Karyotypic study of 3 species of Neolissocheilus hexagonolepis, Puntius ticto and P. chola belong... more Karyotypic study of 3 species of Neolissocheilus hexagonolepis, Puntius ticto and P. chola belonging to family Cyprinidae, from Arunanchal Pradesh, India, were carried out. The diploid chromosome number in Neolissocheilus hexagonolepis was 100 with a chromosomal formula of 32m 16sm 6st 46T and fundamental arm number (FN) as 148. The other 2 species, Puntius ticto and P. chola have 50 chromosome with chromosomal formula of 28m 16sm 6st (FN 94) and 2m 2sm 46T (FN 54), respectively. The evolutionary significance of these 3 karyotypes was discussed.
The stream loach, Schistura reticulofasciata has high demand in ornamental fish trade due to its ... more The stream loach, Schistura reticulofasciata has high demand in ornamental fish trade due to its mesmerizing colorful banding pattern and size. In recent times, its abundance has declined severely in its habitat, and presently it has been assessed as vulnerable fish. Despite its threatened status, no nucleotide sequence information from this fish is publicly available in GenBank and the BOLD System. Here we describe the first complete mitogenome of S. reticulofasciata. The resulting circular mitogenome of S. reticulofasciata is 16,581 in length, comprising 13 protein-coding genes (PCG), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (rRNA), one replication origin (OL) and one control region (D-loop). The overall genome size, gene arrangement, A + T content, AT-skew, GC-skew and partiality towards A and T in mitogenome were similar to those of other Schistura species. Phylogenetic analysis confirmed the high sequence similarity and conserved synteny among the Schistura species. The primary genetic data developed in this study could be successively applied for species identification, genetic diversity studies and the formulation of effective conservation strategies for steam loaches.
Transcriptome profiling has been used to decipher the novel mechanisms behind immune responses of... more Transcriptome profiling has been used to decipher the novel mechanisms behind immune responses of the fishes. However, the molecular mechanism underlining immune response in mahseer is not studied so far. Fishes are greatly affected by bacterial pathogens such as Aeromonas hydrophila. In this study, transcriptome response of golden mahseer (Tor putitora) infected with A. hydrophila was examined using paired end Illumina sequencing of liver tissue to understand the immune response of the fish. The de novo assembly generated 61,042 unigenes ranging from 200 to 9322 bp in length and an average length of 463 bp. The gene ontology annotations resulted a total of 131,826 term assignments to the annotated transcriptome including 60,846 (46.16%) allocations from the biological process; 21,603 (16.39%) from molecular function and 49,377 (37.46%) from cellular components. Differential gene expression analysis of the transcriptome data from challenged and control group revealed 1104 upregulate...
Indian snow trout, Schizothorax richardsonii is distributed in fast flowing torrential snow-fed s... more Indian snow trout, Schizothorax richardsonii is distributed in fast flowing torrential snow-fed streams, rivers and lakes in various altitudes of the Himalayas. We developed fifteen microsatellite markers from approximately 32923-expressed sequence tags (ESTs) of common carp, Cyprinus carpio and evaluated eight of them in 42 unrelated specimens of S. richardsonii. The number of alleles per locus ranged from 3 to 6. The observed heterozygosity (Ho) ranged from 0.099-0.937 and the expected heterozygosity (He) ranged from 0.675-0.755. Because of high level of polymorphism the microsatellite markers reported here would be useful to study population genetics and linkage mapping of Indian Snow Trout.
In the Kumaon region of Uttarakhand Himalayas, coldwater fish species (Cyprinidae) is widespread ... more In the Kumaon region of Uttarakhand Himalayas, coldwater fish species (Cyprinidae) is widespread and endemic in the natural waterbodies system. In order to test the genetic relationship among the four predominant fish species, viz.,Tor putitora (golden mahseer), Schizothorax richardsonii (snow trout), Raiamus bola (Indian trout), and Garra gotyla (garra), an investigation was carried out using RAPD-PCR and targeted mitochondrial DNA- PCR analysis. The phylogenetic trees based on RAPD-PCR, by using 11 randon primers, targeted mitochondrial DNA-PCR, and 12S rRNA sequence showed a consistent result of forming two separate monophyletic groups consisting of T. putitora with S. richardsonii and Garra species with R. bola. The present investigation concluded that both the methods could be a valuable tool for studying molecular systematics and establishing the taxonomic position among cyprinids coldwater fish species of India.
