FishMap: A Community Resource for Zebrafish Genomics

Abstract

An enormous amount of information on a genomics scale is available for zebrafish (Danio rerio), which is a well-studied model organism for human diseases. However, a majority of this annotation is scattered in obscure data sources. There have been limited efforts to present it on a unified and integrated platform, which would help to understand the biological processes in this organism better. FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. The datasets have been methodically collected from various resources and supplementary information of publications and mapped to the zebrafish genome. The data are organized into nine major sections, which include comparative genomics, mapping and sequencing, gene and gene predictions, expression and regulation, and variation and repeats. A number of unique sections have been incorporated, which include tracks on noncoding gene annotation, location of retrovirus/transposon integrations in the genome, and their flanking genomic sequences and novel transcripts. The datasets are linked to related data sources. FishMap is built on the Gbrowse, which is a part of the Generic Model Organism Database Consortium Project. The resource also features a Web-based BLAST server for sequence homology search and a gene ID converter that would enable users to sift through different interchangeable gene annotation identifier systems. The database is amenable to programmatic access through the Distributed Annotation System as well as BioMoby protocols, thus making it a central community resource that can be integrated with existing data mining and analysis workflows. We hope that FishMap would be an integral resource for community participation in zebrafish genomics. The resource is freely available at http://miracle.igib.res.in/fishmap, or at http://fishmap.igib.res.in.

Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

“…Fish Map is a unified and centralized resource for storage, retrieval, and display of genomic information on zebrafish. FishMap is built on the Gbrowse, and is a part of the Generic Model Organism Database Consortium Project (GMOD) (Meli et al 2008). cBARBEL (Catfish Breeder and Researched Bioinformatics Entry Location) is an important catfish genome database and represents one of the first comprehensive bioinformatic databases for an aquaculture species (Lu et al 2010).…”

“…In contrast to other fishes, zebrafish have determinate growth, the number of muscle fibers is established and fixed at the time of the birth; and growth is solely due to hypertrophy of fibers already formed (Du 2004). This condition does not provide a general model for muscle growth since Table 1 The main web-based data sites currently available for zebrafish and aquacultured fishes (according to Briggs 2002;Clark 2003;Meli et al 2008;Johansen et al 2009;Lu et al 2010 it only reaches a modest ultimate body size (3-5 cm) (Johnston 1999;Mommsen 2001). However muscle differentiation, somite formation and subsequent differentiation of myoblasts are under the control of complex signaling pathways and of myogenic regulatory factors that are similar in all teleosteos (Du 2004).…”

Chromosome Evolution in African Cichlid Fish: Contributions from the Physical Mapping of Repeated DNAs

“…In addition, some species of Cichlidae, principally the tilapiines, are very important for aquaculture and fisheries, and the Nile tilapia, Oreochromis niloticus , represents one of the most widely farmed freshwater fish in the world [FAO, 2006]. Although the genomes of several African cichlid species will soon be sequenced [proposal by The International Cichlid Genome Consortium, 2006], knowledge of cichlid genomes is rather preliminary, and far behind pufferfish (Tetraodon nigroviridis) [Jaillon et al, 2004], zebrafish (Danio rerio) [Meli et al, 2008] and medaka (Oryzias latipes) [Kasahara et al, 2007]. So it is therefore of particular interest to investigate the chromosome structure of some representative taxa of the Cichlidae clade.…”

Anti-cancer Drug Discovery: Update and Comparisons in Yeast, Drosophila, and Zebrafish

“…With a large zebrafish genome database available at the Zebrafish Information Network (ZFIN) and at the FishMap website [40, 41], important details are now available to the research community. Additionally, optical clarity of zebrafish embryos and larvae allows visualization of expression of fluorescent protein-tagged transgene and in vivo observation of morphological defects.…”