메뉴 건너뛰기




Volumn 45, Issue 8, 2013, Pages 884-890

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; COPY NUMBER VARIATION; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME SIZE; NONHUMAN; PLANT GENETICS; PLANT GENOME; PRIORITY JOURNAL; SELECTIVE SWEEP; SWEDEN;

EID: 84881026985     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2678     Document Type: Article
Times cited : (300)

References (45)
  • 1
    • 80053612343 scopus 로고    scopus 로고
    • A map of local adaptation in Arabidopsis thaliana
    • Fournier-Level, A. et al. A map of local adaptation in Arabidopsis thaliana. Science 334, 86-89 (2011).
    • (2011) Science , vol.334 , pp. 86-89
    • Fournier-Level, A.1
  • 2
    • 80053587873 scopus 로고    scopus 로고
    • Adaptation to climate across the Arabidopsis thaliana genome
    • Hancock, A.M. et al. Adaptation to climate across the Arabidopsis thaliana genome. Science 334, 83-86 (2011).
    • (2011) Science , vol.334 , pp. 83-86
    • Hancock, A.M.1
  • 3
    • 77649215261 scopus 로고    scopus 로고
    • The scale of population structure in Arabidopsis thaliana
    • Platt, A. et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 6, e1000843 (2010).
    • (2010) PLoS Genet , vol.6
    • Platt, A.1
  • 5
    • 77953233453 scopus 로고    scopus 로고
    • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    • Atwell, S. et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627-631 (2010).
    • (2010) Nature , vol.465 , pp. 627-631
    • Atwell, S.1
  • 6
    • 84856270364 scopus 로고    scopus 로고
    • Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel
    • Horton, M.W. et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat. Genet. 44, 212-216 (2012).
    • (2012) Nat. Genet , vol.44 , pp. 212-216
    • Horton, M.W.1
  • 7
    • 68249140383 scopus 로고    scopus 로고
    • The 1001 Genomes Project for Arabidopsis thaliana
    • Weigel, D. & Mott, R. The 1001 Genomes Project for Arabidopsis thaliana. Genome Biol. 10, 107 (2009).
    • (2009) Genome Biol , vol.10 , pp. 107
    • Weigel, D.1    Mott, R.2
  • 8
    • 79959974750 scopus 로고    scopus 로고
    • Reference-guided assembly of four diverse Arabidopsis thaliana genomes
    • Schneeberger, K. et al. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl. Acad. Sci. USA 108, 10249-10254 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 10249-10254
    • Schneeberger, K.1
  • 9
    • 80053132716 scopus 로고    scopus 로고
    • Multiple reference genomes and transcriptomes for Arabidopsis thaliana
    • Gan, X. et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419-423 (2011).
    • (2011) Nature , vol.477 , pp. 419-423
    • Gan, X.1
  • 10
    • 80053384429 scopus 로고    scopus 로고
    • Whole-genome sequencing of multiple Arabidopsis thaliana populations
    • Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43, 956-963 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 956-963
    • Cao, J.1
  • 11
    • 84874991260 scopus 로고    scopus 로고
    • Patterns of population epigenomic diversity
    • Schmitz, R.J. et al. Patterns of population epigenomic diversity. Nature 495, 193-198 (2013).
    • (2013) Nature , vol.495 , pp. 193-198
    • Schmitz, R.J.1
  • 12
    • 79955468851 scopus 로고    scopus 로고
    • The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
    • Hu, T.T. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476-481 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 476-481
    • Hu, T.T.1
  • 13
    • 2542487363 scopus 로고    scopus 로고
    • Genome size variation among accessions of Arabidopsis thaliana
    • Schmuths, H., Meister, A., Horres, R. & Bachmann, K. Genome size variation among accessions of Arabidopsis thaliana. Ann. Bot. 93, 317-321 (2004).
    • (2004) Ann. Bot , vol.93 , pp. 317-321
    • Schmuths, H.1    Meister, A.2    Horres, R.3    Bachmann, K.4
  • 14
    • 34948853236 scopus 로고    scopus 로고
    • Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
    • Davison, J., Tyagi, A. & Comai, L. Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana. BMC Plant Biol. 7, 44 (2007).
    • (2007) BMC Plant Biol , vol.7 , pp. 44
    • Davison, J.1    Tyagi, A.2    Comai, L.3
  • 15
    • 0030087850 scopus 로고    scopus 로고
    • RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4
    • Copenhaver, G.P. & Pikaard, C.S. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. Plant J. 9, 259-272 (1996).
    • (1996) Plant J , vol.9 , pp. 259-272
    • Copenhaver, G.P.1    Pikaard, C.S.2
  • 16
    • 0014422789 scopus 로고
    • Specific gene amplification in oocytes. Oocyte nuclei contain extrachromosomal replicas of the genes for ribosomal RNA
    • Brown, D.D. & Dawid, I.B. Specific gene amplification in oocytes. Oocyte nuclei contain extrachromosomal replicas of the genes for ribosomal RNA. Science 160, 272-280 (1968).
