메뉴 건너뛰기




Volumn 8, Issue 1, 2016, Pages 243-252

Gene networks in the wild: Identifying transcriptional modules that mediate coral resistance to experimental heat stress

Author keywords

Coexpression; Phenotypic plasticity; Standing variation

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTOME;

EID: 85020324656     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv258     Document Type: Article
Times cited : (61)

References (51)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11:R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 2
    • 61349113311 scopus 로고    scopus 로고
    • Systems genetics of complex traits in Drosophila melanogaster
    • Ayroles JF, et al. 2009. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet. 41:299-307.
    • (2009) Nat Genet. , vol.41 , pp. 299-307
    • Ayroles, J.F.1
  • 3
    • 0035859018 scopus 로고    scopus 로고
    • Ecosystems: Reef corals bleach to survive change
    • Baker AC. 2001. Ecosystems: Reef corals bleach to survive change. Nature 411:765-766.
    • (2001) Nature , vol.411 , pp. 765-766
    • Baker, A.C.1
  • 5
    • 37549030093 scopus 로고    scopus 로고
    • Adaptation from standing genetic variation
    • Barrett RDH, Schluter D. 2008. Adaptation from standing genetic variation. Trends Ecol Evol. 23:38-44.
    • (2008) Trends Ecol Evol. , vol.23 , pp. 38-44
    • Barrett, R.D.H.1    Schluter, D.2
  • 6
    • 84872855352 scopus 로고    scopus 로고
    • Genomic basis for coral resilience to climate change
    • Barshis DJ, et al. 2013. Genomic basis for coral resilience to climate change. Proc Natl Acad Sci U S A. 110:1387-1392.
    • (2013) Proc Natl Acad Sci U S A. , vol.110 , pp. 1387-1392
    • Barshis, D.J.1
  • 7
    • 84979861930 scopus 로고    scopus 로고
    • Rapid acclimation ability mediated by transcriptome changes in reef-building corals
    • Bay RA, Palumbi SR. 2015. Rapid acclimation ability mediated by transcriptome changes in reef-building corals. Genome Biol Evol. 7:1602-1612.
    • (2015) Genome Biol Evol. , vol.7 , pp. 1602-1612
    • Bay, R.A.1    Palumbi, S.R.2
  • 8
    • 57049092878 scopus 로고    scopus 로고
    • The take and give between retrotransposable elements and their hosts
    • Beauregard A, Curcio MJ, Belfort M. 2008. The take and give between retrotransposable elements and their hosts. Annu Rev Genet. 42: 587-617.
    • (2008) Annu Rev Genet. , vol.42 , pp. 587-617
    • Beauregard, A.1    Curcio, M.J.2    Belfort, M.3
  • 10
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B Methodol. 57:289-300.
    • (1995) J R Stat Soc B Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 80054976678 scopus 로고    scopus 로고
    • The evolution of gene expression levels in mammalian organs
    • Brawand D, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
    • (2011) Nature , vol.478 , pp. 343-348
    • Brawand, D.1
  • 12
    • 0033800838 scopus 로고    scopus 로고
    • Stress and transposable elements: Co-evolution or useful parasites?
    • Capy P, Gasperi G, Biémont C, Bazin C. 2000. Stress and transposable elements: Co-evolution or useful parasites? Heredity 85:101-106.
    • (2000) Heredity , vol.85 , pp. 101-106
    • Capy, P.1    Gasperi, G.2    Biémont, C.3    Bazin, C.4
  • 13
    • 80051873100 scopus 로고    scopus 로고
    • Rapid range shifts of species associated with high levels of climate warming
    • Chen IC, Hill JK, Ohlemüller R, Roy DB, Thomas CD. 2011. Rapid range shifts of species associated with high levels of climate warming. Science 333:1024-1026.
    • (2011) Science , vol.333 , pp. 1024-1026
    • Chen, I.C.1    Hill, J.K.2    Ohlemüller, R.3    Roy, D.B.4    Thomas, C.D.5
  • 14
    • 77951716714 scopus 로고    scopus 로고
    • Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory
    • Chevin LM, Lande R, Mace GM. 2010. Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory. PLoS Biol. 8:e1000357.
