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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 JOHN OLAYINKA ATOYEBI on May 14, 2012 at 1:00pm

Dear Colleagues, Its good to rejoin this group once again after sometime of absence, since CBOL conference in Taiwan. Looking forward to a good networking and collaboration.

JOHN

Comment by Pete Hollingsworth on March 23, 2012 at 12:36pm

matK sequence alignments added to the Connect 'Plants' group front page. These are helpful for primer design and assessing levels of mismatch between primers and a given taxonomic group

Comment by Pete Hollingsworth on February 21, 2012 at 8:43am

Some primers and protocols for matK DNA barcoding in land plants are now posted on the 'Plants' group page

Comment by rohini khanapurkar on December 17, 2011 at 1:38pm

i also wanted to knw wt shud be the appropriate sample size to barcode a particular plant species.

Comment by rohini khanapurkar on December 17, 2011 at 1:27pm

hello all,

I wanted to ask if ITS2 alone can be used as barcoding region for medicinal plants, or atleast can it be used as an identifying marker for medicinal plants, please reply as soon as possible,thanking you.

 

Comment by Angelia Yulita on November 13, 2011 at 3:41am

Hello all !

I'm coming from Indonesia and now is proposed to barcoding some tree species in java island.

 

I am a newbie !! So please you guys humbly help me with support, discussion and any information about plant barcoding.

 

Nice to see you guys !!

 

Best regards,

Angelia.

Comment by Jivan Shakya on November 4, 2011 at 6:19am

Hello all,

 

I am from Nepal and currently undertaking the pilot project on barcoding medicinal plants of Nepal. The pilot project aims to barcode Asparagus racemosus, Dactylorhiza hatagirea and Choerospondias axillaris on the basis of rbcL, matK, psbA_trnH and ITS2 seqences.

 

I am new to barcoding and have been getting some basics from the literatures. I look forward to getting valuable support from the group members in terms of knowldege sharing.

 

Regards

Jivan Shakya

Comment by Kristinn P Magnusson on October 24, 2011 at 5:53pm
Botany-position in Iceland, Curator/Researcher
The Akureyri Division of the Icelandic Institute of Natural History invites applications for the
position of Curator/Researcher in Vascular plant biology.
The successful applicant is expected to curate the Vascular plants-collections held at the
Institute, furthermore to conduct research on the taxonomy of Icelandic vascular plants.
Applicants should hold a PhD in Botany and have some experience in vascular plant-research
with particular reference to their taxonomy and distribution. Familiarity with molecular
methodology is preferable.
Probable salaries range from ISK 352,000 (2200 €, 3000 $) to ISK 468,000 (2900 €, 4000 $)
per month.
Applications should be sent by e-mail to nia@ni.is, or by mail to: The Icelandic Institute of
Natural History, Akureyri Division, Borgir vid Nordurslod, IS-600 Akureyri, Iceland.
Application should include: resume, cover letter and names and contact information of two
references.
Application deadline is December 2nd 2011.
The Icelandic Institute of Natural History (http://en.ni.is/) is a governmental research institute
doing basic research in the fields of Botany, Zoology and Geology. The institute is located in
Reykjavik and Akureyri. At the institute the largest collections in Iceland of Icelandic
Vascular plants are kept, totaling some 65,000 herbarium sheets. At the Akureyri Division the
Fungi and Lichen-herbaria are located along with a part of the Vascular plant collection.
There are good working facilities for morphological examinations of the specimens and a well
equipped molecular laboratory which is operated in cooperation with the University of
Akureyri (www.unak.is/english ).
More information can be obtained from Dr. Kristinn J. Albertsson, Director of the Akureyri
Division, kralb@ni.is, tel. +354 4600500
Comment by Dhivya on November 1, 2010 at 12:08pm
Hi all!
Im Dhivya...Mphil Scholar... i need a DNA isolation protocol to isolate DNA from the dried parts of plant tissues which are comprised of highly acidic and phenolic compounds... also if anyone have an idea about extracting DNA from the traditional indian forms of herbal medicines, pls let me know...it ll b helpful for me to carryout my research work...
Comment by Pradeep Kumar Divakar on October 1, 2010 at 10:22am
Hi to all, i am especially working on loci screening to obtain best maker for DNA barcode.
 

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