Molecular characterization of coldwater fishes of district Uttarkashi, Uttarakhand using DNA Barcoding

Abstract

We explored fish fauna Ganga and Yamuna river in Uttarkashi district of Uttarakhand, to establish the molecular taxonomy database. A total of 133 samples were collected from various sampling sites along the entire stretch of rivers in district Uttarkashi. A region of cytochrome c-oxidase unit I (COI) gene (655 bp) was amplified using PCR and sequenced (DNA Barcoded). All the sequences have been uploaded into the NCBI GenBank (accession number assigned). Analysis of data generated showed that these 133 samples belonged to 22 species of 4 orders, 14 genera and 8 families. The genetic variability (K2P distance) distribution analysis was also carried out. The average mean distance of 22 species is 0.219 with 0.014 standard error. The mean genetic distance between 22 species ranged from 0.010%-0.362% while the mean genetic distance within the species ranged from 0.0006%-0.0048%. The lowest pairwise genetic distance observed in Schizothorax sinuatus and Schizothorax progastus i.e. 0.010% with 0.003 standard error indicating a closer phylogenetic relationship between Schizothorax sinuatus and Schizothorax progastus than other species which was confirmed by the genetic distance data. Maximum divergence were observed between Danio devario and Channa gachua i.e. 0.362% with 0.028 standard error. The maximum sequence divergence within the species is observed in Barilius bendelisis with 0.0048% while minimum sequence divergence is observed in Tor putitora with 0.0006 of cyprinidae family. Our data suggests that there is high inter-specific sequence divergence as compared to intra-specific sequence divergence and also conclude that COI sequencing (barcoding) was found to be suitable for the identification of fresh water fish species.

Assessing impact of dams on genetic diversity of native fish Mastacembelus armatus in river Yamuna using mitochondrial DNA cytochrome-b sequences as a molecular marker

“…Samples size was standard, n=6, but this was in compliance with our efforts to protect biodiversity. DNA extraction, PCR and DNA sequencing: Total genomic DNA was isolated from fish fin by using the standard phenol-chloroform isolation protocol as used earlier by Thapliyal et al 2015. In short, DNA was isolated from sample and checked on 1.5% Agarose Gel.…”

Status and Scope of Conventional Morphometry and its Integration with Bar Coding in Jammu and Kashmir (J&K) Fisheries.

“…Meanwhile many other researchers working on barcoding have confirmed its role in correct identification of fishes 56,57,58,59,60 and also that barcoding enhances the global data base for quick identification of fishes, validates the checklist of fish fauna of the area, identifies invasive species and helps in formulation of conservation strategies. 61,62 Jammu & Kashmir at a Glance Jammu & Kashmir, the northernmost state in India, is located between 32.17" and 36.58" north latitude and between 73.26" and 80.30" east to west longitude.…”