Microarrays for comparative and ecological genomics: Beyond single-species applications of array technologies

Journal of Fish Biology

Volumn 72, Issue 9, 2008, Pages 2407-2434

  Kassahn, K S ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Cross species; Heterologous microarray experiments; Microarrays; Multispecies microarrays; Next generation sequencing technologies; Teleost fishes

Indexed keywords

TELEOSTEI;

EID: 44949151534     PISSN: 00221112     EISSN: 10958649     Source Type: Journal    
DOI: 10.1111/j.1095-8649.2008.01890.x     Document Type: Review

References (93)

1. Adjaye, J., Herwig, R., Herrmann, D., Wruck, W., BenKahla, A., Brink, T., Nowak, M., Carnwath, J., Hultschig, C., Niemann, H. Lehrach, H 2004). Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics 5, 83.
2. Andolfatto, P. Przeworski, M 2000). A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156, 257 268.
3. Aubin-Horth, N., Letcher, B. H. Hofmann, H. A 2005). Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon. Journal of Heredity 96, 261 278.
4. Bar-Or, C., Bar-Eyal, M., Gal, T. Z., Kapulnik, Y., Czosnek, H. Koltai, H 2006). Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results. BMC Genomics 7, 110.
5. Bar-Or, C., Czosnek, H. Koltai, H 2007). Cross-species microarray hybridizations: a developing tool for studying species diversity. Trends in Genetics 23, 200 207.
6. Bindner, H 2006a). GeneChip microarrays - signal intensities, RNA concentrations and probe sequences. Journal of Physics: Condensed Matter 18, S537 S566.
7. Bindner, H 2006b). Thermodynamics of competitive surface adsorption on DNA microarrays. Journal of Physics: Condensed Matter 18, S491 S523.
8. Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S. Van de Peer, Y 2006). The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biology 7, R43.
9. Bock, C. Lengauer, T 2008). Computational epigenetics. Bioinformatics 24, 1 10.
10. Brodsky, L. I., Jacob-Hirsch, J., Avivi, A., Trakhtenbrot, L., Zeligson, S., Amariglio, N., Paz, A., Korol, A. B., Band, M., Rechavi, G. Nevo, E 2005). Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression. Proceedings of the National Academy of Sciences of the United States of America 102, 17047 17052.
11. Brunelle, B., Nicholson, T. Stephens, R 2004). Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis. Genome Biology 5, R42.
12. Buckley, B. A 2007). Comparative environmental genomics in non-model species: using heterologous hybridization to DNA-based microarrays. Journal of Experimental Biology 210, 1602 1606.
13. Cassar-Malek, I., Passelaigue, F., Bernard, C., Leger, J. Hocquette, J. F 2007). Target genes of myostatin loss-of-function in muscles of late bovine fetuses. BMC Genomics 8, 63.
14. Chismar, J. D., Mondala, T., Fox, H., Roberts, E., Langford, D., Masliah, E., Salomon, D. R. Head, S. R 2002). Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. Biotechniques 33, 516 524.
15. Christoffels, A., Koh, E. G. L., Chia, J. M., Brenner, S., Aparicio, S. Venkatesh, B 2004). Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Molecular Biology and Evolution 21, 1146 1151.
16. Cossins, A. R. Crawford, D. L 2005). Fish as models for environmental genomics. Nature Reviews Genetics 6, 324 333.
17. Crow, K. D. Wagner, G. P 2006). What is the role of genome duplication in the evolution of complexity and diversity? Molecular Biology and Evolution 23, 887 892.
18. Crow, K. D., Stadler, P. F., Lynch, V. J., Amemiya, C. Wagner, G. P 2006). The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Molecular Biology and Evolution 23, 121 136.
19. Donoghue, P. C. J. Purnell, M. A 2005). Genome duplication, extinction and vertebrate evolution. Trends in Ecology & Evolution 20, 312 319.
20. Draghici, S., Khatri, P., Eklund, A. C. Szallasi, Z 2006). Reliability and reproducibility issues in DNA microarray measurements. Trends in Genetics 22, 101 109.
21. Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., Doxiadis, G. M., Bontrop, R. E. Paabo, S 2002). Intra- and interspecific variation in primate gene expression patterns. Science 296, 340 343.
22. Evertsz, E. M., Au-Young, J., Ruvolo, M. V., Lim, A. C. Reynolds, M. A 2001). Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays. Biotechniques 31, 1182 1192.
23. Feder, M. E. Mitchell-Olds, T 2003). Evolutionary and ecological functional genomics. Nature Reviews Genetics 4, 651 657.
24. Froschauer, A., Braasch, I. Volff, J. N 2006). Fish genomes, comparative genomics and vertebrate evolution. Current Genomics 7, 43 57.
