Plant barcoding primers and protocols

Replies to This Discussion

Permalink Reply by Lee Weigt on December 17, 2009 at 9:42am

attached is one of our basic CTAB Plant DNA extraction protocols at the Smithsonian's LAB - cross posting with another group.
Lee

Attachments:

• Plant_CTAB_protocol.pdf, 246 KB

Permalink Reply by Anoop.B.S. on March 14, 2012 at 12:32pm

thanks..

Permalink Reply by Paulo Baleeiro on July 27, 2010 at 11:01am

does anyone has a good protocol for species complex delimitation??

Permalink Reply by Birgit Gemeinholzer on October 1, 2010 at 11:08am

Hi Paulo,

we made a trial of examining different DNA extraction protocols/kits throughout different plant groups - the Machery & Nagel Nucleo Spin Plant II kit worked best for routine applications. Highest yields always were received by CTAB, however, the DNA is quite dirty, often causing problems for subsequent applications. Purification after DNA isolation cannot be recommended as you loose too much DNA and the quality is not much better afterwards.
cheers,

Birgit

Permalink Reply by Gillian Dean on October 5, 2010 at 12:17am

We are looking into possibilities for generating barcode data from 3500 Indonesian plant species and we are considering sending our samples out for DNA extracting and sequencing.

Does anyone have suggestions for service labs who could help us?

Also, if we were to do the work in Indonesia, I want to move to a kit that uses column-based extraction rather than phenol-chloroform protocol. DO people have suggestions for kits that are good for a wide range of species? I usually use Qiagen, but they are on the expensive side.

Thanks so much, Gill (cross posted with Lab Operations).

Permalink Reply by Chrissen E. C. Gemmill on June 14, 2011 at 4:57pm

Hi there Gillian, I am at the University of Waikato in New Zealand and our facility is very good. I am using ITS and a number of cpDNA markers with good results.

http://bio.waikato.ac.nz/sequence/

 

We have switched to MoBio kits (I think) - better results on dried leaves and cheaper than Qiagen, at least in our experience. Will confirm and get back to you.

Permalink Reply by Gillian Dean on June 14, 2011 at 11:09pm

Hi Chrissen - thanks for the reply.

I took a look at the sequencing facility, thanks.

I'd be glad to hear what kit you are using - I had a small samples of that kit but it was hard to determine how it compared to Qiagen with just a few extractions.

Thanks very much!

Gill

Permalink Reply by Chrissen E. C. Gemmill on June 14, 2011 at 11:14pm

Hi again, it is a BioLine plant isolation kit - we are getting fabulous results. 

http://www.bioline.com/h_prod_detail_ld.asp?itemid=140

Sadly our DNA sequencing Unit can't take overseas samples just now...but are looking at getting the permits again to do so.

Permalink Reply by Gillian Dean on June 14, 2011 at 11:18pm

Great, I will check it out. I do like BioLine products.

What plants families are you working on? We have a barcoding project which has a real range of families so we need something that works across the board.

Thanks!

Permalink Reply by Chrissen E. C. Gemmill on June 18, 2011 at 10:56pm

Hi there, not sure if my reply made it through??? Pittosporaceae, Lauraceaea, Winteraceae and others :-)

 

Permalink Reply by Gillian Dean on June 28, 2011 at 2:01am

No, it didn't get through - but now i have seen it :) interesting to know what groups you work on, thanks!

Permalink Reply by Dhivya on October 27, 2010 at 11:58am

Hi,

I'm Dhivya
My work is Authentication of Indian Medicinal Herbal Products which are in the form of Churnas, Capsules, Leghyam etc. This work is performed to identify the medicinal plants from their adulterants to ensure the safety and efficacy of the drugs.

Im in need of a DNA ISOLATION Protocol by which i can isolate the DNA from the dried parts of the plant tissue, from the processed medicinal preparations like Churnas, Leghyam Capsules etc., Please help me in this regard.


Regards,
Dhivya.S

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