Phenotypic Plasticity of the Drosophila Transcriptome
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments. We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological, social, nutritional, chemical, and physical environments; and we compared the phenotypically plastic transcripts to genetically variable transcripts in a single environment. The environmentally sensitive transcriptome consists of two transcript categories, which comprise ∼15% of expressed transcripts. Class I transcripts are genetically variable and associated with detoxification, metabolism, proteolysis, heat shock proteins, and transcriptional regulation. Class II transcripts have low genetic variance and show sexually dimorphic expression enriched for reproductive functions. Clustering analysis of Class I transcripts reveals a fragmented modular organization and distinct environmentally responsive transcriptional signatures for the four fitness-related traits. Our analysis suggests that a restricted environmentally responsive segment of the transcriptome preserves the balance between phenotypic plasticity and environmental canalization.
Vyšlo v časopise:
Phenotypic Plasticity of the Drosophila Transcriptome. PLoS Genet 8(3): e32767. doi:10.1371/journal.pgen.1002593
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002593
Souhrn
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments. We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological, social, nutritional, chemical, and physical environments; and we compared the phenotypically plastic transcripts to genetically variable transcripts in a single environment. The environmentally sensitive transcriptome consists of two transcript categories, which comprise ∼15% of expressed transcripts. Class I transcripts are genetically variable and associated with detoxification, metabolism, proteolysis, heat shock proteins, and transcriptional regulation. Class II transcripts have low genetic variance and show sexually dimorphic expression enriched for reproductive functions. Clustering analysis of Class I transcripts reveals a fragmented modular organization and distinct environmentally responsive transcriptional signatures for the four fitness-related traits. Our analysis suggests that a restricted environmentally responsive segment of the transcriptome preserves the balance between phenotypic plasticity and environmental canalization.
Zdroje
1. BradshawAD 1965 Evolutionary significance of phenotypic plasticity in plants. Advances in Genetics 13 115 155
2. WaddingtonCH 1942 Canalization of developmnet and the inheritance of acquired characters. Nature 150 563 565
3. WaddingtonCH 1959 Canalization of development and genetic assimilation of acquired characters. Nature 183 1654 1655
4. GibsonG 2009 Decanalization and the origin of complex disease. Nat Rev Genet 10 134 140
5. LeeCKWeindruchRProllaTA 2000 Gene-expression profile of the ageing brain in mice. Nat Genet 25 294 297
6. ZouSMeadowsSSharpLJanLYJanYN 2000 Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc Natl Acad Sci U S A 97 13726 13731
7. CaoSXDhahbiJMMotePLSpindlerSR 2001 Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98 10630 10635
8. PletcherSDMacdonaldSJMarguerieRCertaUStearnsSC 2002 Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr Biol 12 712 723
9. SambandanDCarboneMAAnholtRRHMackayTFC 2008 Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster. Genetics 179 1079 1088
10. VinuelaASnoekLBRiksenJAKammengaJE 2010 Genome-wide gene expression regulation as a function of genotype and age in C. elegans. Genome Res 20 929 937
11. LevineMTEckertMLBegunDJ 2011 Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia. Mol Biol Evol 28 249 256
12. AyrolesJFCarboneMAStoneEAJordanKWLymanRF 2009 Systems genetics of complex traits in Drosophila melanogaster. Nat Genet 41 299 307
13. StoneEAAyrolesJF 2009 Modulated modularity clustering as an exploratory tool for functional genomic inference. PLoS Genet 5 e1000479 doi:10.1371/journal.pgen.1000479
14. BushatiNCohenSM 2007 microRNA functions. Annu Rev Cell Dev Biol 23 175 205
15. RoySErnstJKharchenkoPVKheradpourPNegreN 2010 Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330 1787 1797
16. SambucettiPLoeschckeVNorryFM 2006 Developmental time and size-related traits in Drosophila buzzatii along an altitudinal gradient from Argentina. Hereditas 143 77 83
17. MenschJLavagninoNCarreiraVPMassaldiAHassonE 2008 Identifying candidate genes affecting developmental time in Drosophila melanogaster: pervasive pleiotropy and gene-by-environment interaction. BMC Dev Biol 8 78
18. ChapmanTLiddleLFKalbJMWolfnerMFPartridgeL 1995 Cost of mating in Drosophila melanogaster females is mediated by male accessory gland products. Nature 373 241 244
19. SohalRSWeindruchR 1996 Oxidative stress, caloric restriction, and aging. Science 273 59 63
20. FontanaLPartridgeLLongoVD 2010 Extending healthy life span–from yeast to humans. Science 328 321 326
21. ClarkAGEisenMBSmithDRBergmanCMOliverB 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450 203 218
22. LarracuenteAMSacktonTBGreenbergAJWongASinghND 2008 Evolution of protein-coding genes in Drosophila. Trends Genet 24 114 123
23. MackayTFCRichardsSStoneEABarbadillaAAyrolesJF 2012 The Drosophila melanogaster Genetic Reference Panel. Nature in press
24. ZhouSStoneEAMackayTFCAnholtRRH 2009 Plasticity of the chemoreceptor repertoire in Drosophila melanogaster. PLoS Genet 5 e1000681 doi:10.1371/journal.pgen.1000681
25. StrodeCWondjiCSDavidJPHawkesNJLumjuanN 2008 Genomic analysis of detoxification genes in the mosquito Aedes aegypti. Insect Biochem Mol Biol 38 113 123
26. FeyereisenR 2006 Evolution of insect P450. Biochem Soc Trans 34 1252 1255
27. ClaudianosCRansonHJohnsonRMBiswasSSchulerMA 2006 A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee. Insect Mol Biol 15 615 636
28. RichardsSGibbsRAWeinstockGMBrownSJDenellR 2008 The genome of the model beetle and pest Tribolium castaneum. Nature 452 949 955
29. RansonHClaudianosCOrtelliFAbgrallCHemingwayJ 2002 Evolution of supergene families associated with insecticide resistance. Science 298 179 181
30. ChintapalliVRWangJDowJA 2007 Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39 715 720
31. ZhangXSHillWG 2007 Competition can maintain genetic but not environmental variance in the presence of stabilizing selection. Evolution 61 1532 1545
32. ViaSGomulkiewiczRDe JongGScheinerSMSchlichtingCD 1995 Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol Evol 10 212 217
33. MackayTFCStoneEAAyrolesJF 2009 The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10 565 577
34. Huang daWShermanBTLempickiRA 2009 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4 44 57
35. Huang daWShermanBTLempickiRA 2009 Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37 1 13
36. YuJPacificoSLiuGFinleyRLJr 2008 DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9 461
37. MuraliTPacificoSYuJGuestSRobertsGG3rd 2011 DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res 39 D736 743
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 3
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- PIF4–Mediated Activation of Expression Integrates Temperature into the Auxin Pathway in Regulating Hypocotyl Growth
- Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations
- A Splice Site Variant in the Bovine Gene Compromises Growth and Regulation of the Inflammatory Response
- Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database