25. Gilad, Y., Rifkin, S. A., Bertone, P., Gerstein, M. White, K. P 2005). Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research 15, 674 680.
26. Girke, T., Todd, J., Ruuska, S., White, J., Benning, C. Ohlrogge, J 2000). Microarray analysis of developing Arabidopsis seeds. Plant Physiology 124, 1570 1581.
27. Gracey, A. Y 2007). Interpreting physiological responses to environmental change through gene expression profiling. Journal of Experimental Biology 210, 1584 1592.
28. Gracey, A. Y., Troll, J. V. Somero, G. N 2001). Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proceedings of the National Academy of Sciences of the United States of America 98, 1993 1998.
29. Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A. Cossins, A. R 2004). Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proceedings of the National Academy of Sciences of the United States of America 101, 16970 16975.
30. Gunnarsson, L., Kristiansson, E., Forlin, L., Nerman, O. Larsson, D. G. J 2007). Sensitive and robust gene expression changes in fish exposed to estrogen - a microarray approach. BMC Genomics 8, 149.
31. Hall, N 2007). Advanced sequencing technologies and their wider impact in microbiology. Journal of Experimental Biology 210, 1518 1525.
32. Hammond, J. P., Broadley, M. R., Craigon, D. J., Higgins, J., Emmerson, Z. F., Townsend, H. J., White, P. J. May, S. T 2005). Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. Plant Methods 1, 10.
33. Hinchliffe, S. J., Isherwood, K. E., Stabler, R. A., Prentice, M. B., Rakin, A., Nichols, R. A., Oyston, P. C. F., Hinds, J., Titball, R. W. Wren, B. W 2003). Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Research 13, 2018 2029.
34. Hittel, D. Storey, K. B 2001). Differential expression of adipose- and heart-type fatty acid binding proteins in hibernating ground squirrels. Biochimica et Biophysica Acta 1522, 238 243.
35. Hogstrand, C., Balesaria, S. Glover, C. N 2002). Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Comparative Biochemistry and Physiology. B 133, 523 535.
36. Huang, G. S., Yang, S. M., Hong, M. Y., Yang, P. C. Liu, Y. C 2000). Differential gene expression of livers from ApoE deficient mice. Life Sciences 68, 19 28.
37. Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S. C., Hoffman, E., Jedlicka, A. E., Kawasaki, E., Martinez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., Quackenbush, J., Scott, A., Wilson, M., Yang, Y., Ye, S. Q. Yu, W 2005). Multiple-laboratory comparison of microarray platforms. Nature Methods 2, 345 350.
38. Jaillon, O., Aury, J. M., Brunet, F., Petit, J. L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., Dossat, C., Segurens, B., Dasilva, C., Salanoubat, M., Levy, M., Boudet, N., Castellano, S., Anthouard, R., Jubin, C., Castelli, V., Katinka, M., Vacherie, B., Biemont, C., Skalli, Z., Cattolico, L., Poulain, J., de Berardinis, V., Cruaud, C., Duprat, S., Brottier, P., Coutanceau, J. P., Gouzy, J., Parra, G., Lardier, G., Chapple, C., McKernan, K. J., McEwan, P., Bosak, S., Kellis, M., Volff, J. N., Guigo, R., Zody, M. C., Mesirov, J., Lindblad-Toh, K., Birren, B., Nusbaum, C., Kahn, D., Robinson-Rechavi, M., Laudet, V., Schachter, V., Quetier, F., Saurin, W., Scarpelli, C., Wincker, P., Lander, E. S., Weissenbach, J. Crollius, H. R 2004). Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946 957.
39. 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 Research 32, e93.
40. Jordan, I. K., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y. Koonin, E 2001). Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. Genome Biology 2, research0053.0051-0053.0059.
41. Kane, M., Jatkoe, T., Stumpf, C., Lu, J., Thomas, J. Madore, S 2000). Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Research 28, 4552 4557.
42. Kassahn, K., Crozier, R., Ward, A., Stone, G. Caley, M 2007a). From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics 8, 358.
43. Kassahn, K. S., Caley, M. J., Ward, A. C., Connolly, A. R., Stone, G. Crozier, R. H 2007b). Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. Molecular Ecology 16, 1749 1763.
44. Kim, C., Joyce, E., Chan, K. Falkow, S 2002). Improved analytical methods for microarray-based genome-composition analysis. Genome Biology 3, research0065.0061-0065.0017.
45. Kirchner, S., McDaniel, N. K., Sugiura, S. H., Soteropoulos, P., Tian, B., Fletcher, J. W. Ferraris, R. P 2007). Salmonid microarrays identify intestinal genes that reliably monitor P deficiency in rainbow trout aquaculture. Animal Genetics 38, 319 331.
