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Systematics

I have special interest in molecular systematics. Analysis of both nuclear and extra nuclear DNA sequence has answered some of the basic questions in coffee phylogenetics. In depth phenetic/phylogentic analysis of mobility/sequence based markers have led to the optimization of number of markers/nucleotide sites to be used for such analysis.

Softwares

I also have particular interest in using / comparing / reviewing various phylogenetic analysis software available elsewhere.

Phylogenetics of Coffee

Beyond the routine analysis, I had a specific interest in comparing the results in terms of different markers and different models used for phylogenetic inference. Some of results are as below

1.Analysis of various marker systems such as RAPD, ISSR, SSR, AFLP revlealed that a multilocus marker particularly involving 'randomness' in its principle such as RAPD and AFLP would be of more informative than the markers, which are specific.

2.A perfect randomisation and multiple regression analysis revealed that optimal coverage of genome is possible with even few (approximately 150 to 200) random markers for phylogenetic analysis

3.Coffee being the recently evolved species, analysis of so called informative domains such as , 'trn' region of rDNA, 16s region of rDNA are found to be not suitable

4.The internal transcribed spacer regions ITS1-5SrDNA-ITS2 region of the nuclear ribosomal DNA was found to be most suitable for investigating Coffee phylogenetics

5.We have also modeled a set of basic assemptions needed for phylogentic analysis with respect to the number of markers in the case of mobility based molecular markers and number of bases in the case of sequence based markers

This work was done at Center for Cellular and Molecular Biology, India.