Connect.BarcodeofLife.net

international online community for dna barcoding professionals

Information

Marine Barcoding

Website: http://marinebarcoding.org
Members: 84
Latest Activity: Oct 7

The PLoS ONE MarBOL Collection

The PLoS MarBOL Collection still has room for more publications. Have a look.
The collection is open, i.e. if you have a marine barcoding manuscript in prep or think about writing one then you might want to consider submitting it to PLoS One and it's MarBOL collection. Simply indicate in the submission system that you want your paper be part of the collection.

Discussion Forum

Primer combinations for marine groups 21 Replies

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.Continue

Started by Dirk Steinke. Last reply by Dirk Steinke Aug 6.

DNA Barcoding Sea Slugs of India 1 Reply

Hi every one,Past 3 years of extensive sea slug collection around Indian waters including the Islands resulted in collecting and documenting 101 species. The network on sea slug barcoding is planning…Continue

Started by Prasanna Kumar. Last reply by Prasanna Kumar Apr 20.

Marine Insects

Is there a taxonomic group called "Marine insects"? Is any lab working towards barcoding insects of marine realm? Thanks for the replyContinue

Tags: insects

Started by Prasanna Kumar Dec 21, 2013.

DNA barcoding Marine Bacteria 3 Replies

Dear allHope all had blast in fourth conference. As dna barcoding technology have been expanded and almost touched every aspects of tree of life, one group that remained hidden is bacteria. Although…Continue

Tags: gene, dna, barcode, rRNA, 16S

Started by Prasanna Kumar. Last reply by Vijaykumar Yogesh Muley Dec 9, 2011.

My Comment Wall

Comment

You need to be a member of Marine Barcoding to add comments!

Comment by Sergio Vargas R. on May 31, 2012 at 11:44pm

Hi Lyndell,

the same came to my mind when I first heard about double inheritance... there are heaps of freeky beasts out there!

As for slimy, I mean with too much mucus (mainly polysacharids). If you are extracting using spin columns and you tend to see (this can be inconsistent) a white precipitate clogging the column you probably have to much mucus in your sample. And the bad part is: all this other stuff can inhibit your PCR. If your samples are rich in mucus, try using a CTAB based DNA extraction. If they are not, try serial dilutions of your stock DNA. If this doesn't work try additives: BSA, betaine, trehalose, DMSO or a mixture of them. If this doesn't work you could try touchdown PCR (I do not recommend this for COI but you could try it), if this doesn't work: jump while pipeting and pray to the good all PCR god. If your samples are not fresh, consider that some are not going to work no matter how hard you try.

hope to hear more on the developments of your project.

sergio

p.s. I do not work with molluscs, btw, I work with corals and sponges.

Comment by Lyndell M. Bade on May 31, 2012 at 2:47pm

Hi Sergio,

Good heavens! Your post stopped me dead in my tracks, and then I spent the rest of the evening in the literature.  I have never heard of this double uniparental inheritance in bivalves, but you are so right!  (My background is more elasmobranch ecology, not molluscan.)  I'm going to look over my sequence results tomorrow and see if it looks like the "second" sequence is consistent.  I've been reading up on this, and I definitely have two species (probably 3) that have this form of mt inheritance.  I think there are ways around getting sequences with both the M-type and F-type together, but I have to do more research to sort that out.  Do you work with molluscs a lot?

As for the tissue samples being slimy, I'm not sure what that means...does it refer to an extra coating on the somatic tissue?  If you could elaborate on that, I'd be very grateful!

Thanks so much...you may have just saved my project!!  :)

Cheers,

Lyndell

Comment by Sergio Vargas R. on May 30, 2012 at 5:28pm

Hi Lyndell,

it seems you are amplifying two copies of the mtDNA, this is, if I'm not wrong, likely in molluscs because you can have both paternally and maternally inherited mtDNA coexisting in the same organism. I think this is tissue specific but I'm not sure on that. It could also be taxon specific, you will need to check. Another possibility is NUMTs and pseudogenes which could cause you the troubles. You can search a bit the literature on mtDNA inheritance in Molluscs for you answer.

