Genomics-enabled research in marine ecology: Challenges, risks and pay-offs

Marine Ecology Progress Series

Volumn 332, Issue , 2007, Pages 249-255

  Hofmann, Gretchen E ^a   Place, Sean P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA microarrays; Gene expression; Genomics; Marine ecology; Transcriptomics

Indexed keywords

DNA; ENVIRONMENTAL CONDITIONS; EQUIPMENT; GENE EXPRESSION; GENOMICS; MARINE ECOSYSTEM; PHYSIOLOGICAL RESPONSE; RANGE SIZE;

INVERTEBRATA;

EID: 34047157533     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps332249     Document Type: Article

References (48)

1. Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nature Rev Genet 7:55
2. Almeida JS, McKillen DJ, Chen YA, Gross PS, Chapman RW, Warr G (2005) Design and calibration of microarrays as universal transcriptomic environmental biosensors. Comp Funct Genom 6:132-137
3. Baker AC (2003) Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annu Rev Ecol Evol Syst 34:661-689
4. Buckley BA, Gracey AY, Somero GN (2006) The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. J Exp Biol 209:2660-2677
5. Chun CK, Scheetz TE, Bonaldo MF, Brown B and 20 others (2006) An annotated cDNA library of juvenile Eupryma scolopes with and without colonization by the symbiont Vibrio fischeri, BioMed Central (BMC) Genom 7:154
6. Clark MS, Clarke A, Cockell CS (2004) Antarctic genomics. Comp Funct Genom 5:230-238
7. Dhar AK, Dettori A, Roux MM, Klimpel KR, Read B (2003) Identification of differentially expressed genes in shrimp (Penaeus stylirostris) infected with white spot syndrome virus by cDNA microarrays. Arch Virol 148:2381-2396
8. Dondero F, Piacentini L, Marsano F, Rebelo M, Vergani L, Venier P, Viarengo A (2006) Gene transcription profiling in pollutant exposed mussels (Mytilus spp.) using a new low-density oligonucleotide microarray. Gene 376:24
9. Feder ME, Mitchell-Olds T (2003) Evolutionary and ecological functional genomics. Nature Rev Genet 4:649-655
10. Feder ME, Walser JC (2005) The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol 18:901-910
11. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
12. Gaston KJ (2003) The structure and dynamics of geographic ranges. Oxford University Press, Oxford
13. Gaylord B, Gaines SD (2000) Temperature or transport? Range limits in marine species mediated solely by flow. Am Nat 155:769-789
14. Gibson G (2002) Microarrays in ecology and evolution: a preview. Mol Ecol 11:17-24
15. Gracey AY, Cossins AR (2003) Application of microarray tech nology in environmental and comparative physiology. Annu Rev Physiol 65:231-259
16. Gracey AY, Troll JV, Somero GN (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci USA 98:1993-1998
17. Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR (2004) Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101:16970-16975
18. Hofmann GE, Burnaford JL, Fielman KT (2005) Genomics-fueled approaches to current challenges in marine ecology, Trends Ecol Evol 20:305-311
19. Jackson RB, Linder CR, Lynch M, Purugganan M, Somerville S, Thayer SS (2002) Linking molecular insight and ecological research. Trends Ecol Evol 17:409-414
20. Jenny MJ, Ringwood AH, Schey K, Warr GW, Chapman RW (2004) Diversity of metallothioneins in the American oyster, Crassostrea virginica, revealed by transcriptomic and proteomic approaches. Eur J Biochem 271:1702-1712
21. Ji W, Zhou W, Gregg K, Yu N, Davis S, Davis S (2004) A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res 32:e93, doi:10.1093/nar/gnh084
22. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients, Science 311:1737-1740
23. Klaper R, Thomas MA (2004) At the crossroads of genomics and ecology: the promise of a canary on a chip. BioScience 54:403-412
24. Marsh AG, Fielman KT (2005) Transcriptome profiling of individual larvae of two different developmental modes in the poecilogonous polychaete Streblospio benedicti (Spionidae). J Exp Zool 304B:238-249
25. McKillen D, Chen Y, Chen C, Jenny M and 7 others (2005) Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. BioMed Central (BMC) Genom 6:34
26. Oleksiak MF, Churchill GA, Crawford DL (2002) Variation in gene expression within and among natural populations, Nat Genet 32:261
27. Oleksiak MF, Roach JL, Crawford DL (2005) Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet 37:67
28. Osovitz CJ, Hofmann GE (2005) Thermal history-dependent expression of the hsp70 gene in purple sea urchins: biogeographic patterns and the effect of temperature acclimation. J Exp Mar Biol Ecol 327:134
29. Osovitz CJ, Hofmann GE (2007) Marine macrophysiology: studying physiological variation across large spatial scales in marine systems. Comp Biochem Physiol
30. Partensky F, Hess WR, Vaulot D (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63:106-127
31. Podrabsky JE, Somero GN (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 207:2237-2254
32. Ranz JM, Machado CA (2006) Uncovering evolutionary patterns of gene expression using microarrays. Trends Ecol Evol 21:29-37
33. Renn S, Aubin-Horth N, Hofmann H (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BioMed Central (BMC) Genom 5:42
34. Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R (2004) When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 134:1683-1696
35. Rodriguez-Lanetty M, Phillips W, Weis V (2006) Transcriptome analysis of a cnidarian - dinoflagellate mutualism reveals complex modulation of host gene expression. Bio-Med Central (BMC) Genom 7:23
36. Rowan R (2004) Coral bleaching: thermal adaptation in reef coral symbionts. Nature 430:742
37. Sagarin RD, Somero GN (2006) Complex patterns of expression of heat-shock protein 70 across the southern biogeographical ranges of the intertidal mussel Mytilus californianus and snail Nucella ostrina. J Biogeogr 33:622-630
38. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
39. Schwarz J, Brokstein P, Manohar C, Coffroth MA, Szmant A, Medina M (2006) Coral reef genomics: developing tools for functional genomics of coral symbiosis. In: Proc 10th Int Coral Reef Symp. Japanese Coral Reef Society, Okinawa, p 274-281
40. Seki M, Narusaka M, Ishida J, Nanjo T and 14 others (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279-292
41. Somero G (2005) Linking biogeography to physiology: evolutionary and acclimatory adjustments of thermal limits. Front Zool 2:1
42. Sorte CJB, Hofmann GE (2005) Thermotolerance and heat-shock protein expression in Northeastern Pacific Nucella species with different biogeographical ranges. Mar Biol 146:985-993
43. Stillman JH, Teranishi KS, Tagmount A, Lindquist EA, Brokstein PB (2006) Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes, Integr Comp Biol 46:919-930
44. Thomas MA, Klaper R (2004) Genomics for the ecological toolbox. Trends Ecol Evol 19:439-445
45. van Straalen NM, Roelofs D (2006) Introduction to ecological genomics. Oxford University Press, Oxford
46. Venter JC, Remington K, Heidelberg JF, Halpern AL and 19 others (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
47. Wilson K, Thorndyke M, Nilsen F, Rogers A, Martinez P (2005) Marine systems: moving into the genomics era. PSZN I: Mar Ecol 26:3-16
48. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288