Glycerol accumulation in blood plasma and modulation in the activities of selected enzymes associ... more Glycerol accumulation in blood plasma and modulation in the activities of selected enzymes associated with glycerol synthesis in the liver under cold temperature were assessed in two freshwater cyprinid fishes, Schizothorax richardsonii (snow trout) and Barilius bendelisis (Indian hill trout). Fishes were collected from Kosi River, Uttarakhand during late October 2011 (water temperature 15-16 0C) and after an acclimatisation for 7 days they were maintained at lower temperature of 5 0C over a period of 96 h. The decrease in temperature triggered higher accumulation of glycerol in the blood plasma of both the species. Glycerol accumulation in plasma was found to be associated with changes in enzyme in the liver. In both the species, liver exhibited higher activities of glycerol-3-phosphate dehydrogenase (GPDH) and higher concentration of dihydroxy acetone phosphate (DHAP) which gets converted into glycerol. The increased activities of different enzymes involved in amino acid metabolis...
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, Jan 19, 2018
The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studi... more The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studied using three mitochondrial genes (CoxI, Cytb, ATPase 6/8). A total of 120 individuals representing nine populations from different drainages of Northeast India were used for the study. Thirty-three distinct haplotypes were identified from concatenated gene analysis. The total haplotype and nucleotide diversities are 0.8880 and 0.0280, respectively. The analysis of molecular variance (AMOVA) reveals that the main variation (89.33%) was among populations. Most of the populations showed high polymorphisms, parsimony and haplotype diversity which indicate genetically healthy stocks in the wild. The genetic differentiation patterns were consistent with geographical distributions. Pairwise F comparison of populations showed significant genetic differentiation (0.9088, p < .05). The pattern of haplotype network and phylogenetic tree revealed six major groups. Results suggested that chocola...
Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviou... more Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.
Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviou... more Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.
This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nu... more This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugeni...
Karyotypic study of 3 species of Neolissocheilus hexagonolepis, Puntius ticto and P. chola belong... more Karyotypic study of 3 species of Neolissocheilus hexagonolepis, Puntius ticto and P. chola belonging to family Cyprinidae, from Arunanchal Pradesh, India, were carried out. The diploid chromosome number in Neolissocheilus hexagonolepis was 100 with a chromosomal formula of 32m 16sm 6st 46T and fundamental arm number (FN) as 148. The other 2 species, Puntius ticto and P. chola have 50 chromosome with chromosomal formula of 28m 16sm 6st (FN 94) and 2m 2sm 46T (FN 54), respectively. The evolutionary significance of these 3 karyotypes was discussed.
The stream loach, Schistura reticulofasciata has high demand in ornamental fish trade due to its ... more The stream loach, Schistura reticulofasciata has high demand in ornamental fish trade due to its mesmerizing colorful banding pattern and size. In recent times, its abundance has declined severely in its habitat, and presently it has been assessed as vulnerable fish. Despite its threatened status, no nucleotide sequence information from this fish is publicly available in GenBank and the BOLD System. Here we describe the first complete mitogenome of S. reticulofasciata. The resulting circular mitogenome of S. reticulofasciata is 16,581 in length, comprising 13 protein-coding genes (PCG), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (rRNA), one replication origin (OL) and one control region (D-loop). The overall genome size, gene arrangement, A + T content, AT-skew, GC-skew and partiality towards A and T in mitogenome were similar to those of other Schistura species. Phylogenetic analysis confirmed the high sequence similarity and conserved synteny among the Schistura species. The primary genetic data developed in this study could be successively applied for species identification, genetic diversity studies and the formulation of effective conservation strategies for steam loaches.
