메뉴 건너뛰기




Volumn 196, Issue 4, 2014, Pages 1145-1152

Opposing forces of A/T-biased mutations and G/C-biased gene conversions shape the genome of the nematode Pristionchus pacificus

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; AT BIAS; CODON; DNA BASE COMPOSITION; GENE CONVERSION; GENETIC ASSOCIATION; HUMAN; MUTATION ACCUMULATION LINE; MUTATION RATE; NATURAL POPULATION; NEMATODE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; POPULATION STRUCTURE; PRIORITY JOURNAL; PRISTIONCHUS; PRISTIONCHUS PACIFICUS; STOP CODON; ANIMAL; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOME; MOLECULAR EVOLUTION; POINT MUTATION; RHABDITIDA;

EID: 84901371009     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.159863     Document Type: Article
Times cited : (38)

References (40)
  • 1
    • 84857551173 scopus 로고    scopus 로고
    • Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity
    • Andersen, E. C., J. P. Gerke, J. A. Shapiro, J. R. Crissman, R. Ghosh et al., 2012 Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat. Genet. 44: 285-290.
    • (2012) Nat. Genet. , vol.44 , pp. 285-290
    • Andersen, E.C.1    Gerke, J.P.2    Shapiro, J.A.3    Crissman, J.R.4    Ghosh, R.5
  • 2
    • 79952255486 scopus 로고    scopus 로고
    • Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes
    • Babbitt, G. A., and C. R. Cotter, 2011 Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes. Genome Biol. Evol. 3: 15-22.
    • (2011) Genome Biol. Evol. , vol.3 , pp. 15-22
    • Babbitt, G.A.1    Cotter, C.R.2
  • 3
    • 20244378694 scopus 로고    scopus 로고
    • Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes
    • Baer, C. F., F. Shaw, C. Steding, M. Baumgartner, A. Hawkins et al., 2005 Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes. Proc. Natl. Acad. Sci. USA 102: 5785-5790.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 5785-5790
    • Baer, C.F.1    Shaw, F.2    Steding, C.3    Baumgartner, M.4    Hawkins, A.5
  • 4
    • 77952980794 scopus 로고    scopus 로고
    • Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
    • Borchert, N., C. Dieterich, K. Krug, W. Schütz, S. Jung et al., 2010 Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res. 20: 837-846.
    • (2010) Genome Res. , vol.20 , pp. 837-846
    • Borchert, N.1    Dieterich, C.2    Krug, K.3    Schütz, W.4    Jung, S.5
  • 6
    • 84864089075 scopus 로고    scopus 로고
    • Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes
    • Denver, D. R., L. J. Wilhelm, D. K. Howe, K. Gafner, P. C. Dolan et al., 2012 Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes. Genome Biol. Evol. 4: 513-522.
    • (2012) Genome Biol. Evol. , vol.4 , pp. 513-522
    • Denver, D.R.1    Wilhelm, L.J.2    Howe, D.K.3    Gafner, K.4    Dolan, P.C.5
  • 7
    • 52949136971 scopus 로고    scopus 로고
    • The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism
    • Dieterich, C., S. W. Clifton, L. N. Schuster, A. Chinwalla, K. Delehaunty et al., 2008 The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat. Genet. 40: 1193-1198.
    • (2008) Nat. Genet. , vol.40 , pp. 1193-1198
    • Dieterich, C.1    Clifton, S.W.2    Schuster, L.N.3    Chinwalla, A.4    Delehaunty, K.5
  • 8
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond, A., and A. Rambaut, 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.1    Rambaut, A.2
  • 9
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian Phylogenetics with BEAUti and the BEAST 1.7
    • Drummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut, 2012 Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29: 1969-1973.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1969-1973
    • Drummond, A.J.1    Suchard, M.A.2    Xie, D.3    Rambaut, A.4
  • 10
    • 48049107322 scopus 로고    scopus 로고
    • The conditioned reconstructed process
    • Gernhard, T., 2008 The conditioned reconstructed process. J. Theor. Biol. 253: 769-778.
    • (2008) J. Theor. Biol. , vol.253 , pp. 769-778
    • Gernhard, T.1
  • 11
    • 34447637881 scopus 로고    scopus 로고
    • The nematode Pristionchus pacificus (Nematoda: Diplogastridae) is associated with the oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan
    • Herrmann, M., W. E. Mayer, R. L. Hong, S. Kienle, R. Minasaki et al., 2007 The nematode Pristionchus pacificus (Nematoda: Diplogastridae) is associated with the oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan. Zoolog. Sci. 24: 883-889.
    • (2007) Zoolog. Sci. , vol.24 , pp. 883-889
    • Herrmann, M.1    Mayer, W.E.2    Hong, R.L.3    Kienle, S.4    Minasaki, R.5
  • 12
    • 77952911606 scopus 로고    scopus 로고
    • Haplotype diversity of the nematode Pristionchus pacificus on Réunion in the Indian Ocean suggests multiple independent invasions
    • Herrmann, M., S. Kienle, J. Rochat, W. E. Mayer, and R. J. Sommer, 2010 Haplotype diversity of the nematode Pristionchus pacificus on Réunion in the Indian Ocean suggests multiple independent invasions. Biol. J. Linn. Soc. Lond. 100: 170-179.
