Question: De novo assembly and marker development for insecticide resistance
0
gravatar for mahnazkiani
10 weeks ago by
mahnazkiani30
United States
mahnazkiani30 wrote:

Hello,

I have a question for designing the experiment, I am interested to design markers for insecticide resistance in an insect that its genome has not been sequenced. I am thinking to sequence the genome, do de novo assembly and then look for variants between tolerant and control insect. Is this sounds practical? How about going through transcriptomics instead?

Appreciate your comments, Mahnaz

sequencing next-gen • 188 views
ADD COMMENTlink modified 9 weeks ago by h.mon9.2k • written 10 weeks ago by mahnazkiani30
2
gravatar for h.mon
9 weeks ago by
h.mon9.2k
Brazil
h.mon9.2k wrote:

I would go for transcriptome sequencing:

  • you will need less sequencing
  • markers are more likely to be "functional" - you can even search for SNPs on genes known to be involved in insecticide resistance
  • you may design an experiment to analyse differential gene expression between control and tolerant and develop markers at the same time
ADD COMMENTlink written 9 weeks ago by h.mon9.2k
1

I can only agree with h.mon.

I recently conducted a study involving a bacterium. I de novo assembled the transcriptome and was able to identify key transcripts that were differentially expressed between the two strains of the bacterium. There are tools like blastx that can help you to understand the functionality of 'unknown' sequences.

To de novo assemble the transcriptome, there are various options:

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Kevin Blighe6.4k
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