Transcriptome profiling has been used to decipher the novel mechanisms behind immune responses of... more Transcriptome profiling has been used to decipher the novel mechanisms behind immune responses of the fishes. However, the molecular mechanism underlining immune response in mahseer is not studied so far. Fishes are greatly affected by bacterial pathogens such as Aeromonas hydrophila. In this study, transcriptome response of golden mahseer (Tor putitora) infected with A. hydrophila was examined using paired end Illumina sequencing of liver tissue to understand the immune response of the fish. The de novo assembly generated 61,042 unigenes ranging from 200 to 9322 bp in length and an average length of 463 bp. The gene ontology annotations resulted a total of 131,826 term assignments to the annotated transcriptome including 60,846 (46.16%) allocations from the biological process; 21,603 (16.39%) from molecular function and 49,377 (37.46%) from cellular components. Differential gene expression analysis of the transcriptome data from challenged and control group revealed 1104 upregulate...
Indian snow trout, Schizothorax richardsonii is distributed in fast flowing torrential snow-fed s... more Indian snow trout, Schizothorax richardsonii is distributed in fast flowing torrential snow-fed streams, rivers and lakes in various altitudes of the Himalayas. We developed fifteen microsatellite markers from approximately 32923-expressed sequence tags (ESTs) of common carp, Cyprinus carpio and evaluated eight of them in 42 unrelated specimens of S. richardsonii. The number of alleles per locus ranged from 3 to 6. The observed heterozygosity (Ho) ranged from 0.099-0.937 and the expected heterozygosity (He) ranged from 0.675-0.755. Because of high level of polymorphism the microsatellite markers reported here would be useful to study population genetics and linkage mapping of Indian Snow Trout.
In the Kumaon region of Uttarakhand Himalayas, coldwater fish species (Cyprinidae) is widespread ... more In the Kumaon region of Uttarakhand Himalayas, coldwater fish species (Cyprinidae) is widespread and endemic in the natural waterbodies system. In order to test the genetic relationship among the four predominant fish species, viz.,Tor putitora (golden mahseer), Schizothorax richardsonii (snow trout), Raiamus bola (Indian trout), and Garra gotyla (garra), an investigation was carried out using RAPD-PCR and targeted mitochondrial DNA- PCR analysis. The phylogenetic trees based on RAPD-PCR, by using 11 randon primers, targeted mitochondrial DNA-PCR, and 12S rRNA sequence showed a consistent result of forming two separate monophyletic groups consisting of T. putitora with S. richardsonii and Garra species with R. bola. The present investigation concluded that both the methods could be a valuable tool for studying molecular systematics and establishing the taxonomic position among cyprinids coldwater fish species of India.
Glycerol accumulation in blood plasma and modulation in the activities of selected enzymes associ... more Glycerol accumulation in blood plasma and modulation in the activities of selected enzymes associated with glycerol synthesis in the liver under cold temperature were assessed in two freshwater cyprinid fishes, Schizothorax richardsonii (snow trout) and Barilius bendelisis (Indian hill trout). Fishes were collected from Kosi River, Uttarakhand during late October 2011 (water temperature 15-16 0C) and after an acclimatisation for 7 days they were maintained at lower temperature of 5 0C over a period of 96 h. The decrease in temperature triggered higher accumulation of glycerol in the blood plasma of both the species. Glycerol accumulation in plasma was found to be associated with changes in enzyme in the liver. In both the species, liver exhibited higher activities of glycerol-3-phosphate dehydrogenase (GPDH) and higher concentration of dihydroxy acetone phosphate (DHAP) which gets converted into glycerol. The increased activities of different enzymes involved in amino acid metabolis...
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, Jan 19, 2018
The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studi... more The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studied using three mitochondrial genes (CoxI, Cytb, ATPase 6/8). A total of 120 individuals representing nine populations from different drainages of Northeast India were used for the study. Thirty-three distinct haplotypes were identified from concatenated gene analysis. The total haplotype and nucleotide diversities are 0.8880 and 0.0280, respectively. The analysis of molecular variance (AMOVA) reveals that the main variation (89.33%) was among populations. Most of the populations showed high polymorphisms, parsimony and haplotype diversity which indicate genetically healthy stocks in the wild. The genetic differentiation patterns were consistent with geographical distributions. Pairwise F comparison of populations showed significant genetic differentiation (0.9088, p < .05). The pattern of haplotype network and phylogenetic tree revealed six major groups. Results suggested that chocola...
Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviou... more Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.
Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviou... more Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.
This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nu... more This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugeni...
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