MetaFishNet: a way to advance fish metabolic modeling

Recently scientists from USA and Germany have constructed a genome-wide fish metabolic network model, MetaFishNet. The recent completion of genome sequencing of five fish species (Danio. rerio, Oryzias latipes, Tetraodon rubripes, T. nigroviridis and Gasterosteus aculeatus) has paved the way for constructing a genome-wide fish metabolic network model.

All metabolic enzymes have been identified from complete genomes by sequence analysis, compounds were then be associated with enzymatic activities and a metabolic network was constructed by linking these compounds and enzymes. The first and primary role of MetaFishNet model is a bioinformatic tool for analyzing high throughput expression data, as well as a framework for future systems studies. This genome-wide model offers a significant expansion of the KEGG zebrafish model. MetaFishNet can be used compare fish and human metabolism to identify the most and least conserved pathways.

This study is published in the November, 2010 issue of Genome Biology.
http://genomebiology.com/2010/11/11/R115

Zv9, the most recent genome assembly for zebrafish.

The zebrafish (Danio rerio) is an important model organism for the study of vertebrate development and disease, organ function, behavior, and toxicology. Some of the features that make the zebrafish so experimentally amenable include its short generation time, large numbers of embryos produced per mating, and the development of transparent embryos outside the mother, allowing all stages of development to be observed. The Sanger Institute started the zebrafish genome sequencing project in 2001 and has released several genome assemblies, the latest is Zv9 .

Ninth assembly, Zv9 of the zebrafish genome released is recently been made available in the UCSC Genome Browser. This assembly comprises a total sequence length of 1.4 Gb in 4,560 scaffolds. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involves sequence alignments as well as cDNA, marker and BAC/Fosmid end sequence placements. The sequences that are based on clone contigs or are linked to chromosomes via markers are named 'Zv9_scaffold' followed by a number. The WGS contigs that could not be placed onto chromosomes are named 'Zv9_NA' followed by a number.

This preliminary assembly was produced by The Wellcome Trust Sanger Institute, UK.

http://www.sanger.ac.uk/Projects/D_rerio/

Genomic signature for fish coping with global warming

Cold-water fish such as salmon thrives in temperatures of 50 to 65 degrees Fahrenheit. According to a new study by NRDC and Defenders of Wildlife, global warming is likely to spur the disappearance of trout and salmon from as much as 18 to 38 percent of their current habitat by the year 2090. The study also found that habitat loss for individual species could be as high as 17 percent by 2030, 34 percent by 2060 and 42 percent by 2090 -- if emissions of heat-trapping pollution such as carbon dioxide are not reduced.

Canadian scientists have identified broad genetic signatures that can predict which fish will live or die before spawning a new generation. The study combined radio tracking of fish caught in the ocean and river with a genomic signature based on 32,000 genes in individual fish. Fish captured on the spawning grounds were tracked with tags. Researchers found that 60 per cent of the fish they tracked had genomic signatures predicting their fate. Genomic signatures are essentially responses of the fish's genome — the full array of genes — to a threat, with genes "turned on to guide the physiological and behavioural responses to the threat." The techniques used in the study have major promise as a new tool to guide fish restoration efforts.

This work represents a breakthrough in tracking how salmon are surviving new stresses from global warming. The study published in the January, 2011 edition of the journal Science.

http://www.sciencemag.org/content/331/6014/214.abstract?sid=2a274bc4-b33a-41e8-80e5-17c675485f80