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

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

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

Journal of Computational Chemistry & Molecular Modeling

Not AvailableTo elicit growth and related functions, the interaction of growth hormone receptor (GHR) with growth hormone (GH) is vital as this contact passes the message downstream to the metabolic pathways. The crystal structure of GHR and GH in Labeo rohita is still vague. This study discusses prediction of 3D structures of GHR and GH, validation of predicted structures and binding affinity of GHR with GH. Discovery studio 4.1 software was used for homology modelling and docking of GHR with GH. The best model for GHR (DOPE score: -16527.1) and GH (DOPE score: -17613.3) were used for docking by ZDOCK pro. The docked complex obtained from the interaction of GHR with GH (GHR-GH, ZDOCK score: 19.26) was refined by RDOCK (RDOCK score: -25.642). The findings revealed that GHR-GH complex is stable and interacting amino acids in GHR are R43, E44, I108, D126, E127, D164, R159, W166, W169, and in GH are F3, L45, K49, P61, R64, D116, G128, K172, T175, R178. The interaction of amino acids in the active pockets of complex and its duration provides insight into the actions of GH in Labeo rohita. In addition, docking of GHR with GH provides information about the type of interaction at the binding sites of ligand and receptor and interacting amino acids viz. PHE3, ALA22, TYR98, LEU114, MET145, VAL149, LEU150 and PHE199. Thus, docking of the GHR with GH is useful in understanding the structural information and developing specific receptor antagonists beside providing support in establishing therapeutic approaches in teleost fishes

Journal of Experimental Zoology, India

Not AvailableExplorations are conducted by the researchers to identify and document the flora and fauna found in different geographic locations of the world. In this process, several new species are discovered every year by the researcher, which are phenotypically and/or genotypically different from other species of their cogners. During 2015-16, fifty-seven new species were discovered from the different parts of the country India out of which, 35 new fish species were recorded during the year 2015 and 22 new species during the year 2016. Most of the new discoveries were from the two biodiversity hotspot areas, North-eastern region and Western Ghats. Family Cyprinidae dominates with 21 new species followed by Badidae with 8 species and Sisoridae with 7 species. These discoveries were mainly from the freshwater (48 species) and marine water (9 species). The collected data was analysed to indicate area-wise species richness. It is evident that about 10 percent of global fish diversity is reported from Indian region, which shows high richness in fish resources and further documentation of newly discovered fishes will strengthen the process of maintaining the register of living fish resources of India

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Not AvailableWorldwide, global databases on fishes lack fish diversity information at regional scale of a country, which hasfascinated many fishery workers to know the regional scale fish diversity. Databases are essential part of thebiodiversity science and have been used widely in the biological research. The present study discusses development,services and utility of the database application (UPFBase) providing information on the freshwater fish biodiversityof Uttar Pradesh. To develop UPFBase, data on the fish biodiversity of this region was compiled from differentsources that include primary data generated from different projects and secondary data from published literatures.The collected data were screened and then digitized. Microsoft ACCESS relational database and Visual Basiclanguage technologies were used for designing and implementing the standalone database application with the datamanagement capability. Presently, UPFBase provides taxonomy, synonyms, local name, common name, morphology,biology, distribution, habitat, economic importance, conservation status and other fishery information on 129 fishesbelonging to 11 orders and 27 families. UPFBase is user friendly and provides ease in working through search,query and action command button tools. It can easily be deployed on the mobile storages devices like CD-ROM,Pen drive, PCMCIA etc and can be installed on any Windows based Intel x86 machines. This version of UPFBasewas built for countries, where computational hardware and software resources are in scare and it is expected that itmight play imperious role in knowing and managing the indigenous fish diversity for decision making and posterity.Not Availabl

