Peyush Punia

DNA barcoding Indian marine fishes.

DNA barcoding has been adopted as a global bio‐identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids representing 79 Genera and 37 Families from the Indian Ocean have been barcoded for the first time using cytochrome c oxidase I gene (COI) of the mtDNA. The species were represented by multiple specimens and a total of 397 sequences were generated. After amplification and sequencing of 707 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two parameter (K2P) distances within species, genera, families, orders were 0.30%, 6.60%, 9.91%, 16.00%, respectively. In addition to barcode‐based species identification system, phylogenetic relationships among the species have also been attempted. The neighbour‐joining tree revealed distinct clusters in concurrence with the taxonomic status of the species.

Molecular identification of five Indian sciaenids (pisces: perciformes, sciaenidae) using RAPD markers

The randomly amplified polymorphic DNA (RAPD) markers were used to detect interspecific genetic variability and genetic relatedness among five Indian sciaenids namely Otolithes cuvieri, Johnieops sina, Johnieops macrorhynus, Johnieops vogleri and Protonibea diacanthus for the first time. Eight RAPD primers (OPA01, OPA06, OPA07, OPA18, OPP12, OPP14, OPP16 and OPP11) generated 40 species specific diagnostic bands. The highest genetic divergence was detected between J. macrorhynus and P. diacanthus (0.586) where as the lowest one was observed between J. sina and J. vogleri (0.274).

Evaluation of Genetic Variation in the Clown Knifefish, Chitala chitala, Using Allozymes, RAPD, and Microsatellites

Twenty-seven enzyme systems, six random amplified polymorphic DNA (RAPD) primers, and two microsatellite loci were tested to determine intraspecific divergence in the natural population of the endangered Indian featherback fish, Chitala chitala, for the first time. The 262 samples of C. chitala were collected from six riverine locations in India: the Satluj, Ganga (Ghagra, Bhagirathi, and Brahmaputra), Mahanadi, and Narmada river systems. The analysis revealed population subdivisions, with an FST value from 0.1235 (95% confidence 0.0868–0.1621) for RAPD and a combined FST of 0.0344 (95% confidence 0.0340–0.0350) for microsatellite loci. An analysis of 38 allozyme loci did not reveal any polymorphism in the samples from any of the riverine localities; a possible explanation for this could be that the ancestors of Chitala could have faced a population reduction in prehistoric periods, as low allozyme variation is also reported for other species of Chitala from south Asia.

DNA barcoding Indian freshwater fishes

Abstract DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.

Isolation and characterization of polymorphic microsatellite loci in yellowtail catfish, Pangasius pangasius (Hamilton, 1822).

A total of nine polymorphic microsatellite loci were obtained from a genomic library of Pangasius pangasius (order Siluriformes, family Pangasiidae). Samples from rivers Bhagirathi (n = 22) and Mahanadi (n = 20) were genotyped for each of the nine microsatellite loci to determine genetic variation. The mean number of alleles per locus was 5.22 in Bhagirathi and 5.78 in Mahanadi; and expected heterozygosity ranged from 0.567 (Bhagirathi) to 0.578 (Bhagirathi). Significant deviation (P < 0.003) from Hardy–Weinberg expectations was evident at three loci, Ppa2 (Bhagirathi), Ppa14 (Mahanadi) and Ppa28 (Bhagirathi and Mahanadi). The identified microsatellite loci were found to be promising for population genetics studies of P. pangasius.

Genetic divergence in natural populations of bronze featherback, Notopterus notopterus (Osteoglossiformes: Notopteridae) from five Indian rivers, analyzed through mtDNA ATPase6/8 regions

The present study characterized 842 bp fragment of mitochondrial ATP synthase 6 and 8 (ATPase6/8) genes in Notopterus notopterus. In all, 97 samples of N. notopterus were collected from five distant rivers; viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi representing 4 river basins in India. The analysis of variation revealed presence of 23 haplotypes in ATPase6/8 gene with haplotype diversity (Hd) of 0.899 and nucleotide diversity (π) of 0.00336. The within population variation which was 41.78% of the total variation of 58.22% was found among population. The Fst value of 0.582 (P < 0.05) of the total population was found significant. The results concluded that the polymorphism in ATPase6/8 gene is a potential marker that is important for determining genetic divergence of wild N. notopterus populations. The findings reveal common ancestry of mahanadi population with the populations in rivers of Indo-Gangetic region. However, long evolutionary isolation must be responsible for the high genetic divergence between N. notopterus in Mahanadi and other regions.