    • (1968) Science , vol.160 , pp. 272-280
    • Brown, D.D.1    Dawid, I.B.2
  • 17
    • 0015235733 scopus 로고
    • Increasing the multiplicity of ribosomal RNA genes in Drosophila melanogaster
    • Tartof, K.D. Increasing the multiplicity of ribosomal RNA genes in Drosophila melanogaster. Science 171, 294-297 (1971).
    • (1971) Science , vol.171 , pp. 294-297
    • Tartof, K.D.1
  • 18
    • 0016286075 scopus 로고
    • A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis
    • Yao, M.C., Kimmel, A.R. & Gorovsky, M.A. A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis. Proc. Natl. Acad. Sci. USA 71, 3082-3086 (1974).
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 3082-3086
    • Yao, M.C.1    Kimmel, A.R.2    Gorovsky, M.A.3
  • 19
    • 84860521732 scopus 로고    scopus 로고
    • Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis
    • Pontvianne, F. et al. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev. 26, 945-957 (2012).
    • (2012) Genes Dev , vol.26 , pp. 945-957
    • Pontvianne, F.1
  • 20
    • 52649099036 scopus 로고    scopus 로고
    • Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana
    • Woo, H.R. & Richards, E.J. Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana. BMC Plant Biol. 8, 92 (2008).
    • (2008) BMC Plant Biol , vol.8 , pp. 92
    • Woo, H.R.1    Richards, E.J.2
  • 21
    • 0036743496 scopus 로고    scopus 로고
    • The control of natural variation in cytosine methylation in Arabidopsis
    • Riddle, N.C. & Richards, E.J. The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162, 355-363 (2002).
    • (2002) Genetics , vol.162 , pp. 355-363
    • Riddle, N.C.1    Richards, E.J.2
  • 22
    • 46249112206 scopus 로고    scopus 로고
    • Low levels of DNA polymerase α induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae
    • Casper, A.M., Mieczkowski, P.A., Gawel, M. & Petes, T.D. Low levels of DNA polymerase α induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae. PLoS Genet. 4, e1000105 (2008).
    • (2008) PLoS Genet , vol.4
    • Casper, A.M.1    Mieczkowski, P.A.2    Gawel, M.3    Petes, T.D.4
  • 23
    • 0141787945 scopus 로고    scopus 로고
    • Disruption of the AtREV3 gene causes hypersensitivity to ultraviolet B light and γ-rays in Arabidopsis: Implication of the presence of a translesion synthesis mechanism in plants
    • Sakamoto, A. et al. Disruption of the AtREV3 gene causes hypersensitivity to ultraviolet B light and γ-rays in Arabidopsis: implication of the presence of a translesion synthesis mechanism in plants. Plant Cell 15, 2042-2057 (2003).
    • (2003) Plant Cell , vol.15 , pp. 2042-2057
    • Sakamoto, A.1
  • 24
    • 31544434491 scopus 로고    scopus 로고
    • Loss of DNA polymerase ζ causes chromosomal instability in mammalian cells
    • Wittschieben, J.P., Reshmi, S.C., Gollin, S.M. & Wood, R.D. Loss of DNA polymerase ζ causes chromosomal instability in mammalian cells. Cancer Res. 66, 134-142 (2006).
    • (2006) Cancer Res , vol.66 , pp. 134-142
    • Wittschieben, J.P.1    Reshmi, S.C.2    Gollin, S.M.3    Wood, R.D.4
  • 25
    • 1542405310 scopus 로고    scopus 로고
    • Eukaryotic MCM proteins: Beyond replication initiation
    • Forsburg, S.L. Eukaryotic MCM proteins: beyond replication initiation. Microbiol. Mol. Biol. Rev. 68, 109-131 (2004).
    • (2004) Microbiol. Mol. Biol. Rev , vol.68 , pp. 109-131
    • Forsburg, S.L.1
  • 26
    • 78951470427 scopus 로고    scopus 로고
    • Conditions under which genome-wide association studies will be positively misleading
    • Platt, A., Vilhjálmsson, B.J. & Nordborg, M. Conditions under which genome-wide association studies will be positively misleading. Genetics 186, 1045-1052 (2010).
    • (2010) Genetics , vol.186 , pp. 1045-1052
    • Platt, A.1    Vilhjálmsson, B.J.2    Nordborg, M.3
  • 27
    • 84871345504 scopus 로고    scopus 로고
    • The nature of confounding in genome-wide association studies
    • Vilhjálmsson, B.J. & Nordborg, M. The nature of confounding in genome-wide association studies. Nat. Rev. Genet. 14, 1-2 (2013).
