FisOmics: A portal of fish genomic resources.

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics/, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements.

An update on mechanism of entry of white spot syndrome virus into shrimps.

Host-parasite relationships can be best understood at the level of protein-protein interaction between host and pathogen. Such interactions are instrumental in understanding the important stages of life cycle of pathogen such as adsorption of the pathogen on host surface followed by effective entry of pathogen into the host body, movement of the pathogen across the host cytoplasm to reach the host nucleus and replication of the pathogen within the host. White Spot Disease (WSD) is a havoc for shrimps and till date no effective treatment is available against the disease. Moreover information regarding the mechanism of entry of White Spot Syndrome Virus (WSSV) into shrimps, as well as knowledge about the protein interactions occurring between WSSV and shrimp during viral entry are still at very meagre stage. A cumulative and critically assessed information on various viral-shrimp interactions occurring during viral entry can help to understand the exact pathway of entry of WSSV into the shrimp which in turn can be used to device drugs that can stop the entry of virus into the host. In this context, we highlight various WSSV and shrimp proteins that play role in the entry mechanism along with the description of the interaction between host and pathogen proteins.

HRGFish: A database of hypoxia responsive genes in fishes.

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene.

Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome.

In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data.

MicroRNAs (miRNAs) are small, non-coding RNA molecules that bind to the mRNA of the target genes and regulate the expression of the gene at the post-transcriptional level. Zebrafish is an economically important freshwater fish species globally considered as a good predictive model for studying human diseases and development. The present study focused on uncovering known as well as novel miRNAs, target prediction of the novel miRNAs and the differential expression of the known miRNA using the small RNA sequencing data of the brain and pineal gland (dark and light treatments) obtained from NCBI SRA. A total of 165, 151 and 145 known zebrafish miRNAs were found in the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Chromosomes 4 and 5 of zebrafish reference assembly GRCz10 were found to contain maximum number of miR genes. The miR-181a and miR-182 were found to be highly expressed in terms of number of reads in the brain and pineal gland, respectively. Other ncRNAs, such as tRNA, rRNA and snoRNA, were curated against Rfam. Using GRCz10 as reference, the subsequent bioinformatic analyses identified 25, 19 and 9 novel miRNAs from the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Targets of the novel miRNAs were identified, based on sequence complementarity between miRNAs and mRNA, by searching for antisense hits in the 3'-UTR of reference RNA sequences of the zebrafish. The discovery of novel miRNAs and their targets in the zebrafish genome can be a valuable scientific resource for further functional studies not only in zebrafish but also in other economically important fishes.

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish.

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.

Assessment of genotoxic and mutagenic potential of hexavalent chromium in the freshwater fish Labeo rohita (Hamilton, 1822).

The present study was undertaken to investigate the genotoxicity and mutagenicity of sublethal concentrations of hexavalent chromium (potassium dichromate) in the Indian major carp, Labeo rohita. The 96 h LC50 value of potassium dichromate estimated was 118 mg L(-1) by probit analysis using SPSS (version 16.0) software. Based on 96 h LC50 value, three sublethal test concentrations of potassium dichromate (29.5, 59.0 and 88.5 mg L(-)(1)) were selected and specimens were exposed in vivo to these test concentrations for 96 h. The mutagenic and genotoxic effects of potassium dichromate were evaluated in gill and blood cells using micronucleus (MN) test and comet assay. In general, significant (p < 0.05) effects due to the concentrations and the exposure durations were observed in exposed specimens. The MN induction was highest at 96 h at all the test concentrations in the peripheral blood. A similar trend was observed for the DNA damage, measured in terms of percentage of tail DNA, in erythrocyte and gill cells. The study indicated hazardous effect of the hexavalent chromium to fish and other aquatic organisms and indirectly to human beings.

In silico analysis of SSRs in mitochondrial genomes of fishes.

The availability of fish mitochondrial (mt) genomes provides an opportunity to explore the simple sequence repeats. In the present study, mt genomes of 85 fish species reported from Indian subcontinent were downloaded from NCBI and computationally analysed for finding SSRs types, frequency of occurrence, mutation and evolutionary adaptation across species. A total of 92 microsatellites in different nucleotide combinations were detected in 59 species. 26 interspersed SSRs, mostly poly (AT)n were found in the D-loop regions in the species of Cyprinidae. Fifty-six SSRs of 12 bp fixed length were observed in eight genes only. Further, identical repeat motifs were found on the same location in ATP6 and ND4 genes, which were biased towards particular habitat. The comparison of ATP6 and ND4 gene sets to other homologous sequences showed point mutations. This study explores the SSRs discovery and their utility as marker for species and population identification.

Mitochondrial 16S rRNA gene-based evolutionary divergence and molecular phylogeny of Barilius spp.

Barilius is an important genus of fish family Cyprinidae, which comprises 22 species from Indian region. This study aimed to characterize five commonly occurring Bariline species, for example, Barilius bakeri. Barilius gatensis. Barilius vagra. Barilius bendelisis and Barilius tileo, across the country using partial mitochondrial 16 S rRNA gene, to estimate the order of inter- and intra-species divergence among these species and to establish phylogenetic and evolutionary relationships. The average inter-specific divergence was estimated as 7.10%. Intra-specific divergence of 0.20% and 0.10% was observed in B. gatensis and B. bendelisis that exhibited three and two haplotypes with 0.70 and 0.60 haplotype diversities, respectively. The NJ and MP phylogenetic trees were constructed using 16 S rRNA sequences along with sequences of the other five Indian cyprinid species retrieved from NCBI. Phylogenetic trees revealed five discrete branches each as a distinct species of the genus and exhibited identical phylogenetic relationship with other cyprinids. The study provided adequate information to distinguish the five Barilius species and indicated the suitability of 16S rRNA gene sequences in genetic divergence and phylogenetic studies.

