De novo assembly and marker development for insecticide resistance

Question

[mahnazkiani]

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

Answer 1

[h.mon]

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

[Kevin Blighe]

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:

• Velvet followed by Oases (https://www.ebi.ac.uk/~zerbino/velvet/)

• TopHat2 / Cufflinks to produce a FASTA reference, and then Kallisto to count abundnces

• Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki)

• Rockhopper (https://cs.wellesley.edu/~btjaden/Rockhopper/)