Genomics for the ecological toolbox

Trends in Ecology and Evolution

Volumn 19, Issue 8, 2004, Pages 439-445

  Thomas, Michael A ^a   Klaper, Rebecca ^b  

^a Nucl Eng Idaho State University   (United States)

^b UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGY; GENE EXPRESSION; GENOME;

EID: 3342951235     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2004.06.010     Document Type: Review

References (70)

1. Stearns S., Magwene P. The naturalist in a world of genomics. Am. Nat. 161:2003;171-180
2. Feder M.E., Mitchell-Olds T. Evolutionary and ecological functional genomics. Nat. Rev. Genet. 4:2003;651-657
3. Klaper R., Thomas M.A. At the crossroads of genomics and ecology: the promise of a canary on a chip. Bioscience. 54:2004;403-412
4. Jackson R.B., et al. Linking molecular insight and ecological research. Trends Ecol. Evol. 17:2002;409-414
5. Diatchenko L., et al. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. U. S. A. 93:1996;6025-6030
6. Rebrikov D.V., et al. Suppression subtractive hybridization. Methods Mol. Biol. 258:2004;107-134
7. Velculescu V.E., et al. Serial analysis of gene expression. Science. 270:1995;484-487
8. Eisen M.B., et al. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:1998;14863-14868
9. Goetz F.W. The 'ups' and 'downs' in using subtractive cloning techniques to isolate regulated genes in fish. Integr. Comp. Biol. 43:2003;16-23
10. Matsumura H., et al. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. U. S. A. 100:2003;15718-15723
11. Draghici S., et al. Global functional profiling of gene expression. Genomics. 81:2003;98-104
12. Moody D., et al. Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genomics. 3:2002;27
13. Miller N.A., et al. Cross-hybridization of closely related genes on high-density macroarrays. Biotechniques. 32:2002;620-625
14. Hedges S.B., Kumar S. Genomics. Vertebrate genomes compared. Science. 297:2002;1283-1285
15. Burt D.W., et al. The dynamics of chromosome evolution in birds and mammals. Nature. 402:1999;411-413
16. Stillman B.A., Tonkinson J.L. Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem. 295:2001;149-157
17. Roethele J., et al. Evidence for broad-scale conservation of linkage map relationships between Rhagoletis pomonella (Diptera: Tephritidae) and Drosophila melanogaster (Diptera: Drosophilidae). Ann. Entomol. Soc. Am. 94:2001;936-947
18. Reysenbach A.L., Shock E. Merging genomes with geochemistry in hydrothermal ecosystems. Science. 296:2002;1077-1082
19. Torsvik V., Ovreas L. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 5:2002;240-245
20. Beja O., et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68:2002;335-345
21. Wellington E.M., et al. Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr. Opin. Microbiol. 6:2003;295-301
22. Moran N.A., et al. A genomic perspective on nutrient provisioning by bacterial symbionts of insects. Proc. Natl. Acad. Sci. U. S. A. 100:2003;14543-14548
23. Halitschke R., et al. Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. VI. Microarray analysis reveals that most herbivore-specific transcriptional changes are mediated by fatty acid-amino acid conjugates. Plant Physiol. 131:2003;1894-1902
24. Izaguirre M.M., et al. Convergent responses to stress. Solar ultraviolet-B radiation and Manduca sexta herbivory elicit overlapping transcriptional responses in field-grown plants of Nicotiana longiflora. Plant Physiol. 132:2003;1755-1767
25. Brazma A., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29:2001;365-371
26. Reineke A., et al. Differential gene expression in two strains of the endoparasitic wasp Venturia canescens identified by cDNA-amplified fragment length polymorphism analysis. Mol. Ecol. 12:2003;3485-3492
27. Donson J., et al. Comprehensive gene expression analysis by transcript profiling. Plant Mol. Biol. 48:2002;75-97
28. Franz O., et al. Verification of differential gene transcription using virtual northern blotting. Nucleic Acids Res. 27:1999;e3
29. Ungerer M.C., et al. Quantitative trait loci for inflorescence development in Arabidopsis thaliana. Genetics. 160:2002;1133-1151
30. Weinig C., et al. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics. 165:2003;321-329
31. Twigger S., et al. Rat genome database (RGD): mapping disease onto the genome. Nucleic Acids Res. 30:2002;125-128
32. Stoll M., et al. New target regions for human hypertension via comparative genomics. Genome Res. 10:2000;473-482
33. Zhu W., et al. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol. 132:2003;469-484
34. Nordborg M., Bergelson J. The effect of seed and rosette cold treatment on germination and flowering time in some Arabidopsis thaliana (Brassicaceae) ecotypes. Am. J. Bot. 86:1999;470
35. Weinig C., et al. QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments. Mol. Ecol. 12:2003;1153-1163
