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Primer combinations for marine groups

This is a bulletin board for adding primers that are used in Marine Barcoding. Please add primer names, sequences and all relevant information you want to share in the reply field.

Replies to This Discussion

Permalink Reply by Lyndell M. Bade on February 14, 2012 at 2:12pm

Hi Erik,

I'm starting my bivalve sequencing tomorrow. I'm very new to this, but I'm starting with the LCO and HCO primers. Have you had luck with those primers and bivalves? Or did you have better luck using the veneroidLCO with the HCO? I'm working on Western Atlantic (US East Coast) species of oysters, bay scallops, hard and soft clams, macoma, stout razor clams, and chiones. I'd greatly appreciate any feedback/ideas/suggestions you may have!

All the Best,

Lyndell

Permalink Reply by Erik M. Pilgrim on February 14, 2012 at 3:30pm

Hi Lyndell,

I've had success with LCO/HCO on a variety of molluscs, so I think you should try those first. Then if things aren't successful you can try some other primer combinations.

Best of Luck,

Erik

Permalink Reply by Lyndell M. Bade on March 6, 2012 at 2:56pm

Hi Erik,

Thanks so much for the encouragement! That was very appreciated. I'm an ecologist and not a molecular biologist, so this is new to me. :) I've since gotten 5/7 spp to work with just basic master mixes and have actually used the bird sexing PCR protocol, and it works just fine! Of course I have yet to sequence those bands, so we'll see. I'm definitely having trouble with Atlantic bay scallops and Baltic macomas. Any suggestions on papers to see re: master mix concentrations and PCR protocols for molluscs? Or have you worked with these spp and have any ideas?

Thanks so much!

Lyndell

Permalink Reply by Lyndell M. Bade on March 6, 2012 at 3:02pm

Has anyone done any work on cownose rays (Rhinoptera bonasus)? Or any rays (eagle, cownose, manta ray) from the Family Myliobatidae? I'm planning on trying the LCO1490 and HCO2198 on those guys, but I just thought I'd see if anyone else has done any work with elasmobranchs... If you have, or know anyone who has, feel free to pass on names/references/ideas!

Thanks Much,

Lyndell

Permalink Reply by Dirk Steinke on March 6, 2012 at 5:42pm

Hi Lyndell,

Actually there are a few other options than the Folmer primers. Either you go with the ones developed by Ward et al 2005 DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B-Biological Sciences 360: 1847-1857.

Or you use a cocktail (most successful here and we've done quite a few rays) from Ivanova et al. 2007 Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7: 544-548.

Dirk

Permalink Reply by Lyndell M. Bade on March 7, 2012 at 8:34pm

Hi Dirk,

These papers are VERY helpful...thanks so much! I took a look at them last night and they're going to be a tremendous help. Thanks again!

All the Best,

Lyndell