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I'm am struggling with genomic DNA extraction from different samples of Pyura chilensis; the DNA is degraded as can be seen on the gel.

We've always used GeneJET Genomic DNA purification Kit (by ThermoFisher), and it works fine for samples from other species; so the kit isn't the problem.

We've always used tissue samples stored in 95% Ethanol (which are washed with water prior to DNA extraction), but the problem persists irrespective of whether the samples are one day old or a few years old. The storage method seems to work fine for gDNA extraction from other species.

Then, my guess is that the problem is with Pyura itself. So I have to figure out if either the extraction or the storage isn't appropriate for Pyura. I read that Pyura has a lot of copper in it. We planned to use a new buffer for storing it: salt Saturated DMSO, containing EDTA.

I would like to ask if any of you have ever worked with this organism (and if you have, then how did you manage to extract DNA from it). Do you have any suggestions on any DNA purification protocols?

enter image description here 1st lane is the ladder (1kb) and last 3 lanes with long blurred thing instead of bands are my DNA samples.

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With reference to your gel photo, the genomic DNA (in the three Pyura sample lanes) does not look badly degraded. If the size marker is 1 Kb ladder, then the majority of the DNA is of high molecular size. During extraction it is common for high molecular weight DNA to become "sheared" to some degree (mechanically broken into smaller fragments). This can appear as the faint downward smear. The lanes may be somewhat over loaded as well. You can try to use more gentle extraction technique and see if it helps to your satisfaction. Any of those you mention will work.

Badly degraded genomic DNA would appear as a more intense "smear" near the lower portion of the 1 Kb size standard.

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This is from a published work by Segovia et al. 2017:

Mantle tissue (0.2 g) from each individual was used to extract DNA using the DNeasy Blood® & Tissue Kit (QIAGEN®, USA) according to the manufacturer’s instructions. Quantity/purity of DNA was measured in Nanodrop 2,000 (Thermo, USA).

They have done SNP identification from the genome. So I assume that their gDNA would have been of decent quality.

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