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Fish as models for environmental genomics

Nature Reviews Genetics volume 6, pages 324–333 (2005)Cite this article

Abstract

Fish offer important advantages for defining the organism–environment interface and responses to natural or anthropogenic stressors. Genomic approaches using fish promise increased investigative power, and have already provided insights into the mechanisms that underlie short-term and long-term environmental adaptations. The range of fish species for which genomic resources are available is increasing, but will require significant further expansion for the optimal application of fish environmental genomics.

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Figure 1: Variation in gene expression within and between closely related species.
Figure 2: Transcript profiling as a phenotyping tool.
Figure 3: Distribution of fish genomic resources.

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Acknowledgements

We thank M. Berenbrink for helpful discussions and comments and anonymous referees for comments. A.R.C. was supported by long-term funding from the UK Natural Environmental Research Council who also have supported the Liverpool Microarray Facility. D.L.C. was supported by grants from the US National Science Foundation Biocomplexity Programme and the US National Heart Lung and Blood Institute.

Author information

Authors and Affiliations

  1. Liverpool Microarray Facility and Centre for BioArray Innovation, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom

    Andrew R. Cossins

  2. Centre for Marine Genomics, Rosenstiel School of Marine and Atmospheric Sciences, 4600 Rickenbacker Causeway, Miami, 33149, Florida, USA

    Douglas L. Crawford

Authors
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Correspondence to Andrew R. Cossins.

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Related links

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FURTHER INFORMATION

dbEST — Database of Expressed Sequence Tags

Fishbase

Gene Ontology

KEGG — Kyoto Encyclopedia of Genes and Genomes

Medaka Genome Project

Tetraodon Genome Browser

The Danio rerio Sequencing Project

The Fugu Genomics Project

Zebrafish Gene Collection

Glossary

FIXATION

The increase in the frequency of a genetic variant in a population to 100%.

FOSMID

A low-copy vector for the construction of stable genomic libraries that uses the Escherichia coli F-factor origin for replication.

GENE ONTOLOGY

A hierarchical organization of concepts and nomenclature for molecular function, biological processes and cellular components. It constitutes a controlled vocabulary with orderly relationships between parent and daughter terms, onto which known genes are mapped, and provides a useful means of categorizing gene lists into functionally meaningful groupings.

GENETIC DRIFT

(Also known as random drift.) A phenomenon whereby the frequency of a gene in a population changes over time because the number of offspring born to parents that carry the gene is subject to chance variation.

HAPPY MAPPING

A simple method for ordering markers and determining the physical distances between them. It uses sub-haploid equivalents of randomly sheared DNA and requires the use of whole-genome amplification methods to carry out many PCR reactions.

HIERARCHICAL ANALYSIS

An organization or 'clustering' of elements that best describes the relationships between them. A tree diagram or dendrogram is frequently used to represent the results of a cluster analysis, with cases of greatest similarity being adjacent to each other.

HOX CLUSTER

A family of genes involved in directing the morphological development of the body during early stages of life. In vertebrates they are clustered together on defined chromosomes and are widely believed to have originated by extensive duplication. The order of developmental expression over time is related to the position on the chromosome.

ISOGENIC

Cells or organisms that are derived from inbreeding or by genetic manipulation, and have identical or almost identical genomes.

KEGG SCHEME

A database comprising a collection of graphical pathway maps for metabolism, regulatory processes and other biological processes.

MORPHOLINO

A non-degradable antisense oligonucleotide in which the sugar component is replaced by a morpholine ring structure. Morpholinos are currently used to block target-gene expression in zebrafish, Xenopus laevis and sea urchins. They bind stably to target mRNAs in order to block translation, and give more consistent phenotypes than traditional antisense oligonucleotides.

NEUTRAL VARIATION

Variation in protein sequence that is not selectively important.

NEUTRAL HYPOTHESIS

An evolutionary model that assumes that the selective advantage of the variation in a trait is insufficient to provide any fitness advantage. Changes in allele frequency are said to be the result of chance alone, or 'drift'.

PARALOGY

Paralogous genes show homology because they originated as a result of duplication of a single ancestral gene.

QTL

(Quantitative trait loci). A genetic locus that is identified through the statistical analysis of quantitative traits (such as height in plants or body weight in animals). These traits are typically affected by more than one gene and also by the environment.

RADIATION HYBRIDS

Cells produced by fusing irradiated donor cells that contain chromosomal fragments with recipient rodent cells to produce a panel of cell lines. Each of these cell lines contains fragments of donor chromosomes, which can be used to screen for physical linkage of genetic or physical markers. The resulting maps are indispensable tools for the positional cloning of candidate genes.

STANDING GENETIC VARIATION

The genetic variation or heterozygosity that occurs between individuals in laboratory or natural populations.

SYTENY

Collinearity in the order of genes (or of other DNA sequences) in a chromosomal region of two species.

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Cossins, A., Crawford, D. Fish as models for environmental genomics. Nat Rev Genet 6, 324–333 (2005). https://doi.org/10.1038/nrg1590

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