from normal protocols for the same, i.e.

1) generate multiple sequence alignment

2) construct phylogenetic tree

3) select tool, e.g. PhyloP conservation score (PHAST)

4) select method (stick with PHAST/phyloP for a moment, could choose LRT or, for instance, something like CONACC

while some tools, e.g. vert30 or some such, are very specifically targeting certain clades, in general most tutorials on this subject will cover these basics and more. does this help at all? if you need more info, sorry/please do let me know.

Best,

VAL

[Buffo]

I edited my question. I'm sorry I didn't get your point.

[LauferVA]

buffo, no worries. based on my edits i think the approach outlined will work well.

best,

VAL

[Buffo]

the process of calculating conservation scores does not, so far as i am aware, change dependent upon functional annotations

I'm not interested in functional annotation, I didn't mention it. Not sure why it might be related to my question.

1) generate multiple sequence alignment

Once again, my aim is to answer if the new introns (SS motifs and the BP, mainly) I found (and the CDS) are conserved in other species, therefore: MSA against what? and how MSA would answer my question?

The same for points 2, 3, and 4. What I need is something like the IAOD DB but including way more species (including parasites).