I would like to do sequencing of a species of Charophyceae, for which, I have collected a few morphologically differing members from different locations. I would like determine if there is any variation in the molecular level between these geographically isolated members. I am not sure whether to sequence the ITS or ISSR region. Kindly guide me.
Thank you
ITS1 and ITS2 are very easy to amplify by PCR just 450 bp very easy to amplify in single reaction and within single chance you can sequence it by forward and backward primers.
Als, ITS 2 database is also available with more than 70000 plant sequences are available.
Some of my publications can give you idea on this. IITS for Tinospora cordifolia and Tinospora sinensis.
Thank you Mr. Devendra. I would also like to know whether it would be suitable for identification of any variation at the sub-species level. Can you refer some papers which have a similar kind of work.
In my experience ITS region is a good marker for the identification at specie level, inversely is not variable at subspecie level (but I'm expert for higher plants and not in algae). In order to quantify the genetic diversity within your taxa I suggest to you to use ITS (nuclear DNA) or matk or other cpDNA in order to characterize every accession/provenance of your specie and, subsequently, make an analysis at population level with ISRR or AFLP.
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