[Taxacom] Illumina seqeuncing

[Bevan Weir]

Hi,

I think this would be very challenging to get enough good quality DNA from such as small specimen. Remember that you will sequence everything including their gut contents, the gut bacteria will be preferentially sequenced due to their high genome copy number.

If you have a big insect you can dissect out the guts, but in this case you will have to just brute force the sequencing by getting really deep coverage, and extracting the DNA from multiple specimens.

Any sequencing provider worth the money you will pay will explain all this to you in your initial consulting meeting.

Cheers,
Bevan


--
Dr Bevan Weir
Research Scientist & Capability Leader, Mycology and Bacteriology
Curator, ICMP culture collection
Systematics Team
Landcare Research

Phone: +64 9 574 4115 Mobile: +64 21 723826 email: weirb at landcareresearch.co.nz
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ICMP culture collection
Fungal and bacterial systematics research
Group publications
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-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Damien HINSINGER
Sent: Wednesday, 19 February 2014 9:12 p.m.
To: TAXACOM taxacom
Subject: Re: [Taxacom] Illumina seqeuncing

One of the most critical factor in next generation sequencing is the quality of the DNA prior to the library construction.
If you are able to extract high weight DNA fragment (at least 10-15 kb), it should be good (the DNA will be fragmented according to the size required by the platform you will use)... But that's the question, could you extract high quality DNA from such specimens ?
Regards, Damien


Le 19 févr. 2014 à 01:54, Aron Katz <aron.d.katz at gmail.com> a écrit :

> I'm considering Illumina sequences, but I'm not sure if small specimens (1-2mm) stored in alcohol are appropriate for this sequencing method.  Does anyone have experience with attaining genome sequence data from small arthropod specimens collected in 95% ethanol? These specimens will be freshly collected and stored at -10degC short term. I'm hoping to avoid having to collect them 'dry'.
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