CAPS Analysis: A Possible Tool to Detect and Group Geminiviruses Infecting Some Fibre Crops and Weeds

Some fibre crops and weeds, showing typical symptoms caused by begomoviruses, were subjected to PCR amplification using different sets of primers specific for DNA A and DNA β molecules of begomoviruses. Restriction digestion of full length DNA A and DNA β using different enzymes revealed variation in restriction profiles amongst the virus isolates in the present study. Moreover, variation in the restriction profile of different DNA β molecule with that of their corresponding reported sequences were also noticed. Cleaved amplified polymorphic sequence (CAPS) analysis of DNA β revealed little or no genetic distance between the begomoviruses infecting Sida acuminata and S. rhombifolia and also among the begomoviruses infecting Urena, Hibiscus cannabinus, and H. sabdariffa. But the same analysis with full length DNA A showed close phylogenetic relationships between begomoviruses infecting H. cannabinus and H. sabdariffa. Hence, for wide spread variation and unavailability of any sequence information CAP analysis might be a useful tool to detect and group