36. Kroymann J., et al. Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc. Natl. Acad. Sci. U. S. A. 100:2003;14587-14592
37. Clauss M.J., Mitchell-Olds T. Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history. Mol. Ecol. 12:2003;1287-1299
38. Kover P.X., Schaal B.A. Genetic variation for disease resistance and tolerance among Arabidopsis thaliana accessions. Proc. Natl. Acad. Sci. U. S. A. 99:2002;11270-11274
39. Kamoun S., et al. Resistance of Nicotiana benthamiana to Phytophthora infestans is mediated by the recognition of the elicitor protein INF1. Plant Cell. 10:1998;1413-1426
40. Rolfe B.G., et al. Proteomic analysis of legume-microbe interactions. Comp. Funct. Genomics. 4:2003;225-228
41. Gazzani S., et al. Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol. 132:2003;1107-1114
42. Thorgaard G.H., et al. Status and opportunities for genomics research with rainbow trout. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133:2002;609-646
43. Stein L.D., et al. The generic genome browser: a building block for a model organism system database. Genome Res. 12:2002;1599-1610
44. Smith L., Greenfield A. DNA microarrays and development. Hum. Mol. Genet. 12:2003;R1-R8
45. Zdobnov E.M., et al. Comparative genome and proteome analysis of anopheles gambiae and Drosophila melanogaster. Science. 298:2002;149-159
46. von Roepenack-Lahaye E., et al. Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol. 134:2004;548-559
47. Bush G.L. Mating behavior, host specificity, and the ecological significance of sibling species in frugivorous flies of the genus Rhagoletis (Diptera-Tephritidae). Am. Nat. 103:1969;669
48. McPheron B.A., et al. Genetic differences between host races of Rhagoletis pomonella. Nature. 336:1988;64-66
49. Feder J., et al. Host fidelity is an effective premating barrier between sympatric races of the apple maggot fly. Proc. Natl. Acad. Sci. U. S. A. 91:1994;7990-7994
50. Linn C. Jr, et al. Fruit odor discrimination and sympatric host race formation in Rhagoletis. Proc. Natl. Acad. Sci. U. S. A. 100:2003;11490-11493
51. Fry J.D. Multilocus models of sympatric speciation: Bush versus Rice versus Felsenstein. Evolution. 57:2003;1735-1746
52. Berlocher S.H., Feder J.L. Sympatric speciation in phytophagous insects: moving beyond controversy? Annu. Rev. Entomol. 47:2002;773-815
53. Feder J.L., et al. Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis. Proc. Natl. Acad. Sci. U. S. A. 100:2003;10314-10319
54. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science. 287:2000;2185-2195
55. Borras T., et al. Transcription profiling in Drosophila eyes that overexpress the human glaucoma-associated trabecular meshwork-inducible glucocorticoid response protein/myocilin (TIGR/MYOC). Genetics. 163:2003;637-645
56. Feany M.B., Bender W.W. A Drosophila model of Parkinson's disease. Nature. 404:2000;394-398
57. Blair Hedges S., Kumar S. Genomic clocks and evolutionary history. Trends Genet. 19:2003;200-206
58. Diagana T.T., et al. Mutation of Drosophila homer disrupts control of locomotor activity and behavioral plasticity. J. Neurosci. 22:2002;428-436
59. Chan B., et al. Courtship and other behaviors affected by a heat-sensitive, molecularly novel mutation in the cacophony calcium-channel gene of Drosophila. Genetics. 162:2002;135-153
60. Caldwell J.C., et al. Dynamic analysis of larval locomotion in Drosophila chordotonal organ mutants. Proc. Natl. Acad. Sci. U. S. A. 100:2003;16053-16058
61. Rayburn L.Y., et al. amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development. Genetics. 163:2003;227-237
62. Grozinger C.M., et al. Pheromone-mediated gene expression in the honey bee brain. Proc. Natl. Acad. Sci. U. S. A. 100:(Suppl. 2):2003;14519-14525
63. Kim Y.-O., et al. A functional genomic screen for cardiogenic genes using RNA interference in developing Drosophila embryos. Proc. Natl. Acad. Sci. U. S. A. 101:2003;159-164
64. Rogers W.E., Siemann E. Effects of simulated herbivory and resources on Chinese tallow tree (Sapium sebiferum, Euphorbiaceae) invasion of native coastal prairie. Am. J. Bot. 90:2003;243-249
65. Siemann E., Rogers W.E. Reduced resistance of invasive varieties of the alien tree Sapium sebiferum to a generalist herbivore. Oecologia. 135:2003;451-457
66. Siemann E., Rogers W.E. Herbivory, disease, recruitment limitation, and success of alien and native tree species. Ecology. 84:2003;1489-1505
67. Morlais I., et al. A targeted approach to the identification of candidate genes determining susceptibility to Plasmodium gallinaceum in Aedes aegypti. Mol. Genet. Genomics. 269:2003;753-764
68. Yan G., Severson D.W. Dynamics of molecular markers linked to the resistance loci in a mosquito-Plasmodium system. Genetics. 164:2003;511-519
69. Holt R.A., et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 298:2002;129-149
70. Gardner M.J., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419:2002;498-511