46. Koskinen, H., Pehkonen, P., Vehniainen, E., Krasnov, A., Rexroad, C., Afanasyev, S., Molsa, H. Oikari, A 2004). Response of rainbow trout transcriptome to model chemical contaminants. Biochemical and Biophysical Research Communications 320, 745 753.
47. Krasnov, A., Koskinen, H., Pehkonen, P., Rexroad, C. E., Afanasyev, S. Molsa, H 2005). Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics 6, 3.
48. Laird, P. W 2003). The power and the promise of DNA methylation markers. Nature Reviews Cancer 3, 253 266.
49. Le Quéré, A., Eriksen, K. A., Rajashekar, B., Schutzenbubel, A., Canback, B., Johansson, T. Tunlid, A 2006). Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays. Molecular Ecology 15, 535 550.
50. Lee, M., Xiang, C. C., Trent, J. M. Bittner, M. L 2007). Performance characteristics of 65-mer oligonucleotide microarrays. Analytical Biochemistry 368, 70 78.
51. Liu, X. S 2007). Getting started in tiling microarray analysis. PLoS Computational Biology 3, 1842 1844.
52. Liu, F., Jenssen, T. K., Trimarchi, J., Punzo, C., Cepko, C. L., Ohno-Machado, L., Hovig, E. Patrick Kuo, W 2007). Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 8, 153.
53. MACQ Consortium (2006). The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 24, 1151 1161.
54. Makalowski, W., Zhang, J. H. Boguski, M. S 1996). Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Research 6, 846 857.
55. Málaga-Trillo, E. Meyer, A 2001). Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. American Zoologist 41, 676 686.
56. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y. J., Chen, Z. T., Dewell, S. B., Du, L., Fierro, J. M., Gomes, X. V., Godwin, B. C., He, W., Helgesen, S., Ho, C. H., Irzyk, G. P., Jando, S. C., Alenquer, M. L. I., Jarvie, T. P., Jirage, K. B., Kim, J. B., Knight, J. R., Lanza, J. R., Leamon, J. H., Lefkowitz, S. M., Lei, M., Li, J., Lohman, K. L., Lu, H., Makhijani, V. B., McDade, K. E., McKenna, M. P., Myers, E. W., Nickerson, E., Nobile, J. R., Plant, R., Puc, B. P., Ronan, M. T., Roth, G. T., Sarkis, G. J., Simons, J. F., Simpson, J. W., Srinivasan, M., Tartaro, K. R., Tomasz, A., Vogt, K. A., Volkmer, G. A., Wang, S. H., Wang, Y., Weiner, M. P., Yu, P. G., Begley, R. F. Rothberg, J. M 2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376 380.
57. McCarroll, S. A. Altshuler, D. M 2007). Copy-number variation and association studies of human disease. Nature Genetics 39, S37 S42.
58. Medhora, M., Bousamra, M., Zhu, D. L., Somberg, L. Jacobs, E. R 2002). Upregulation of collagens detected by gene array in a model of flow-induced pulmonary vascular remodeling. American Journal of Physiology. Heart and Circulatory Physiology 282, H414 H422.
59. Miller, N. A., Gong, Q., Bryan, R., Ruvolo, M., Turner, L. A. LaBrie, S. T 2002). Cross-hybridization of closely related genes on high-density macroarrays. Biotechniques 32, 620 625.
60. Moody, D., Zou, Z. McIntyre, L 2002). Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genomics 3, 27.
61. Nieto-Díaz, M., Pita-Thomas, W. Nieto-Sampedro, M 2007). Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays. BMC Genomics 8, 89.
62. Nowrousian, M., Ringelberg, C., Dunlap, J. C., Loros, J. L. Kuck, U 2005). Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora. Molecular Genetics and Genomics 273, 137 149.
63. Oleksiak, M. F., Kolell, K. J. Crawford, D. L 2001). Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Marine Biotechnology 3, S203 S211.
64. Oleksiak, M. F., Roach, J. L. Crawford, D. L 2005). Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nature Genetics 37, 67 72.
65. Oshlack, A., Chabot, A. E., Smyth, G. K. Gilad, Y 2007). Using DNA microarrays to study gene expression in closely related species. Bioinformatics 23, 1235 1242.
66. Picard, D. J. Schulte, P. M 2004). Variation in gene expression in response to stress in two populations of Fundulus heteroclitus. Comparative Biochemistry and Physiology A 137, 205 216.
67. Podrabsky, J. E. Somero, G. N 2004). Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. Journal of Experimental Biology 207, 2237 2254.
68. Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D. Brown, P. O 1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genetics 23, 41 46.
69. Ranz, J. M., Castillo-Davis, C. I., Meiklejohn, C. D. Hartl, D. L 2003). Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742 1745.
