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Volumn 70, Issue 3, 2016, Pages 696-706

Genome-wide patterns of regulatory divergence revealed by introgression lines

Author keywords

cis Regulation; Gene expression; Hybrid misregulation; Solanum lycopersicum; Solanum pennellii; trans regulation

Indexed keywords

CLADISTICS; DIVERGENCE; EVOLUTION; FRUIT; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; HYBRID; INTROGRESSION; PHENOTYPE; REPRODUCTIVE ISOLATION;

EID: 84959419922     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12875     Document Type: Article
Times cited : (22)

References (49)
  • 1
    • 33847207839 scopus 로고    scopus 로고
    • Lethality in Drosophila melanogaster/Drosophila simulans species hybrids is not associated with substantial transcriptional misregulation
    • Barbash, D. A., and J. G. Lorigan . 2007. Lethality in Drosophila melanogaster/Drosophila simulans species hybrids is not associated with substantial transcriptional misregulation. J. Exp. Zool. Part B 308B: 74-84.
    • (2007) J. Exp. Zool. Part , vol.308B , pp. 74-84
    • Barbash, D.A.1    Lorigan, J.G.2
  • 3
    • 84942239590 scopus 로고    scopus 로고
    • Regulatory divergence between parental alleles determines gene expression patterns in hybrids
    • Combes, M.-C., Y. Hueber, A. Dereeper, S. Rialle, J.-C. Herrera, and P. Lashermes . 2015. Regulatory divergence between parental alleles determines gene expression patterns in hybrids. Genome Biol. Evol. 7: 1110-1121.
    • (2015) Genome Biol. Evol. , vol.7 , pp. 1110-1121
    • Combes, M.-C.1    Hueber, Y.2    Dereeper, A.3    Rialle, S.4    Herrera, J.-C.5    Lashermes, P.6
  • 5
    • 84886360274 scopus 로고    scopus 로고
    • cis- and trans-Regulation in Drosophila Interspecific Hybrids
    • in Chen, Z. J. and J. A. Birchler, eds. . John Wiley & Sons, Inc, Ames, Iowa, USA.
    • Coolon, J. D. and P. J. Wittkopp . 2013. cis- and trans-Regulation in Drosophila Interspecific Hybrids. Pp. 37-57 in Chen, Z. J. and J. A. Birchler, eds. Polyploid and hybrid genomics. John Wiley & Sons, Inc, Ames, Iowa, USA.
    • (2013) Polyploid and hybrid genomics , pp. 37-57
    • Coolon, J.D.1    Wittkopp, P.J.2
  • 7
    • 34249770724 scopus 로고
    • A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes
    • Eshed, Y., and D. Zamir . 1994. A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes. Euphytica 79: 175-179.
    • (1994) Euphytica , vol.79 , pp. 175-179
    • Eshed, Y.1    Zamir, D.2
  • 8
    • 0028846653 scopus 로고
    • An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL
    • Eshed, Y., and D. Zamir .. 1995. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141: 1147-1162.
    • (1995) Genetics , vol.141 , pp. 1147-1162
    • Eshed, Y.1    Zamir, D.2
  • 9
    • 1342288026 scopus 로고    scopus 로고
    • affyanalysis of Affymetrix GeneChip data at the probe level
    • Gautier, L., L. Cope, B. M. Bolstad, and R. A. Irizarry . 2004. affyanalysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315.
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 10
    • 26444519157 scopus 로고    scopus 로고
    • The quantitative genetics of transcription
    • Gibson, G., and B. Weir . 2005. The quantitative genetics of transcription. Trends Genet. 21: 616-23.
    • (2005) Trends Genet. , vol.21 , pp. 616-623
    • Gibson, G.1    Weir, B.2
  • 12
    • 78049444770 scopus 로고    scopus 로고
    • Widespread over-expression of the X chromosome in sterile F1 hybrid mice
    • Good, J. M., T. Giger, M. D. Dean, and M. W. Nachman . 2010. Widespread over-expression of the X chromosome in sterile F1 hybrid mice. PLos Genet. 6: e1001148.
    • (2010) PLos Genet. , vol.6 , pp. e1001148
    • Good, J.M.1    Giger, T.2    Dean, M.D.3    Nachman, M.W.4
  • 13
    • 84859208133 scopus 로고    scopus 로고
    • Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance
    • Gruber, J. D., K. Vogel, G. Kalay, and P. J. Wittkopp . 2012. Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance. PLos Genet. 8: e1002497.
    • (2012) PLos Genet. , vol.8 , pp. e1002497
    • Gruber, J.D.1    Vogel, K.2    Kalay, G.3    Wittkopp, P.J.4
  • 16
    • 35548955944 scopus 로고    scopus 로고
    • Genome clashes in hybrids: insights from gene expression
