I just now came across a paper where the authors have barcoded the genus cymbopogon using ISSR markers. However, how they have performed this barcoding analysis with binary data is not clarified clearly. I am enclosing the mentioned paper and also the ss of the ascribed barcode with my question. If anybody can help to perform this analysis it will be of great help.
I have just attached an article that may help. With my best wishes
Data Comparative Assessment of Genetic Diversity in Tomato Cultiv...
Dear Sir,
Thanks for the link, I am well versed with these softwares, but my point is in that mentioned paper authors have claimed that they have performed barcoding using ISSR marker data which is essentially binary. In that paper, they have no where mentioned how they have got that barcode. My question is how to do that using binary matrix, as according to my knowledge (I may be wrong) barcoding is possible using DNA sequence datas.
Dear Paromik, I attached the pdf of an article relative to an ISSR work I made some years ago. I hope it will be of some help for you.
Hi:)
This is easier than it might seem :)
to produce such a barcode picture of issr you need to use 0-1 results matrix, place it in a table, fill all grids which contain 1 with black and 0 with white, change frames into white , and work a little bit with height and width and that's it;) please see in the file
Paromik, I think that the simple method shown by Maja can be effective for your purposes. As regards my paper, in the table at the end of the article further information is provided. In bold are reported private bands, namely those bands that are species-exclusive.
It is interesting. But can we take ISSR data for reliable barcoding
ISSR or RAPD monomorphic bands can be taken for barcoding.But very uncertain. If someone is lucky they may get ITS region or Knox region after sequencing.Only then those bands can be declared as barcoad band. But before starting the experiments some information of the regions in the family may be obtained. I mean the bp values of the specific bands in the family. It is possible collect it from NCBI data base.
DNA barcoding is a proposal to use a marker (in tha animal kingdom a mitochondrial fragmento of the CO1 gene) as a standard for species ID. To use ISSRs would be a lot more work, I have used 5 od these and found much less resolution than with mtDNA. Hope this helps.
I got 700 bp band as the barcoding band for Garcinia which is a ITS region.Actually we were getting 700bp band as monomorphic in many primers used to study RAPD as well as in ISSR FOR 10 SPECIES. Finally we wanted to know what is this region and finally we found this region as ITS region by sequencing.In this way some monomorphic bands which appears repetitively may be the genius specific band.But ofcourse it is a little uncertain. But i wanted to tell that it is possible wit ISSR &RAPD MARKERS.
To all
ISSR are 20/30 times more resolutive than any markers (even microsats) BUT they give"only" a phenotypic information and not a genotypic one.
If you wish to separate species, they are extremely efficient but if you search for a phylogenetic information, most of time they are useless.
Barcode (based on a single gene such as Cox1 or ITS) provide extremely rough results which in some case may separate well defined species (most of time species which are easy to separate using morphological work, except in very few cases).
Finally, barcode is ok to separate species which are separated from at least 3 to 4 millions years. ISSR are extremely sensitive and are able to separate any close species (you can forget RAPD....they are not reproducible). None of these two approach are suitable to build a phylogeny.
I published more than 20 papers using barcoding and/or ISSR which are available in my profile.
Cheers from Luc
Sir LuC Legal , what about SCoT orDAMD markers? Recently SCoT has proved to be reliable marker? Can it be used?
This paper is not dealing with typical DNA barcoding work. Reveals the efficiency of ISSR markers in fingerprinting. Please go with chloroplast loci (rbcL/matK/trnH-psbA) or other loci like ITS/ITS2 or tiered approach (rbcL+ITS2) for proper species discrimination.
I do really think that ISSR/RAPD is the best for barcoding. Anyway, I hope the attached paper may give you quick comparative answer
Data Comparative Assessment of Genetic Diversity in Tomato Cultiv...
Hi
Here there are two concepts i.e.
1. DNA barcoding (Studying the Phylogenetic relationship of Different Species -- Interspecies study based on sequence variation information of conserved regions i.e. chloroplast/mitochondria specific markers, ITS and ETS)
2. Molecular barcoding (Characterization of germplasm varieties, mostly of one species by variation of allelic profile captured by molecular markers (RAPD/ISSR/SRAP/SSR) from the respective samples -- Intraspecies study)
In fact as mentioned in the paper enclosed, the ISSR barcodes are the corresponding Molecular Fingerprints generally considered as GENOTYPE of that variety(s). This is general molecular characterization work done and capturing the allelic variation being shown by ISSR markers as a source of variation for constructing the Dendrogram. The differential ISSR allelic profile present in binary format can be used for generating molecular barcodes if you have computed the molecular weight of those bands (polymorphic + monomorphic) on the gel.
Good Luck
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