    • (2010) PLoS Biol. , vol.8 , pp. e1000357
    • Chevin, L.M.1    Lande, R.2    Mace, G.M.3
  • 15
    • 84890546613 scopus 로고    scopus 로고
    • Systems genetics approaches to understand complex traits
    • Civelek M, Lusis AJ. 2014. Systems genetics approaches to understand complex traits. Nat Rev Genet. 15:34-48.
    • (2014) Nat Rev Genet. , vol.15 , pp. 34-48
    • Civelek, M.1    Lusis, A.J.2
  • 16
    • 0034817039 scopus 로고    scopus 로고
    • High temperatures tolerated by a diverse assemblage of shallow-water corals in American Samoa
    • Craig P, Birkeland C, Belliveau S. 2001. High temperatures tolerated by a diverse assemblage of shallow-water corals in American Samoa. Coral Reefs 20:185-189.
    • (2001) Coral Reefs , vol.20 , pp. 185-189
    • Craig, P.1    Birkeland, C.2    Belliveau, S.3
  • 17
    • 34548487517 scopus 로고    scopus 로고
    • Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors
    • de la Vega E, Degnan BM, Hall MR, Wilson KJ. 2007. Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors. Fish Shellfish Immunol. 23:1072-1088.
    • (2007) Fish Shellfish Immunol. , vol.23 , pp. 1072-1088
    • De La Vega, E.1    Degnan, B.M.2    Hall, M.R.3    Wilson, K.J.4
  • 18
    • 50049109156 scopus 로고    scopus 로고
    • Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata
    • DesalvoMK, et al. 2008. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. Mol Ecol. 17:3952-3971.
    • (2008) Mol Ecol. , vol.17 , pp. 3952-3971
    • Desalvo, M.K.1
  • 19
    • 84933557745 scopus 로고    scopus 로고
    • Genomic determinants of coral heat tolerance across latitudes
    • Dixon GB, et al. 2015. Genomic determinants of coral heat tolerance across latitudes. Science 348:1460-1462.
    • (2015) Science , vol.348 , pp. 1460-1462
    • Dixon, G.B.1
  • 20
    • 84877759683 scopus 로고    scopus 로고
    • Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish
    • Filteau M, Pavey SA, St-Cyr J, Bernatchez L. 2013. Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish. Mol Biol Evol. 30:1384-1396.
    • (2013) Mol Biol Evol. , vol.30 , pp. 1384-1396
    • Filteau, M.1    Pavey, S.A.2    St-Cyr, J.3    Bernatchez, L.4
  • 21
    • 34249012056 scopus 로고    scopus 로고
    • Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments
    • Ghalambor CK, McKay JK, Carroll SP, Reznick DN. 2007. Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Funct Ecol. 21:394-407.
    • (2007) Funct Ecol. , vol.21 , pp. 394-407
    • Ghalambor, C.K.1    McKay, J.K.2    Carroll, S.P.3    Reznick, D.N.4
  • 22
    • 0032080772 scopus 로고    scopus 로고
    • Activation of plant retrotransposons under stress conditions
    • GrandbastienMA. 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3:181-187.
    • (1998) Trends Plant Sci. , vol.3 , pp. 181-187
    • Grandbastien, M.A.1
  • 23
    • 67650264382 scopus 로고    scopus 로고
    • A quantitative survey of local adaptation and fitness trade-offs
    • Hereford J. 2009. A quantitative survey of local adaptation and fitness trade-offs. Am Nat. 173:579-588.
    • (2009) Am Nat. , vol.173 , pp. 579-588
    • Hereford, J.1
  • 24
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. 2008. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44-57.
    • (2008) Nat Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 25
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals
    • Jaenisch R, Bird A. 2003. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat Genet. 33:245-254.
    • (2003) Nat Genet. , vol.33 , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 26
    • 9944247694 scopus 로고    scopus 로고
    • Conceptual issues in local adaptation
    • Kawecki TJ, Ebert D. 2004. Conceptual issues in local adaptation. Ecol Lett. 7:1225-1241.
    • (2004) Ecol Lett. , vol.7 , pp. 1225-1241
    • Kawecki, T.J.1    Ebert, D.2