    • Landry, C., D. Hartl, and J. Ranz . 2007. Genome clashes in hybrids: insights from gene expression. Heredity 99: 483-493.
    • (2007) Heredity , vol.99 , pp. 483-493
    • Landry, C.1    Hartl, D.2    Ranz, J.3
  • 17
    • 33645131133 scopus 로고    scopus 로고
    • Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila
    • Landry, C. R., P. J. Wittkopp, C. H. Taubes, J. M. Ranz, A. G. Clark, and D. L. Hartl . 2005. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171: 1813-1822.
    • (2005) Genetics , vol.171 , pp. 1813-1822
    • Landry, C.R.1    Wittkopp, P.J.2    Taubes, C.H.3    Ranz, J.M.4    Clark, A.G.5    Hartl, D.L.6
  • 18
    • 84896735766 scopus 로고    scopus 로고
    • Voom: precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law, C. W., Y. Chen, W. Shi, and G. K. Smyth . 2014. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15: R29.
    • (2014) Genome Biol. , vol.15 , pp. R29
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 20
    • 40749108388 scopus 로고    scopus 로고
    • Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri
    • Malone, J. H., T. H. Chrzanowski, and P. Michalak . 2007. Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri. PLoS One 2: e781.
    • (2007) PLoS One , vol.2 , pp. e781
    • Malone, J.H.1    Chrzanowski, T.H.2    Michalak, P.3
  • 22
    • 84891688517 scopus 로고    scopus 로고
    • The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression
    • Meiklejohn, C. D., J. D. Coolon, D. L. Hartl, and P. J. Wittkopp . 2014. The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Res. 24: 84-95.
    • (2014) Genome Res. , vol.24 , pp. 84-95
    • Meiklejohn, C.D.1    Coolon, J.D.2    Hartl, D.L.3    Wittkopp, P.J.4
  • 23
    • 0038420716 scopus 로고    scopus 로고
    • Genome-wide patterns of expression in Drosophila pure species and hybrid males
    • Michalak, P., and M. A. Noor . 2003. Genome-wide patterns of expression in Drosophila pure species and hybrid males. Mol. Biol. Evol. 20: 1070-1076.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1070-1076
    • Michalak, P.1    Noor, M.A.2
  • 25
    • 13744262010 scopus 로고    scopus 로고
    • Genetics of hybrid incompatibility between Lycopersicon esculentum and L. hirsutum
    • Moyle, L. C., and E. B. Graham . 2005. Genetics of hybrid incompatibility between Lycopersicon esculentum and L. hirsutum. Genetics 169: 355-373.
    • (2005) Genetics , vol.169 , pp. 355-373
    • Moyle, L.C.1    Graham, E.B.2
  • 26
    • 52049098877 scopus 로고    scopus 로고
    • Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses
    • Moyle, L. C., and T. Nakazato . 2008. Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses. Genetics 179: 1437-1453.
    • (2008) Genetics , vol.179 , pp. 1437-1453
    • Moyle, L.C.1    Nakazato, T.2
  • 28
    • 84915749250 scopus 로고    scopus 로고
    • Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect
    • Muir, C. D., J. B. Pease, and L. C. Moyle . 2014. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae). Genetics 198: 1629-1643.
    • (2014) Lycopersicon; Solanaceae). Genetics , vol.198 , pp. 1629-1643
    • Muir, C.D.1    Pease, J.B.2    Moyle, L.C.3
  • 29
    • 41749111578 scopus 로고    scopus 로고
    • Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes
    • Nakazato, T., M. Bogonovich, and L. C. Moyle . 2008. Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes. Evolution 62: 774-792.
    • (2008) Evolution , vol.62 , pp. 774-792
    • Nakazato, T.1    Bogonovich, M.2    Moyle, L.C.3
  • 30
    • 33845664381 scopus 로고    scopus 로고
    • Gene expression divergence and the origin of hybrid dysfunctions
    • Ortz-Barrientos, D., B. A. Counterman, and M. A. Noor . 2007. Gene expression divergence and the origin of hybrid dysfunctions. Genetica 129: 71-81.
    • (2007) Genetica , vol.129 , pp. 71-81
    • Ortz-Barrientos, D.1    Counterman, B.A.2    Noor, M.A.3
  • 31
    • 84955703917 scopus 로고    scopus 로고
    • Phylogenomics reveals three sources of adaptive variation during a rapid radiation
    • Pease, J. B., D. C. Haak, M. W. Hahn, and L. C. Moyle . 2016. Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biol. 14: e1002379, doi:10.1371/journal.pbio.1002379.
    • (2016) PLoS Biol , vol.14 , pp. e1002379
    • Pease, J.B.1    Haak, D.C.2    Hahn, M.W.3    Moyle, L.C.4
  • 34