    • (2013) Nat. Rev. Genet , vol.14 , pp. 1-2
    • Vilhjálmsson, B.J.1    Nordborg, M.2
  • 29
    • 77949423534 scopus 로고    scopus 로고
    • Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
    • Meer, M.V., Kondrashov, A.S., Artzy-Randrup, Y. & Kondrashov, F.A. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature 464, 279-282 (2010).
    • (2010) Nature , vol.464 , pp. 279-282
    • Meer, M.V.1    Kondrashov, A.S.2    Artzy-Randrup, Y.3    Kondrashov, F.A.4
  • 30
    • 0036479020 scopus 로고    scopus 로고
    • The extent of linkage disequilibrium in Arabidopsis thaliana
    • Nordborg, M. et al. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30, 190-193 (2002).
    • (2002) Nat. Genet , vol.30 , pp. 190-193
    • Nordborg, M.1
  • 31
    • 22744434580 scopus 로고    scopus 로고
    • The pattern of polymorphism in Arabidopsis thaliana
    • Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005).
    • (2005) PLoS Biol , vol.3
    • Nordborg, M.1
  • 32
    • 34548016343 scopus 로고    scopus 로고
    • Recombination and linkage disequilibrium in Arabidopsis thaliana
    • Kim, S. et al. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 39, 1151-1155 (2007).
    • (2007) Nat. Genet , vol.39 , pp. 1151-1155
    • Kim, S.1
  • 33
    • 84874076180 scopus 로고    scopus 로고
    • Visualization of SNPs with t-SNE
    • Platzer, A. Visualization of SNPs with t-SNE. PLoS ONE 8, e56883 (2013).
    • (2013) PLoS ONE , vol.8
    • Platzer, A.1
  • 34
    • 27544437635 scopus 로고    scopus 로고
    • Genomic scans for selective sweeps using SNP data
    • Nielsen, R. et al. Genomic scans for selective sweeps using SNP data. Genome Res. 15, 1566-1575 (2005).
    • (2005) Genome Res , vol.15 , pp. 1566-1575
    • Nielsen, R.1
  • 35
    • 77649260327 scopus 로고    scopus 로고
    • Population differentiation as a test for selective sweeps
    • Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402 (2010).
    • (2010) Genome Res , vol.20 , pp. 393-402
    • Chen, H.1    Patterson, N.2    Reich, D.3
  • 36
    • 34547108086 scopus 로고    scopus 로고
    • Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
    • Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338-342 (2007).
    • (2007) Science , vol.317 , pp. 338-342
    • Clark, R.M.1
  • 37
    • 0034603206 scopus 로고    scopus 로고
    • Integrated cytogenetic map of chromosome arm 4S of A. Thaliana: Structural organization of heterochromatic knob and centromere region
    • Fransz, P.F. et al. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100, 367-376 (2000).
    • (2000) Cell , vol.100 , pp. 367-376
    • Fransz, P.F.1
  • 38
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 39
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAM-tools
    • Li, H. et al. The Sequence Alignment/Map format and SAM-tools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 40
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 491-498
    • Depristo, M.A.1
  • 41
    • 84892675055 scopus 로고    scopus 로고
    • TE-Locate: A tool to locate and group transposable element occurrences using paired-end next-generation sequencing data
    • Platzer, A., Nizhynska, V. & Long, Q. TE-Locate: a tool to locate and group transposable element occurrences using paired-end next-generation sequencing data. Biology 1, 395-410 (2012).
    • (2012) Biology , vol.1 , pp. 395-410
    • Platzer, A.1    Nizhynska, V.2    Long, Q.3
  • 42
    • 0040124427 scopus 로고
    • Linkage disequilibrium due to random genetic drift in finite subdivided populations
    • Ohta, T. Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proc. Natl. Acad. Sci. USA 79, 1940-1944 (1982).
    • (1982) Proc. Natl. Acad. Sci. USA , vol.79 , pp. 1940-1944
    • Ohta, T.1
  • 43
    • 78650727753 scopus 로고    scopus 로고
    • Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome
    • Cockram, J. et al. Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome. Proc. Natl. Acad. Sci. USA 107, 21611-21616 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 21611-21616
    • Cockram, J.1
  • 44
    • 84857238825 scopus 로고    scopus 로고
    • Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
    • Mangin, B. et al. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity 108, 285-291 (2012).
    • (2012) Heredity , vol.108 , pp. 285-291
    • Mangin, B.1
  • 45
    • 35349012592 scopus 로고    scopus 로고
    • Genome-wide detection and characterization of positive selection in human populations
    • Sabeti, P.C. et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-918 (2007).
    • (2007) Nature , vol.449 , pp. 913-918
    • Sabeti, P.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.