Genomic approaches with natural fish populations from polluted environments

Environmental Toxicology and Chemistry

Volumn 30, Issue 2, 2011, Pages 283-289

  Bozinovic, Goran ^a   Oleksiak, Marjorie F ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MIAMI   (United States)

Author keywords

Fundulus heteroclitus; Genomics; Natural populations; Pollution

Indexed keywords

BIOLOGICAL COMPLEXITY; BIOLOGICAL MECHANISMS; CANDIDATE GENES; FISH POPULATIONS; FUNDULUS HETEROCLITUS; GAIN INSIGHT; GENOMIC RESPONSE; GENOMICS; GENOTYPING; NATURAL POPULATION; TRANSCRIPTOMICS;

FISHERIES; LIVING SYSTEMS STUDIES; POLLUTION;

GENE EXPRESSION;

TRANSCRIPTOME;

CYPRINID; GENE EXPRESSION; GENOMICS; POLLUTION EFFECT; POLYMORPHISM;

ARTICLE; ATLANTIC COD; CYPRINODONTIFORMES; ENVIRONMENT; FISH; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC POLYMORPHISM; GENOMICS; GENOTYPE; MICROARRAY ANALYSIS; MICROGADUS TOMCOD; NATURAL POPULATION; NONHUMAN; PHENOTYPE; PLATICHTHYS FLESUS; PLEURONICHTHYS VERTICALIS; POLLUTANT; POLLUTION; POPULATION GENETICS; PRIORITY JOURNAL; TRANSCRIPTOMICS; WATER POLLUTION;

ANIMALS; ENVIRONMENTAL POLLUTANTS; FISHES; GENE EXPRESSION PROFILING; GENETICS, POPULATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROARRAY ANALYSIS; WATER POLLUTANTS; WATER POLLUTION;

FUNDULUS HETEROCLITUS;

EID: 78651352523     PISSN: 07307268     EISSN: 15528618     Source Type: Journal    
DOI: 10.1002/etc.403     Document Type: Article

References (43)

1. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. 2003. The power and promise of population genomics: From genotyping to genome typing. Nat Rev Genet 4: 981-994.
2. Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D. 2009. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol 18: 3128-3150.
3. Cossins AR, Crawford DL. 2005. Fish as models for environmental genomics. Nat Rev Genet 6: 324-333.
4. Oleksiak MF. 2010. Genomic approaches with natural fish populations. J Fish Biol 76: 1067-1093.
5. Oleksiak MF, Kolell KJ, Crawford DL. 2001. Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar Biotechnol (NY) 3: S203-211.
6. Morozova O, Hirst M, Marra MA. 2009. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10: 135-151.
7. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17: 1636-1647.
8. Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, Glover E, Silander T, Craven MW, Reddy JK, Jovanovich SB, Bradfield CA. 2001. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol 60: 1189-1194.
9. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tannant R, Stoll R, Barrett JC, Blanchard K, Paules RS, Afshari CA. 2002. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 67: 219-231.
10. Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nat Genet 32: 261-266.
11. Oleksiak MF, Roach JL, Crawford DL. 2005. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet 37: 67-72.
12. Williams TD, Gensberg K, Minchin SD, Chipman JK. 2003. A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquat Toxicol 65: 141-157.
13. Falciani F, Diab AM, Sabine V, Williams TD, Ortega F, George SG, Chipman JK. 2008. Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants. Aquat Toxicol 90: 92-101.
14. Baker ME, Ruggeri B, Sprague LJ, Eckhardt-Ludka C, Lapira J, Wick I, Soverchia L, Ubaldi M, Polzonetti-Magni AM, Vidal-Dorsch D, Bay S, Gully JR, Reyes JA, Kelley KM, Schlenk D, Breen EC, Sasik R, Hardiman G. 2009. Analysis of endocrine disruption in Southern California coastal fish using an aquatic multispecies microarray. Environ Health Perspect 117: 223-230.
15. Lie KK, Lanzen A, Breilid H, Olsvik PA. 2009. Gene expression profiling in Atlantic cod (Gadus morhua L.) from two contaminated sites using a custom-made cDNA microarray. Environ Toxicol Chem 28: 1711-1721.
16. Burnett KG, Bain LJ, Baldwin WS, Callard GV, Cohen S, Di Giulio RT, Evans DH, Gomez-Chiarri M, Hahn ME, Hoover CA, Karchner SI, Katoh F, Maclatchy DL, Marshall WS, Meyer JN, Nacci DE, Oleksiak MF, Rees BB, Singer TD, Stegeman JJ, Towle DW, Van Veld PA, Vogelbein WK, Whitehead A, Winn RN, Crawford DL. 2007. Fundulus as the premier teleost model in environmental biology: Opportunities for new insights using genomics. Comp Biochem Physiol Part D Genomics Proteomics 2: 257-286.
17. Powers DA, Ropson I, Brown DC, van Beneden R, Cashon R, Gonzalez-Villasenor LA, DiMichele JA. 1986. Genetic variation in Fundulus heteroclitus: Geographic distribution. Am Zool 26: 131-144.
18. Van Veld PA, Nacci DE. 2008. Toxicity resistance. In Di Giulio RT, Hinton DE, eds, The Toxicology of Fishes. Taylor and Francis, Boca Raton, FL, USA, pp 597-641.
19. Roling JA, Bain LJ, Gardea-Torresdey J, Key PB, Baldwin WS. 2007. Using mummichog (Fundulus heteroclitus) arrays to monitor the effectiveness of remediation at a superfund site in Charleston, South Carolina, U.S.A. Environ Toxicol Chem 26: 1205-1213.
20. Fisher MA, Oleksiak MF. 2007. Convergence and divergence in gene expression among natural populations exposed to pollution. BMC Genomics 8: 108.
21. Oleksiak MF. 2008. Changes in gene expression due to chronic exposure to environmental pollutants. Aquat Toxicol 90: 161-171.
22. Pruell RJ, Norwood CB, Bowen RD, Boothman WS, Rogerson PF, Hackett M, Butterworth BC. 1990. Geochemical study of sediment contamination in New Bedford Harbor, Massachusetts. Mar Environ Res 29: 77-102.
23. Wolfe DA, Long ER, Thursby GB. 1996. Sediment toxicity in the Hudson-Raritan Estuary: Distribution and correlations with chemical contamination. Estuaries 19: 901-912.
24. Bieri RH, Hein C, Huggett RJ, Shou P, Slone H, Smith H, Su C-W. 1986. Polycyclic Aromatic Hydrocarbons in Surface Sediments from the Elizabeth River Subesturary. Int J Environ Anal Chem 26: 97-113.
25. Bozinovic G, Oleksiak MF. 2010. Embryonic gene expression among pollutant resistant and sensitive Fundulus heteroclitus populations. Aquat Toxicol 98: 221-229.
26. Carlson EA, Roy NK, Wirgin II. 2009. Microarray analysis of polychlorinated biphenyl mixture-induced changes in gene expression among Atlantic tomcod populations displaying differential sensitivity to halogenated aromatic hydrocarbons. Environ Toxicol Chem 28: 759-771.
27. Storz JF. 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol Ecol 14: 671-688.
28. Stinchcombe JR, Hoekstra HE. 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100: 158-170.
29. Hoffman JI, Amos W. 2005. Microsatellite genotyping errors: Detection approaches, common sources and consequences for paternal exclusion. Mol Ecol 14: 599-612.
30. Hauser L, Seeb JE. 2008. Advances in molecular technology and their impact on fisheries genetics. Fish Fish 9: 473-486.
31. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
32. Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad KT, Fevolden SE, Berg PR, Lien S. 2008. Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genet 9: 18.
33. Ragoussis J. 2009. Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 10: 117-133.
34. De la Vega FM, Lazaruk KD, Rhodes MD, Wenz MH. 2005. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP genotyping assays and the SNPlex genotyping system. Mutat Res 573: 111-135.
35. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
36. Theodorakis CW, Lee KL, Adams SM, Law CB. 2006. Evidence of altered gene flow, mutation rate, and genetic diversity in redbreast sunfish from a pulp-mill-contaminated river. Environ Sci Technol 40: 377-386.
37. Makinen HS, Cano JM, Merila J. 2008. Identifying footprints of directional and balancing selection in marine and freshwater three-spined stickleback (Gasterosteus aculeatus) populations. Mol Ecol 17: 3565-3582.
38. Nielsen EE, Hemmer-Hansen J, Poulsen NA, Loeschcke V, Moen T, Johansen T, Mittelholzer C, Taranger GL, Ogden R, Carvalho GR. 2009. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol 9: 276.
39. Rogers SM, Bernatchez L. 2007. The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonus sp. Salmonidae) species pairs. Mol Biol Evol 24: 1423-1438.
40. Vasemagi A, Nilsson J, Primmer CR. 2005. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.). Mol Biol Evol 22: 1067-1076.
41. Williams LM, Oleksiak MF. 2008. Signatures of selection in natural populations adapted to chronic pollution. BMC Evol Biol 8: 282.
42. Jelinek R. 2005. The contribution of new findings and ideas to the old principles of teratology. Reprod Toxicol 20: 295-300.
43. Ayroles JF, Carbone MA, Stone EA, Jordan KW, Lyman RF, Magwire MM, Rollmann SM, Duncan LH, Lawrence F, Anholt RR, Mackay TF. 2009. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet 41: 299-307.