Problems in DNA barcoding

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Comment by C.Vadivalagan on May 8, 2012 at 1:19pm

Dear all,

        I Have completed my molecular Biology work now am planing to move on computation work (Barcoding) now i done molecular Phylogeny and protein Docking but i didnt get any idea about coding software. 

can you sagest coding software, its very useful for completing my research.

Thanking you all

with regards,

Chithravel Vadivalagan

 

Comment by Rakshit Ojha on April 29, 2012 at 9:24am

hello everybody,

i am working with some museum ant specimens which are around 30-40 years old (when collected) and the ants are alcohol preserved and the alcohol is not changed for past 28 years. I am facing problems to extract DNA from them, is there any protocol through which i can extract DNA from such old samples...if any please suggest. Thank you all. 

Comment by Prasanna Kumar on December 7, 2011 at 11:56am

@  Gaikwad Swapnil Sopan

Thanx for the reply. Even though MLGS is recommended, u would agree that we need single or not more than two gene markers to call it as barcode. I personally felt that if we pin point a particular locus, we could sort it out. Thanx for the reply.

Comment by Prasanna Kumar on December 7, 2011 at 11:53am

@ Hi Chelzie

I am please to know that u have made progress in bacterial barcoding. I like to see ur abstracts as i could not download it from the web. I missed the conference due to last minute emergency. Else we would heve met. Plz mail the your abstracts to marinemicrobiology@gmail.com. As rpoB's efficacy in delineating bacilli and other bacterial species has been well established, what are the difficulties you are facing? What sort of improvements should one be expecting? like to discuss further with u. Thanx for the reply.

Comment by Gaikwad Swapnil Sopan on December 7, 2011 at 1:11am

Hi Prasanna Kumar,

Story of bacteria is really different.....if you look at the intraspecies divergences. I do agree with  Chelzie Crenna Darusallam   rpoB is better marker. However, for bacteria MLST approach is followed i.e. multiple locus sequence typing and thus status of new species is confimed. And further this is approved by DNA DNA hybridisation.

I hope this will help you,

Keep posting,

Swapnil

Comment by Chelzie Crenna Darusallam on December 7, 2011 at 12:46am

Hi Prasanna Kumar,

I am working in marine bacteria and assessed DNA barcode (rpoB gene) to identify (you can found my abstract poster in the conference web -C7). The rpoB showed promising result however as the new marker it still need some improvement(s). The idea for DNA barcode for bacteria is find the core gene (as has been described in Rodoni's presentation in the conference)..I am very pleased to discussed further with you.

Comment by Prasanna Kumar on December 6, 2011 at 11:57pm

Hi hope all had blast in fourth conference. As dna barcoding technology have been expanded and it almost touched every aspects of tree of life, but one group that remained isolated is bacteria. Although the problems of barcoding bacteria is discussed @ http://www.ccdb.ca/pa/ge/research/domains-of-life/archea-and-bacteria, the article promises to define a barcode gene for this prokaryotic group in near future. I wish to know is there any such gene in practice? I am very much interested to define and produce DNA barcodes for bacteria, especially for marine bacteria. I hold 84species of freshly isolated marine bacteria from bay of bengal and its respective 16SrRNA sequences. Many species in same family shared 2% to 0.5% variation which overcame the species boundary of 3% variations. I kindly request all members in this group to help me define and target a particular gene for bacterial barcoding. I have rpoB gene in mind, and have either positive points nor negative points to support or oppose it. So please help me to sort out the problem? could this be solved?, is another question poping up now.

:-)

Thanks for the reply.

Comment by Gaikwad Swapnil Sopan on April 2, 2010 at 1:19am

Yes, I have checked the orientation, it is prefect. But I can't deny the fact of pseudogen. i hope to solve the same.
Thanks for the response. Hope to see more inputs from you.
Keep posting.

Comment by Julie Stahlhut on April 1, 2010 at 11:23am

Hi, Gaikwad! I've seen this too, and here are two suggestions:

First, if you're assembling forward and reverse sequences from tracefiles, make sure that your DNA analysis program has not reversed their directions. If it has, it's usually easy to find a "reverse" function to put the sequences in their proper orientations. This often solves the problem.

Another possibility is that you are amplifying pseudogenes (numts). This may be more difficult to solve; you might have to try amplifying and sequencing with different primers.

Which insect taxa are you trying to barcode?


-- Julie Stahlhut