Regarding the gills, here's the trick again from the diagnostic lab protocols,
Originally Posted by danfive
I worked with PCR from gills, as well. They are not very difficult but you should consider that the gills may contain a lot of blood and the iron in the hemolymph/globin is a PCR inhibitor---solution to problem: cut small sections of gill (i.e. 0.1g) and soak in pure water for 20 minutes. Take your tissue and just about any DNA extraction procedure will work and give you good quality DNA from there. To be extra secure you can use a Clontech Chromaspin Column-100 to purify your DNA a step further.
Same trick for RNA, cut into small fragments and soak 20 min, then proceed with homogenization and Trizol extraction. Won't need the clontech column for additional clean-up.