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Plants

Members: 124
Latest Activity: Oct 12, 2016

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

Started by Mohamed Awad May 15, 2014. 0 Replies

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

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

Started by Muhammad Zafar Saleem Feb 26, 2013. 0 Replies

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

Plant barcoding primers and protocols

Started by Karen James. Last reply by Anoop.B.S. Mar 14, 2012. 15 Replies

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

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

Started by Le Ngoc Trieu Mar 6, 2012. 0 Replies

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

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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!
Comment by David E. Schindel on November 24, 2009 at 9:42am
I'm very glad to see that the barcoding botanists have created an online group. I tried to answer Diego's question but I'm neither a botanist nor a lab person. Here's what I said and I invite others to provide a real answer:


I'm not a specialist but I know that normal barcoding does not involve cloning, so you will probably be sending PCR products to your sequencing lab. People do cloning when they are concerned with pseudogenes but this is not normal practice for barcoding most specimens.

As far as I know, there are no problems aligning matK using the BOLD system. Let's see what the specialists say when I forward your question to them.

David
Comment by Diego Pignataro on November 23, 2009 at 11:35pm
Hi!, first..thanks for create this group!!

I am currently developing a DNA barcode project in plants. We have had some problems with our PCR amplification with matK locus. but finally we go it. Now our main problem is to find a cheap place to send our sequences, Macrogene its an option but I receive any other option.

For sequencing service...do you send directly your isolated PCR products or the plasmid dna after cloning procedures?, we have both, but for the following samples..should we continue with all the cloning process?, the last one..do you think we gonna need an additional sofware like codonaligner to analyse our sequences? or can we do everything over the boldsystems web page?.

Hope to here from you soon.

Thanks again for your time!

Best regards,


Diego Pignataro
 

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