Question: Shall I take vigna angularis or vigna radiata as a reference for vigna munga
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gravatar for rprog008
18 months ago by
rprog00870
rprog00870 wrote:

Dear member,

I want to annotate transcript sequence (FASTA file) of Vigna Mungo obtained from Trinity. In NCBI there is reference genome of Vigna radiata and Vigna angularis.

Can anyone please suggests which one shall I take and why.

Thanks in advance

rna-seq annotation • 297 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by rprog00870

You would generally take the genome of the species that is evolutionarily closer to your species of interest. In this case it looks like they are all Vigna species so either should work.

Ideally you would assemble your data with trinity and then use these species to annotate the assembled transcripts (not sure if that is what you had in mind or you were just thinking of aligning to transcriptome of one of the known species).

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax87k

Thank you for your reply :) Yes, you are right. At first I have assembled my data with trinity. Now I want to annotate the assembled transcript.

ADD REPLYlink written 18 months ago by rprog00870

There are all three genomes finished, am I right?

In this case, build phylogenetic tree of all three ones

and see, which one - Vigna radiata or Vigna angularis is closer to Vigna Mungo.

ADD REPLYlink modified 18 months ago • written 18 months ago by natasha.sernova3.7k

[edited] Yes three genomes of three species namely V. angularis, V. radiata and V. unguiculata are available :)

Thanks I will do try to build phylogenetic tree and proceed further now :)

ADD REPLYlink modified 18 months ago • written 18 months ago by rprog00870

Thanks @natasha.sernova and @ genomax I found one literature, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147568, where they have reported Vigna munga is closely related with Vigna radiata ( figure 3 and 4) :) Is it ok, if I take vigna radiata for annotating vigna mungo sequence and i will cite this paper.

ADD REPLYlink written 18 months ago by rprog00870

Please do not add answers unless you're answering the top-level question.

ADD REPLYlink modified 18 months ago • written 18 months ago by RamRS28k

if I take vigna radiata for annotating vigna mungo sequence

You are still going to have to do a lot of blasting, sequence comparisons in order to annotate transcripts from your species. While related your species could have differences, data you have may not be complete etc.

I am not sure if you can use a tool like RATT (http://ratt.sourceforge.net/ ). That may make things easier.

ADD REPLYlink written 18 months ago by genomax87k
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