[kerplunk412]

Thank you K.

So which kit do you would suggest? Or which company...

F

Sorry I didn't respond to this earlier. The NEXTflex PCR-Free DNA-Seq kit from Bioo Scientific is what I would recommend, but please note that I work for Bioo Scientific. I believe Illumina and a couple of other companies offer similar kits. Feel free to PM me if you would like more information.

No matter which company you go with, I highly recommend PCR-free, using Covaris to shear your DNA. This eliminates concern of insertion bias and PCR bias, and I am fairly sure PCR-free is generally accepted to show the most even coverage over AT and GC rich regions. If you can get 100-200 ng of DNA from an individual I think PCR-free or very low cycle PCR library prep from an individual is feasible.

[SNPsaurus]

I would definitely be concerned with the presence of gut bacteria and endosymbionts. We do a lot of small insect genotyping by sequencing, and small insects have a higher probability of having lots of food DNA, gut bacteria, Wolbachia... you name it.

Can you get embryos from one female? A little heterozygosity would pale in comparison to having 2/3rds your reads go to species different from the one you are interested in assembling. Heads are another option. Samples sourced from heads have been very clean.

[Hamid]

Hi Francicco,

Shearing DNA with Covaris AFA is concentration independent. You can optimize your desired shearing size range and distribution using a higher concentration of ~1g of any control DNA, and then use the same settings to shear your limited mass DNA.

Thank you

Hamid