At the bench, you could clone if you don't have many samples... is time consuming but it could even more time consuming trying to solve the problem by other means.

If your beasts are too slimy I would recommend you to use a plant DNA kit to wash the polysacharid away, generally any CTAB based DNA extraction protocol would help you.

hope it helps,

sergio

Comment by Lyndell M. Bade on May 30, 2012 at 5:17pm

Hi Sergio,

Thank you for commenting.  I'm happy to supply more information...I appreciate any suggestions or advice anyone has!  I am working on bivalves, sequencing the COI first as part of a diet study.  I am using the Folmer et al. 1994/Hebert et al. 1993 primers (LCO1490 and HCO2198).  I am just not getting very clean sequence results, even though I have good bands on my gels after PCR.  The hard and soft-shelled clams (Mercenaria mercenaria and Mya arenaria) are really quite good...but my oyster (Crassostrea virginica) results are inconsistent/fragmented and the stout razor clams (Tagelus plebius) are very poor quality.  Even when I do have pretty good sequence results, they look "muddy" and I can see what is probably 2 different sequence "signatures", if that makes sense.

I'm trying to determine if I should use different primer combinations, or if I have some level of contamination.  I know this is a lot to throw out, and it's difficult to explain in a comment!  I guess one of my main questions is whether or not I could have a band on the gel but not have the best primer match to get really clean sequence results.  Perhaps that explains my fragmented results?

I'm not getting any good PCR results from bay scallops (Argopecten irradians concentricus) or baltic macoma clams (Macoma balthica).  It looks like I need different primers or annealing temperatures for those.  There's just too many variables!

Any thoughts or ideas would be appreciated!  Feel free to send me a message or post on my wall if that's easier.  Thanks much!

Best,

Lyndell

Comment by Sergio Vargas R. on May 30, 2012 at 4:05pm

Hi Lyndell,

could you elaborate a bit on you sequencing problems? it may be easier to help you if provide more info.

sergio

Comment by Lyndell M. Bade on May 30, 2012 at 3:55pm

Prasanna, were you able to get some help re: your question below about marine egg mass barcoding and manuscripts?  And if so, did you find papers and/or did you publish your work?  (I notice that comment was from a year ago.)  I'm interested in your findings and protocol.  I'm working with bivalves and having a hard time getting good sequencing results, so I'm troubleshooting and trying to find people to brainstorm with!  If you have papers you can recommend or would be willing to msg about this, please let me know. 

Cheers,

Lyndell

Comment by Roy Palmer on August 10, 2011 at 5:55pm

Australian Fish Names Committee

Always on the look out for connection between Bar Code of Life and making testing easier

Comment by Prasanna Kumar on June 10, 2011 at 10:26am

Hi to every one

Sub: need suggestions in making a manuscript

Just as hobby, I have barcoded molluscan egg masses and making a manuscript. I have produced 29 barcodes which shows closely similarity with Babylonia spirata, Harpa sp., Murex pecten and Hemifusus sp during BLAST search. I have two questions..

 

1) can any one suggest a model manuscript for this topic, as I could not locate one in internet. (i.e., with regard to marine egg mass barcoding)..

2) what are the justification one can give to barcode egg mass form marine environment in introduction of the manuscript.

 

Cheers

Comment by Prasanna Kumar on May 28, 2011 at 3:44am

Dear Dirk

 

thanks for the directions.

cheers

Comment by Dirk Steinke on May 27, 2011 at 12:23pm

Dear Prasanna,

 

In principle the collection is open to such papers. You would have to submit your manuscript to PLoS ONE as any other regular submission and indicate that you like to contribute to the collection. There is a field in the submission system asking for this. As soon as your paper is formally accepted I will be contacted if I accept it as part of the collection.

 

Members (84)

 
 
 

Translate

Tory's site-wide code

New to the Connect network?


Watch our Intro Webinar


Introduce yourself to the Connect community


Write a blog post


Ask a question

Tory's code

© 2014   Created by Mike Trizna.   Powered by

Badges  |  Report an Issue  |  Terms of Service