Genetic variation in wild and hatchery population of Catla catla (Hamilton, 1822) analyzed through mtDNA cytochrome b region.

Catla (Catla catla) is a one of the most harvested Indian major carps and is widely cultured fish species in Indian subcontinent. In the present study, genetic variability between hatchery and wild stocks of Catla was surveyed using sequence data of mitochondrial DNA of partial 307 bp of cytochrome b region. A total of 174 Catla individuals were examined from three different river basins and hatcheries. Significant genetic heterogeneity was observed for the sequence data (FST = 0.308, p ≤ 0.001). However, analysis of molecular variance (AMOVA) resulted in insignificant genetic differentiation among the samples of three rivers and culture zones (FCT = -0.10, p = 0.44). The result suggested a significant genetic variation within different riverine system, low genetic differentiation among samples from river basins and a lack of genetic variation in hatchery populations.

Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences.

The population structure and genetic diversity of Rohu (Labeo rohita Hamilton, 1822) was studied by analysis of the partial sequences of mitochondrial DNA cytochrome b region. We examined 133 samples collected from six locations in three geographically isolated rivers of India. Analysis of 11 haplotypes showed low haplotype diversity (0.00150), nucleotide diversity (π) (0.02884) and low heterogeneity value (0.00374). Analysis of molecular variance (AMOVA) revealed the genetic diversity of L. rohita within population is very high than between the populations. The Fst scores (-0.07479 to 0.07022) were the indication of low genetic structure of L. rohita populations of three rivers of India. Conspicuously, Farakka-Bharuch population pair Fst score of 0.0000, although the sampling sites are from different rivers. The phylogenetic reconstruction of unique haplotypes revealed sharing of a single central haplotype (Hap_1) by all the six populations with a point mutations ranging from 1-25 nucleotides.

Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region.

In order to assess the DNA sequence variation and phylogenetic relationship among five tuna species (Auxis thazard, Euthynnus affinis, Katsuwonus pelamis, Thunnus tonggol, and T. albacares) out of all four tuna genera, partial sequences of the mitochondrial DNA (mtDNA) D-loop region were analyzed. The estimate of intra-specific sequence variation in studied species was low, ranging from 0.027 to 0.080 [Kimura's two parameter distance (K2P)], whereas values of inter-specific variation ranged from 0.049 to 0.491. The longtail tuna (T. tonggol) and yellowfin tuna (T. albacares) were found to share a close relationship (K2P = 0.049) while skipjack tuna (K. pelamis) was most divergent studied species. Phylogenetic analysis using Maximum-Likelihood (ML) and Neighbor-Joining (NJ) methods supported the monophyletic origin of Thunnus species. Similarly, phylogeny of Auxis and Euthynnus species substantiate the monophyly. However, results showed a distinct origin of K. pelamis from genus Thunnus as well as Auxis and Euthynnus. Thus, the mtDNA D-loop region sequence data supports the polyphyletic origin of tuna species.

Genetic stock structure of Osteobrama belangeri (Valenciennes, 1844) in Indian region.

Osteobrama belangeri is an important medium carp endemic to Manipur state in India Myanmar and Yunnan Province of China. Although the species is listed as Near Threatened species according to IUCN status with sizeable population available in Myanmar, it is Extinct in the Wild in Manipur. An 842 bp segment ATP synthase 6/8 region of mtDNA was sequenced and analysed for 56 O. belangeri individuals. Analysis of population differentiation showed no significant genetic differentiation between the four sampling localities (ΦST = -0.034, p = 0.819). Results were further corroborated by a non-significant nearest neighbour statistics (Snn = 0.223, p = 0.897) and exact test of population differentiation (p = 0.893). Phylogeographic analysis revealed two haplogroups, but there was no obvious phylogeographic pattern separating the sampling localities. The present study suggests a single panmictic population of O. belangeri in Indian region.

Genetic differentiation in Indian Major Carp, Cirrhinus mrigala (Hamilton, 1822) from Indian Rivers, as revealed by direct sequencing analysis of mitochondrial Cytochrome b region.

A 307 bp segment of Cytochrome b gene of mtDNA was sequenced and analyzed for 90 individuals of Cirrhinus mrigala collected across the three rivers, namely Ganges, Narmada and Brahmaputra. Analyses revealed the presence of 14 haplotypes with haplotype diversity (h) ranging from 0.304 to 0.692, and nucleotide diversity (π) 0.002-0.043. The majority of variation was found within the population (96.21%), and the FST value (0.035) as well as the value of exact test of population differentiation (0.893) were found to be insignificant (p<0.05). Analysis of molecular variance (AMOVA) also indicated insignificant differentiation among sub-populations. Generally, low genetic differences were observed even though those populations were from different geographic locations. The present study suggests a single panmictic population of C. mrigala across the three rivers of India.

Historic demography and phylogenetic relationship of Euthynnus species based on COI sequence analyses.

Euthynnus species are epipelagic migratory tuna species, with global distribution. They occur in the open waters but usually remain close to the shoreline. In present study, historic demography and phylogenetic relationship of Euthynnus species were examined using sequence data from portions of the mitochondrial COI gene. A total of 35 sequences were retrieved from NCBI. Mismatch distribution analyses suggested a late Pleistocene population expansion of E. affinis and E. alletteratus. Neutrality test for E. alletteratus fails to reject the null hypothesis of neutral evolution while COI sequences of E. affinis are found to be at genetic equilibrium. Phylogenetic analysis suggest that E. alletteratus is the most ancestral species while E. affinis is more closely related to E. lineatus than E. alletteratus.

Cytochrome Oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas.

Tunas are commercially important fishery worldwide. There are at least 13 species of tuna belonging to three genera, out of which genus Thunnus has maximum eight species. On the basis of their availability, they can be characterised as oceanic such as Thunnus albacares (yellowfin tuna) or coastal such as Thunnus tonggol (longtail tuna). Although these two are different species, morphological differentiation can only be seen in mature individuals, hence misidentification may result in erroneous data set, which ultimately affect conservation strategies. The mitochondrial DNA cytochrome oxidase c subunit 1 (COI) gene is one of the most popular markers for population genetic and phylogeographic studies across the animal kingdom. The present study aims to study the sequence conservation and variation in mitochondrial Cytochrome Oxidase I (COI) between these two species of tuna. COI sequence analysis of yellowfin and longtail revealed the close relationship between them in Thunnus genera. The present study is the first direct comparison of mitochondrial COI sequences of these two tuna species.

Evolutionary history and phylogenetic relationship between Auxis thazard and Auxis rochei inferred from COI sequences of mtDNA.

Tunas of the genus Auxis are cosmopolitan species and the smallest members of the tribe Thunnini, the true tunas. In the present study, COI sequences of mtDNA were employed to examine the evolutionary history and phylogenetic relationship between A. thazard and A. rochei. A total of 29 COI sequences were retrieved from NCBI. Historic demographic analyses of sequence data showed that A. thazard has undergone sudden population expansion in the past while population size of A. rochei has been remain constant for long period. Non-significant value of Tajimas's D (P = 0.22400) and Fu's FS (P = 0.21400) test fail to reject the null hypothesis of neutral evolution for A. rochei. Phylogenetic analyses of nucleotide sequences demonstrated separate clusters for both species and are strongly supported by 98% bootstrap value. The results of the present study suggest the recent founding of A. thazard in world ocean while A. rochei represents the ancestral species.

In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.