Induction of micronuclei and nuclear lesions in Channa punctatus following exposure to carbosulfan, glyphosate and atrazine.

The genotoxic effects of commonly used agricultural pesticides viz., carbosulfan, glyphosate, and atrazine, were evaluated in Channa punctatus (Pisces, Perciformes) using micronucleus (MN) test and induction of nuclear lesions (NL). The 96 h LC50 value were estimated by probit analysis as 0.27, 32.0 and 42.0 mg L(-1), respectively, for carbosulfan, glyphosate, and atrazine using semi-static bioassays. Based on these values, three sublethal test concentrations of carbosulfan (0.07, 0.13, 0.20 mg L(-1)), glyphosate (8.1, 16.3, 24.4 mg L(-1)) and atrazine (10.6, 21.2, 31.8 mg L(-1)) corresponding to », ½ and ¾ of the LC50 of the pesticides respectively, were selected for exposure for 96 h. Peripheral blood samplings were taken at intervals of 24 h for assessment of MN and NL frequencies. Considerably higher genotoxic damage was induced by carbosulfan as compared to glyphosate and atrazine. There were significant effects (p < 0.01) of concentrations in all the treated groups. The induction of MN and NL was highest at 96 h pesticide exposure at all test concentrations. The nuclear abnormalities recorded in this study, such as blebbed-, lobed-, notched- and bi-nuclei, other than micronuclei, are indicators of genotoxic damage.

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.

BACKGROUND: Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. DESCRIPTION: FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. CONCLUSIONS: FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

UNLABELLED: DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. AVAILABILITY: The database is available for free at http://mail.nbfgr.res.in/fbis/

Fish Karyome: A karyological information network database of Indian Fishes.

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation.

A total of 1671 ESTs of Labeo rohita were retrieved from dbEST database and analysed for functional annotation using various computational approaches. The result indicated 1387 non-redundant (184 contigs and 1203 singletons) putative transcripts with an average length of 542 bp. These 1387 transcript sequences were matched with Refseq_RNA, UniGene and Swiss-Prot on high threshold cut-off for functional annotation along with help of gene ontology and SSRs markers. We developed extensive Perl programming based modules for processing all alignment files, comparing and extracting common hits from all files on a threshold, evaluating statistics for alignment results and assigning gene ontology terms. In this study, 92 putative transcripts predicted as orthologous genes and among those, 44 putative transcripts were annotated with gene ontology terms. The annotated orthologous gene of our result associated with some very important proteins of L. rohita involved in biotic and abiotic stresses and glucose metabolism of spermatogenic cells etc. The unidentified transcripts, if found important in expression profiling can be vital resource after re-sequencing. The predicted genes can further be used for enhancing productivity and controlling disease of L. rohita.

Toxicity of the herbicide atrazine: effects on lipid peroxidation and activities of antioxidant enzymes in the freshwater fish Channa punctatus (Bloch).

The present study was undertaken to evaluate the toxicity and effects of a commercial formulation of the herbicide atrazine (Rasayanzine) on lipid peroxidation and antioxidant enzyme system in the freshwater air breathing fish Channa punctatus. The 12, 24, 48, 72 and 96 h LC(50) of atrazine, calculated by probit analysis, were determined to be 77.091, 64.053, 49.100, 44.412 and 42.381 mg·L(-1), respectively, in a semi static system with significant difference (p < 0.05) in LC(10-90) values obtained for different times of exposure. In addition to concentration and time dependent decrease in mortality rate, stress signs in the form of behavioral changes were also observed in response to the test chemical. In fish exposed for 15 days to different sublethal concentrations of the herbicide (1/4 LC(50) = ∼10.600 mg·L(-1), 1/8 LC(50) = ∼5.300 mg·L(-1) and 1/10 LC(50) = ∼4.238 mg·L(-1)) induction of oxidative stress in the liver was evidence by increased lipid peroxidation levels. The antioxidants superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) responded positively in a concentration dependent pattern, thus, suggesting the use of these antioxidants as potential biomarkers of toxicity associated with contaminations exposure in freshwater fishes.

Nucleotide sequences and chromosomal localization of 45S and 5S rDNA in Neolissochilus hexagonolepis (Pisces, Cyprinidae), using dual-color fish.

Dual-color fluorescence in situ hybridization (FISH) was performed to study the simultaneous localization of major (45S) and minor (5S) family ribosomal RNA genes on chromosomes of Neolissochilus hexagonolepis. The partial 45S (18S, ITS 1, 5.8S, ITS 2 and 28S) and complete 5S (coding and NTS) rDNA units were amplified, sequenced, analyzed, and mapped on the metaphase chromosomes. The complete 18S, 5.8S and partial 28S rDNAs were 1849 bp, 157 bp and 1819 bp long, respectively. Internal transcribed spacers, namely ITS 1 (828 bp) and ITS 2 (359 bp), showed significant nucleotide variations from other fish species listed in NCBI database. The 5S rDNA contained an identical coding region of 120 bp and a highly divergent, non-transcribed 81-bp spacer. The specimens of N. hexagonolepis showed six bright fluorescent signals of 18S, while the 5S signals were present only on one pair of chromosomes. Subsequent analyses between conventional Ag-NORs and 18S rDNA FISH strongly suggested the possible inactivation of one pair of NORs that was localized at a telomeric position of a submetacentric chromosome. The sequencing and chromosomal localization of 45S and 5S rDNAs may serve as a useful genetic marker in taxonomic classification as well as in phylogenetic and evolutionary studies.