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Plants

Members: 116
Latest Activity: Sep 2

New primers and protocols for matK DNA barcoding

These pdfs detail clade-specific primer sets & protocols for the matK barcode region in land plants. These protocols were developed by Alan Forrest, in collaboration with Luke Dunning, Aron Fazekas, Lianming Gao, Sean Graham, Mehrdad Hajibabaei, Pete Hollingsworth, Maria Kuzmina and Damon Little, and the work was funded by the Gordon and Betty Moore Foundation,

If you use these primers please send an email to barcoding@rbge.ac.uk. This is to enable us to provide protocol updates and to solicit feedback on how well the primers perform.

Angiosperm_matK_RBGE_PROTOCOLv1.0.pdf

Gymnosperm_matK_RBGE_PROTOCOLv1.0.pdf

Hornwort_matK_RBGE_PROTOCOLv1.0.pdf

Fern_matK_RBGE_PROTOCOLv1.0.pdf

Liverwort_matK_RBGE_PROTOCOLv.1.1.pdf

Moss_matK_RBGE_PROTOCOLv1.0.pdf

The folder below contains the matK sequence alignments which were used for primer design. These alignments are useful for designing further taxon-specific primers and also for assessing levels of primer mismatch

matK_alignments_used_for_primer_design.zip

Discussion Forum

DNA Barcoding within species

in the definition of DNA barcoding (its for species identification) what about using it withen speciesContinue

Started by Mohamed Awad May 15.

Hi Dears I want to start the plant DNA barcoding of pakistani spp of flowering plants

Hiwhat primers sequence set may I use PCR conditions DNA extraction protocols Need yours healpZafar Continue

Started by Muhammad Zafar Saleem Feb 26, 2013.

Plant barcoding primers and protocols 15 Replies

Please use this space to discuss primers and protocols. To start things off, here are the most up-to-date…Continue

Started by Karen James. Last reply by Anoop.B.S. Mar 14, 2012.

PCR condition for amplication matK gene with pair of primers trnK3914F and trnK2R in Panax genus

I'm investigating phylogenetic in Panax genus (Araliaceae). I tried some published PCR condition for amplification matK gene with pair of specific primers trnK3914F (5’-TGG GTT GCT AAC TCA ATG G-3’)…Continue

Started by Le Ngoc Trieu Mar 6, 2012.

My Comment Wall

Comment

You need to be a member of Plants to add comments!

Comment by Paula on August 27, 2010 at 2:11am
Hi Olivier and everybody
I am from the University of the Free State, Bloemfontein, South Africa. We have been busy for a few year sequencing plants from the Hyacinthaceae and Amaryllidaceae in South Africa, but started only recently implementing those sequences for Barcoding.

Olivier, we must make contact some time. I met Michelle about two weeks ago when she presented a talk for us. As I said, we work on the above families, and especially the genera Clivia and Lachenalia, but will expad in these families with time. I hope our work does not overlap with your work...

My e-mail address is spiesp@ufs.ac.za

Kind regards,
Paula
Comment by Shoupu He on August 26, 2010 at 8:43pm
Hi all!
I work on cotton in China. I'm very interested in DNA barcoding because we have abundant cotton germplasm. I hope this approach could work on cotton.

Best regards

Dennis He
Comment by Olivier Maurin on August 21, 2010 at 4:23am
Hello all, I work at the University of Johannesburg with Michelle van der Bank, and we wanted to share with you the latest development in regards to plant DNA barcoding in South Africa. Best wishes to all. Olivier
Please feel free to visit and comment on:
http://www.toyotaoutreach.com/
Comment by Diego Pignataro on March 2, 2010 at 4:02pm
hi everybody!

I am in France until the end of May, if there is anybody who works with plant barcoding I would like to visit the lab and share experiences, or if somebody know about one laboratory near Toulouse will be perfect!

Best regards for everybody

Diego
Comment by Hemant Kawalkar on December 23, 2009 at 7:18am
Hi, It feels great to look at the response to Diego's question. I have planned to barcode Indian Drimia species. I am new to DNA barcoding and look forward to get help form this group if at all i face a problem in my work.... Hope every thing goes well.... thanks Karen for making this group!! :)
Comment by Diego Pignataro on December 2, 2009 at 1:54pm
Thanks a lot for all comments and advices!!, hope everything work well for all of you!.

Keep in touch.

Best regards for all,

Diego
Comment by Nadeesha Lewke Bandara on December 2, 2009 at 9:57am
Hi everyone,
about diego;s problem- If you have access to ABI SEQUENCER MACHINE you can do it by your self.IF you have PCR products, before sending to the sequencer you should puriefy PCR products.protocols use for purification depends on the lab.I'm doing matk sequencing for genus Onobrychis using ABI 3730 machine.but my lab not doing commercial sequencing.
Cheers.
Comment by Rasika Bhagwat on December 2, 2009 at 8:52am
Hi
I am Rasika, working at NCL in India. I am working on plant DNA barcoding.
Comment by Luz Ruiz Maqueda on November 25, 2009 at 2:47pm
Hi everyone!
About Diego's question, I sent to Macrogen because it was cheaper from other options... about the programs to align, there are many options to align, all of them are online and they are free of charge, like bioedit (windows plataform, http://www.mbio.ncsu.edu/BioEdit/bioedit.html), clc sequence viewer (for the three plataforms: windows, mac and linux, http://www.clcbio.com/index.php?id=28). If you have money to buy software, I recomend you DNAstar.
Hope this is useful to you.
Cheers!
Comment by Karen James on November 24, 2009 at 1:00pm
Thanks for joining, Diego. Glad to hear you're starting a new project. I suggest starting with the current protocols (pdf) provided on the CBOL Plant Working Group page. At the PWG pre-conference workshop we were told that's where all the up to date info is.

David's right - you'd send your PCR products to your organisation's sequencing lab, or if you don't have one, you should contact the folks at Guelph (e.g. Mehrdad Hajibabaei) and see if they might be able to sequence your products for you.

Most of us are either only just beginning or about to begin working with plant barcodes in BOLD so we'll have to see how that goes!
 

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