Efficiency of different COI markers in DNA barcoding of freshwater prawn species
R. Udayasuriyan, P. Saravana Bhavan, C. Vadivalagan and G. Rajkumar
Five species of prawns (Macrobrachium rosenbergii, Macrobrachium malcolmsonii, Macrobrachium lamarrei, Macrobrachium lamarrei lamarroids and Caridina gracilipes) were identified morphologically, and molecularly discriminated by mt-COI gene with four different sets of universal primers (LCO1490 & HCO2198, COIa & COIf, CrustF1 & HCO2198 and CrustF2 & HCO2198) in order to find out the best suited primer set. The primer sets, LCO1490 & HCO2198 and COIa & COIf was worked well in all subjected species. In terms of number of sequences the former primer set was found to be better than that of the latter primer set. But in terms of quality of phylogenetic information (synonymous and non-synonymous substitutions, saturations, transitional and transvertional type substitutions, divergence rates and phylogenetic tree topology just the reverse was resulted. Therefore, the primer set COIa & COIf showed more significant results in non-synonymous substitution, saturations, transvertional type substitution and divergence rates when compared with LCO1490 & HCO2198.