  • 27
    • 84882450971 scopus 로고    scopus 로고
    • Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments
    • Kenkel CD, Meyer E, MatzMV. 2013. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol Ecol. 22:4322-4334.
    • (2013) Mol Ecol. , vol.22 , pp. 4322-4334
    • Kenkel, C.D.1    Meyer, E.2    Matz, M.V.3
  • 28
    • 0036526266 scopus 로고    scopus 로고
    • Acclimation and adaptive responses of woody plants to environmental stresses
    • Kozlowski TT, Pallardy SG. 2002. Acclimation and adaptive responses of woody plants to environmental stresses. Bot Rev. 68:270-334.
    • (2002) Bot Rev. , vol.68 , pp. 270-334
    • Kozlowski, T.T.1    Pallardy, S.G.2
  • 29
    • 85045952710 scopus 로고    scopus 로고
    • Evolutionary comparison of transcriptome sequences from four clades of coral endosymbionts in the genus Symbiodinium: A search for genes involved in the thermotolerance of clade D
    • Ladner JT, Barshis DJ, Palumbi SR. 2012. Evolutionary comparison of transcriptome sequences from four clades of coral endosymbionts in the genus Symbiodinium: A search for genes involved in the thermotolerance of clade D. Patricia J Gumport Vice Provost Grad. Educ. 133-168.
    • (2012) Patricia J Gumport Vice Provost Grad. Educ. , pp. 133-168
    • Ladner, J.T.1    Barshis, D.J.2    Palumbi, S.R.3
  • 30
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder P, Horvath S. 2008. WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9:559.
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 31
    • 85026988855 scopus 로고    scopus 로고
    • Genome-environment associations in sorghum landraces predict adaptive traits
    • Lasky JR, et al. 2015. Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv. 1:e1400218.
    • (2015) Sci Adv. , vol.1 , pp. e1400218
    • Lasky, J.R.1
  • 32
    • 58049220322 scopus 로고    scopus 로고
    • A meta-analysis of local adaptation in plants
    • Leimu R, Fischer M. 2008. A meta-analysis of local adaptation in plants. PLoS One 3:e4010.
    • (2008) PLoS One , vol.3 , pp. e4010
    • Leimu, R.1    Fischer, M.2
  • 33
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 34
  • 35
    • 0026591963 scopus 로고
    • The evolutionary maintenance of alternative phenotypes
    • Moran NA. 1992. The evolutionary maintenance of alternative phenotypes. Am Nat. 139:971-989.
    • (1992) Am Nat. , vol.139 , pp. 971-989
    • Moran, N.A.1
  • 36
    • 0036789519 scopus 로고    scopus 로고
    • Variation in gene expression within and among natural populations
    • Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nat Genet. 32:261-266.
    • (2002) Nat Genet. , vol.32 , pp. 261-266
    • Oleksiak, M.F.1    Churchill, G.A.2    Crawford, D.L.3
  • 37
    • 79955888491 scopus 로고    scopus 로고
    • Do fluctuating temperature environments elevate coral thermal tolerance?
    • Oliver TA, Palumbi SR. 2011. Do fluctuating temperature environments elevate coral thermal tolerance? Coral Reefs 30:429-440.
    • (2011) Coral Reefs , vol.30 , pp. 429-440
    • Oliver, T.A.1    Palumbi, S.R.2
  • 38
    • 84914103725 scopus 로고    scopus 로고
    • The population genetics of evolutionary rescue
    • Orr HA, Unckless RL. 2014. The population genetics of evolutionary rescue. PLoS Genet. 10:e1004551.
    • (2014) PLoS Genet. , vol.10 , pp. e1004551
    • Orr, H.A.1    Unckless, R.L.2
  • 39
    • 84901216800 scopus 로고    scopus 로고
    • Mechanisms of reef coral resistance to future climate change
    • Palumbi SR, Barshis DJ, Traylor-Knowles N, Bay RA. 2014. Mechanisms of reef coral resistance to future climate change. Science 344:895-898.
    • (2014) Science , vol.344 , pp. 895-898
    • Palumbi, S.R.1    Barshis, D.J.2    Traylor-Knowles, N.3    Bay, R.A.4
  • 40
    • 84876835091 scopus 로고    scopus 로고
    • Evolutionary change during experimental ocean acidification
