Application of environmental dna for studying freshwater fish diversity in Gobind Sagar and Pong reservoirs

Abstract

The main objective of the present study was to assess the potential of environmental DNA metabarcoding for the detection of target exotic species (H. molitrix and C. carpio) and overall fish diversity in Pong and Gobind Sagar reservoirs. Water samples were collected from Gobind Sagar and Pong reservoirs. eDNA was extracted and PCR was done to partially amplify the 12S rRNA gene from the isolated eDNA by using teleost-specific primers described by Valentini et al. (2016). Sequencing was done on Illumina HiSeq platform. Both the target fishes i.e. H. molitrix and C. carpio were detected in both Pong and Gobind Sagar reservoirs. Other important fish species like L. rohita, L. catla, M. armatus, P. sarana, X. cancila, C. punctata, P. sophore and L. bata were also detected. Two invasive species, O. niloticus and H. nobilis were detected from Pong and Gobind Sagar reservoirs respectively. Another aspect of the present study was to design primer pair specific for H. molitrix to be sequenced on the NGS platform. The designed carp ND2 primer pair successfully amplified H. molitrix DNA. The last objective of the study was to assess the phylogenetic distribution of T. putitora and S. seenghala from the Pong and Gobind Sagar reservoirs using 12S rRNA gene fragment. Phylogenetic analysis was carried out in MEGA 11. For S. seenghala, the phylogenetic tree indicated that S. seenghala is more closely related to S. acicularis. For T. putitora, the phylogenetic tree indicated T. putitora and T. tor are more closely related than other mahseer species. newline