We simultaneously extract DNA from fish fins, muscle, and eggs using the CTAB protocol or the Qiagen DNEasy blood and tissue kit, and get good results for the first two, while the DNA from eggs is smeary and has very low quality readings. Does anyone know what's in the eggs that is causing this, and have you come across an extraction procedure that significantly improves the situation? (by the way, the eggs were preserved in ethanol, RNAlater and Allprotect reagent, but the genomic DNA is consistently poor).
Eggs have a lot of protein. If you are using DNAeasy, you have 3 possibilities: (1) add β-mercaptoethanol to the lysis buffer(disruption of disulfide bonds), (2) repeated wash of the column, (3) decrease ammount of sample. Otherwise you may use standard phenol/chloroform (recommended for the preotein rich samples) and add 1/24 of isoamyl alcohol (increases protein migration to the organic phase).
Some fish eggs (salmonid ones) have a very strong "capsule" (zona radiata, zona radiata externa and vitelline membrane) which are impermeable to most substances (the salmonids' vitelline membrane is even known to be impermeable to water and the zona radiata externa prevents the whole capsule to be digested by external proteolytic treatments). Accordingly, preservative substances won't be efficient if you don't preliminarily break the capsule.
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