    • 84926507971 scopus 로고    scopus 로고
    • limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie, M. E., B. Phipson, D. Wu, Y. Hu, C. W. Law, W. Shi, and G. K. Smyth . 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43:e47.
    • (2015) Nucleic Acids Res , vol.43 , pp. e47
    • Ritchie, M.E.1    Phipson, B.2    Wu, D.3    Hu, Y.4    Law, C.W.5    Shi, W.6    Smyth, G.K.7
  • 35
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D., D. J. McCarthy, and G. K. Smyth . 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 36
    • 33750204290 scopus 로고    scopus 로고
    • Genetics of global gene expression
    • Rockman, M. V., and L. Kruglyak . 2006. Genetics of global gene expression. Nat. Rev. Genet. 7: 862-872.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 862-872
    • Rockman, M.V.1    Kruglyak, L.2
  • 37
    • 37249075841 scopus 로고    scopus 로고
    • Extensive additivity of gene expression differentiates subspecies of the house mouse
    • Rottscheidt, R., and B. Harr . 2007. Extensive additivity of gene expression differentiates subspecies of the house mouse. Genetics 177: 1553-1567.
    • (2007) Genetics , vol.177 , pp. 1553-1567
    • Rottscheidt, R.1    Harr, B.2
  • 40
    • 84864834178 scopus 로고    scopus 로고
    • cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids
    • Shi, X., D. W. Ng, C. Zhang, L. Comai, W. Ye, and Z. J. Chen . 2012. cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat. Commun. 3: 950.
    • (2012) Nat. Commun. , vol.3 , pp. 950
    • Shi, X.1    Ng, D.W.2    Zhang, C.3    Comai, L.4    Ye, W.5    Chen, Z.J.6
  • 41
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth, S. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3. 139-140.
    • (2004) Stat. Appl. Genet. Mol. Biol. 3 , pp. 139-140
    • Smyth, S.1
  • 42
    • 65549086559 scopus 로고    scopus 로고
    • A yeast hybrid provides insight into the evolution of gene expression regulation
    • Tirosh, I., S. Reikhav, A. A. Levy, and N. Barkai . 2009. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324: 659-662.
    • (2009) Science , vol.324 , pp. 659-662
    • Tirosh, I.1    Reikhav, S.2    Levy, A.A.3    Barkai, N.4
  • 44
    • 67649884531 scopus 로고    scopus 로고
    • Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility
    • Walia, H., C. Josefsson, B. Dilkes, R. Kirkbride, J. Harada, and L. Comai . 2009. Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr. Biol. 19: 1128-1132.
    • (2009) Curr. Biol. , vol.19 , pp. 1128-1132
    • Walia, H.1    Josefsson, C.2    Dilkes, B.3    Kirkbride, R.4    Harada, J.5    Comai, L.6
  • 45
    • 85193403130 scopus 로고    scopus 로고
    • Evolution of gene expression
    • in Losos, J. B., D. A. Baum, D. J. Futuyma, H. E. Hoekstra, R. E. Lenski, A. J. Moore, C. L. Peichel, D. Schluter, and M. C. Whitlock, eds., Princeton University Press, Princeton New Jersey, USA.
    • Wittkopp, P. J. 2013. Evolution of gene expression. Pp. 413-419 in Losos, J. B., D. A. Baum, D. J. Futuyma, H. E. Hoekstra, R. E. Lenski, A. J. Moore, C. L. Peichel, D. Schluter, and M. C. Whitlock, eds. The Princeton guide to evolution, Princeton University Press, Princeton New Jersey, USA.
    • (2013) The Princeton guide to evolution , pp. 413-419
    • Wittkopp, P.J.1
  • 46
    • 3042722019 scopus 로고    scopus 로고
    • Evolutionary changes in cis and trans gene regulation
    • Wittkopp, P. J., B. K. Haerum, and A. G. Clark . 2004. Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
    • (2004) Nature , vol.430 , pp. 85-88
    • Wittkopp, P.J.1    Haerum, B.K.2    Clark, A.G.3
  • 47
    • 39749116219 scopus 로고    scopus 로고
    • Regulatory changes underlying expression differences within and between Drosophila species
    • Wittkopp, P. J., B. K. Haerum, and A. G. Clark . 2008. Regulatory changes underlying expression differences within and between Drosophila species. Nat. Genet. 40: 346-350.
    • (2008) Nat. Genet. , vol.40 , pp. 346-350
    • Wittkopp, P.J.1    Haerum, B.K.2    Clark, A.G.3
  • 48
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray, G. A. 2007. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8: 206-216.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 206-216
    • Wray, G.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.