    • Pespeni MH, et al. 2013. Evolutionary change during experimental ocean acidification. Proc Natl Acad Sci U S A. 110:6937-6942.
    • (2013) Proc Natl Acad Sci U S A. , vol.110 , pp. 6937-6942
    • Pespeni, M.H.1
  • 41
    • 84874423696 scopus 로고    scopus 로고
    • Variation in the transcriptional response of threatened coral larvae to elevated temperatures
    • Polato NR, Altman NS, Baums IB. 2013. Variation in the transcriptional response of threatened coral larvae to elevated temperatures. Mol Ecol. 22:1366-1382.
    • (2013) Mol Ecol. , vol.22 , pp. 1366-1382
    • Polato, N.R.1    Altman, N.S.2    Baums, I.B.3
  • 42
    • 77953599934 scopus 로고    scopus 로고
    • Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata
    • Portune KJ, Voolstra CR, Medina M, Szmant AM. 2010. Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata. Mar Genomics. 3:51-62.
    • (2010) Mar Genomics. , vol.3 , pp. 51-62
    • Portune, K.J.1    Voolstra, C.R.2    Medina, M.3    Szmant, A.M.4
  • 43
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team. Vienna (Austria): R Foundation for Statistical Computing.
    • R Development Core Team. 2008. R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
    • (2008) R: A Language and Environment for Statistical Computing
  • 44
    • 79953014657 scopus 로고    scopus 로고
    • Local adaptation in marine invertebrates
    • Sanford E, Kelly MW. 2011. Local adaptation in marine invertebrates. Annu Rev Mar. Sci. 3:509-535.
    • (2011) Annu Rev Mar. Sci. , vol.3 , pp. 509-535
    • Sanford, E.1    Kelly, M.W.2
  • 45
    • 84925425962 scopus 로고    scopus 로고
    • The role of transcriptome resilience in resistance of corals to bleaching
    • Seneca FO, Palumbi SR. 2015. The role of transcriptome resilience in resistance of corals to bleaching. Mol Ecol. 24:1467-1484.
    • (2015) Mol Ecol. , vol.24 , pp. 1467-1484
    • Seneca, F.O.1    Palumbi, S.R.2
  • 46
    • 77649199218 scopus 로고    scopus 로고
    • The physiology of climate change: How potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'
    • Somero GN. 2010. The physiology of climate change: How potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'. J Exp Biol. 213:912-920.
    • (2010) J Exp Biol. , vol.213 , pp. 912-920
    • Somero, G.N.1
  • 47
    • 0038725000 scopus 로고    scopus 로고
    • Acclimation capacity underlies susceptibility to climate change
    • Stillman JH. 2003. Acclimation capacity underlies susceptibility to climate change. Science 301:65.
    • (2003) Science , vol.301 , pp. 65
    • Stillman, J.H.1
  • 48
    • 34547144147 scopus 로고    scopus 로고
    • Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana
    • Swindell WR, Huebner M, Weber AP. 2007. Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana. Heredity 99:143-150.
    • (2007) Heredity , vol.99 , pp. 143-150
    • Swindell, W.R.1    Huebner, M.2    Weber, A.P.3
  • 49
    • 74549224369 scopus 로고    scopus 로고
    • Effects of temperature on gene expression in embryos of the coral Montastraea faveolata
    • Voolstra CR, et al. 2009. Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. BMC Genomics 10:627.
    • (2009) BMC Genomics , vol.10 , pp. 627
    • Voolstra, C.R.1
  • 50
    • 0042697343 scopus 로고    scopus 로고
    • The evolution of transcriptional regulation in eukaryotes
    • Wray GA, et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 20:1377-1419.
    • (2003) Mol Biol Evol. , vol.20 , pp. 1377-1419
    • Wray, G.A.1
  • 51
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene coexpression network analysis
    • Zhang B, Horvath S. 2005. A general framework for weighted gene coexpression network analysis. Stat Appl Genet Mol Biol. 4:1128..
    • (2005) Stat Appl Genet Mol Biol. , vol.4 , pp. 1128
    • Zhang, B.1    Horvath, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.