70. Relógio, A., Schwager, C., Richter, A., Ansorge, W. Valcarcel, J 2002). Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Research 30, e51.
71. Renn, S. C. P., Aubin-Horth, N. Hofmann, H. A 2004). Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5, 42.
72. de Reyniès, A., Geromin, D., Cayuela, J.-M., Petel, F., Dessen, P., Sigaux, F. Rickman, D 2006). Comparison of the latest commercial short and long oligonucleotide microarray technologies. BMC Genomics 7, 51.
73. Rise, M. L., Jones, S. R., Brown, G. D., von Schalburg, K. R., Davidson, W. S. Koop, B. F 2004a). Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiological Genomics 20, 21 35.
74. Rise, M. L., von Schalburg, K. R., Brown, G. D., Mawer, M. A., Devlin, R. H., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, A. R., Hunt, P., Shukin, R., Zeznik, J. A., Nelson, C., Jones, S. R. M., Smailus, D. E., Jones, S. J. M., Schein, J. E., Marra, M. A., Butterfield, Y. S. N., Stott, J. M., Ng, S. H. S., Davidson, W. S. Koop, B. F 2004b). Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Research 14, 478 490.
75. Roest Crollius, H. Weissenbach, J 2005). Fish genomics and biology. Genome Research 15, 1675 1682.
76. Rotchell, J. M. Ostrander, G. K 2003). Molecular markers of endocrine disruption in aquatic organisms. Journal of Toxicology and Environmental Health. Part B, Critical Reviews 6, 453 495.
77. Ryan, D., Rahimi, M., Lund, J., Mehta, R. Parviz, B. A 2007). Toward nanoscale genome sequencing. Trends in Biotechnology 25, 385 389.
78. Saetre, P., Lindberg, J., Leonard, J. A., Olsson, K., Pettersson, U., Ellegren, H., Bergstrom, T. F., Vila, C. Jazin, E 2004). From wild wolf to domestic dog: gene expression changes in the brain. Brain Research. Molecular Brain Research 126, 198 206.
79. von Schalburg, K., Rise, M., Cooper, G., Brown, G., Gibbs, A. R., Nelson, C., Davidson, W. Koop, B 2005). Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6, 126.
80. Schena, M., Shalon, D., Davis, R. W. Brown, P. O 1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467 470.
81. Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T. Petronis, A 2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Research 34, 528 542.
82. Sen Sarma, M., Whitfield, C. W. Robinson, G. E 2007). Species differences in brain gene expression profiles in honey bees. BMC Genomics 8, 202.
83. Shah, G. R., Azizian, M., Bruch, D., Mehta, R. Kittur, D 2004). Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform - preliminary results. Clinical Transplantation 18, 76 80.
84. Sidow, A 1996). Gen(om)e duplications in the evolution of early vertebrates. Current Opinion in Genetics and Development 6, 715 722.
85. Stafford, P. Brun, M 2007). Three methods for optimization of cross-laboratory and cross-platform microarray expression data. Nucleic Acids Research 35, e72.
86. Tsoi, S. C. M., Cale, J. M., Bird, I. M., Ewart, V., Brown, L. L. Douglas, S 2003). Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection. Marine Biotechnology 5, 545 554.
87. Veldhoen, N., Skirrow, R. C., Ji, L., Domanski, D., Bonfield, E. R., Bailey, C. M. Helbing, C. C 2006). Use of heterologous cDNA arrays and organ culture in the detection of thyroid honnone-dependent responses in a sentinel frog, Rana catesbeiana. Comparative Biochemistry and Physiology D 1, 187 199.
88. Walker, S. J., Wang, Y. L., Grant, K. A., Chan, F. Hellmann, G. M 2006). Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. Journal of Neuroscience Methods 152, 179 189.
89. Wang, Z., Lewis, M., Nau, M., Arnold, A. Vahey, M 2004). Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip(R) platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples. BMC Bioinformatics 5, 165.
90. Williams, T. D., Gensberg, K., Minchin, S. D. Chipman, J. K 2003). A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquatic Toxicology 65, 141 157.
91. Woo, Y., Affourtit, J., Daigle, S., Viale, A., Johnson, K., Naggert, J. Churchill, G 2004). A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. Journal of Biomolecular Techniques 15, 276 284.
92. Wu, L. Y., Thompson, D. K., Li, G. S., Hurt, R. A., Tiedje, J. M. Zhou, J. Z 2001). Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology 67, 5780 5790.
93. Zou, J., Young, S., Zhu, F., Xia, L., Skeans, S., Wan, Y. T., Wang, L. Q., McClanahan, T., Gheyas, F., Wei, D., Garlisi, C., Jakway, J. Umland, S 2002). Identification of differentially expressed genes in a monkey model of allergic asthma by microarray technology. Chest 121, 26S 27S.