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Not AvailableBackground. The Ganga River (Ganges) is known of its rich fish diversity which is adversely affected by degrading environmental and ecological conditions. There are more than 300 exotic fish species in India. Many of them (particularly Cyprinus carpio) escaped from confinement and are now present in the Ganga River, challenging its ecological equilibrium. The aim of this project was to study the population characteristics of Cyprinus carpio (i.e., the abundance, size range, food and feeding, gonado-somatic index (GSI), gonad maturity stage, maturity and breeding) and the altered fishery dynamics. Materials and Methods. The commercially caught fishes, including the exotic ones, were identified, examined and measured. Important indices such as: the abundance index of exotic fishes, the gonado-somatic index (IG), as well as the gonad maturity stage of the escapee C. carpio were determined. The gut content was also analyzed to identify food items and there after the food richness, diet breadth, and gut repletion index (GRI%) were calculated using the Simpson's diversity index. Results. C. carpio introduced about sixty years ago for aquaculture has now been found to invade into the Ganga, the largest river of the country contributing significantly to the fishery. The abundance index of C. carpio ranged from 12.2% to 45.5% in 250 km long river stretch of the Ganga River flowing along Kanpur to Varanasi in the state of Uttar Pradesh. The gut content analysis revealed the presence of Eichhornia (9.8%), Pistia (11.6%), Nymphaea (8.5%), annelids worms (7.8%), algae (20.2%), mud and detritus (14.8%). The calculated diet breadth ranged from 0.82% to 0.91%; food richness ranged from 12 to 16, and the gut repletion index (GRI%) was 100% at different sampling sites. Mature females represented all the six reproductive stages with varying gonado-somatic index (IG) (0.5 to 30) in different catches. Presence of spent, ripe, and mature females was recorded. Conclusion. Abundance of exotic fish primarily C. carpio and Oreochromisniloticus in the fishery of the Ganga River was observed. The gonado-somatic index (IG) and the presence of all the six gonadal stages confirmed that C. carpio established its breeding population. The dominant catch of exotic fishes negatively impacted on the important indigenous fishes particularly Indian major carps (Catla catla, Labeo rohita, and Cirrhinus mrigala). The change in dynamics of the fishery due to the presence of common carp attracted attention to conserve rich indigenous germplasm facing threats of shifting from their natural habitats .Not Availabl

A regional information system on fishes from the Western Ghats, India: Its design, implementation and utility

1305-1309Present study discusses design and implementation of an information system for fish biodiversity of Western Ghats region. The system was developed by collating data from published reliable sources and applying Visual Basic language, MSACESS database and ADOBE image technologies for the Windows platform. The system through different search options provides ability to browse taxonomic, distribution, conservation status, morphology, environment and other fishery information of fish species of interest with good quality images. It incorporates information on 373 fish species belonging to 45 families and 141 genus. Of the 373 fish species,141 are endemic to this region and 8 are exotic. This serves as fish checklist resource of this region

Community Ecology

Not AvailableLuni is an ecologically fragile and ephemeral saline river of socio-economic significance for indigenous peoples of the Thar Desert, India. The present study aims for mapping the ichthyofaunal diversity of an unexplored river Luni and its relationship with habitat parameters based on field surveys conducted from October, 2018 to November, 2019. The diverse habitats of river Luni support 27 fish species and the highest diversity was recorded from midstream segment (19 species) followed by downstream (14 species). The index of diversity (H = 2.35) and dominance (D = 0.133) indicated rich fish diversity and even distribution. The relational analysis of habitat variables with abundance of cyprinids revealed, altitude and oxidation reduction potential as the key drivers for its distribution in the upstream segment of the river. This study provides an evidence for establishment of invasive species especially Oreochromis mossambicus and its impact on the fish assemblage structure of arid river Luni. The major anthropogenic factors threatening biodiversity and pristine habitats are mining, release of effluents and excess canal water, unplanned developmental activities in the riparian corridor and establishment of non-native species. The baseline information generated on fish assemblage pattern and habitat status of the river Luni can assist in formulating strategies for the conservation and management of this riverine ecosystem to support the livelihood of local communities

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Not AvailableCyprinus carpio is world’s most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from “Gene” and “RefSeq” databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi

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Not AvailableSeveral 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.CABin Scheme of ICAR, implemented through ICAR-IASRI, New Delhi