    • (2010) Biol. J. Linn. Soc. Lond. , vol.100 , pp. 170-179
    • Herrmann, M.1    Kienle, S.2    Rochat, J.3    Mayer, W.E.4    Sommer, R.J.5
  • 13
    • 77958465787 scopus 로고    scopus 로고
    • High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes
    • Howe, D. K., C. F. Baer, and D. R. Denver, 2010 High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes. Genome Biol. Evol. 2: 29-38.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 29-38
    • Howe, D.K.1    Baer, C.F.2    Denver, D.R.3
  • 15
    • 67650064592 scopus 로고    scopus 로고
    • Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    • Keightley, P. D., U. Trivedi, M. Thomson, F. Oliver, S. Kumar et al., 2009 Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19: 1195-1201.
    • (2009) Genome Res. , vol.19 , pp. 1195-1201
    • Keightley, P.D.1    Trivedi, U.2    Thomson, M.3    Oliver, F.4    Kumar, S.5
  • 16
    • 33646106807 scopus 로고    scopus 로고
    • Relative contribution of homologous recombination and non-homologous end-joining to DNA double-strand break repair after oxidative stress in Saccharomyces cerevisiae
    • Letavayová, L., E. Marková, K. Hermanská, V. Vlčková, D. Vlasáková et al., 2006 Relative contribution of homologous recombination and non-homologous end-joining to DNA double-strand break repair after oxidative stress in Saccharomyces cerevisiae. DNA Repair 5: 602-610.
    • (2006) DNA Repair , vol.5 , pp. 602-610
    • Letavayová, L.1    Marková, E.2    Hermanská, K.3    Vlčková, V.4    Vlasáková, D.5
  • 18
    • 84863229351 scopus 로고    scopus 로고
    • Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by re-sequencing Landsberg erecta and all four products of a single meiosis
    • Lu, P., X. Han, J. Qi, J. Yang, A. J. Wijeratne et al., 2011 Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by re-sequencing Landsberg erecta and all four products of a single meiosis. Genome Res. 22: 508-518.
    • (2011) Genome Res. , vol.22 , pp. 508-518
    • Lu, P.1    Han, X.2    Qi, J.3    Yang, J.4    Wijeratne, A.J.5
  • 19
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • Lunter, G., and M. Goodson, 2011 Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21: 936-939.
    • (2011) Genome Res. , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 21
    • 77955090647 scopus 로고    scopus 로고
    • Evolution of the mutation rate
    • Lynch, M., 2010a Evolution of the mutation rate. Trends Genet. 26: 345-352.
    • (2010) Trends Genet. , vol.26 , pp. 345-352
    • Lynch, M.1
  • 22
    • 75749103383 scopus 로고    scopus 로고
    • Rate, molecular spectrum, and consequences of human mutation
    • Lynch, M., 2010b Rate, molecular spectrum, and consequences of human mutation. Proc. Natl. Acad. Sci. USA 107: 961-968.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 961-968
    • Lynch, M.1
  • 23
  • 24
    • 0038543069 scopus 로고    scopus 로고
    • Biased gene conversion: Implications for genome and sex evolution
    • Marais, G., 2003 Biased gene conversion: implications for genome and sex evolution. Trends Genet. 19: 330-338.
    • (2003) Trends Genet. , vol.19 , pp. 330-338
    • Marais, G.1
  • 25
    • 84876684114 scopus 로고    scopus 로고
    • Unraveling the evolutionary history of the nematode Pristionchus pacificus: From lineage diversification to island colonization
    • McGaughran, A., K. Morgan, and R. J. Sommer, 2013 Unraveling the evolutionary history of the nematode Pristionchus pacificus: from lineage diversification to island colonization. Ecol. Evol. 3: 667-675.
    • (2013) Ecol. Evol. , vol.3 , pp. 667-675
    • McGaughran, A.1    Morgan, K.2    Sommer, R.J.3
  • 26
    • 79961041294 scopus 로고    scopus 로고
    • Mutation rates and intraspecific divergence of the mitochondrial genome of Pristionchus pacificus
    • Molnar, R. I., G. Bartelmes, I. Dinkelacker, H. Witte, and R. J. Sommer, 2011 Mutation rates and intraspecific divergence of the mitochondrial genome of Pristionchus pacificus. Mol. Biol. Evol. 28: 2317-2326.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2317-2326
    • Molnar, R.I.1    Bartelmes, G.2    Dinkelacker, I.3    Witte, H.4    Sommer, R.J.5
  • 27
    • 84855438947 scopus 로고    scopus 로고
    • Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out-crossing
    • Morgan, K., A. McGaughran, L. Villate, M. Herrmann, H. Witte et al., 2012 Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out-crossing. Mol. Ecol. 21: 250-266.
    • (2012) Mol. Ecol. , vol.21 , pp. 250-266
    • Morgan, K.1    McGaughran, A.2    Villate, L.3    Herrmann, M.4    Witte, H.5
  • 28
    • 78651159254 scopus 로고
    • The genetic structure of natural populations of Drosophila melanogaster
    • Mukai, T., 1964 The genetic structure of natural populations of Drosophila melanogaster. Genetics 50: 1-19.
    • (1964) Genetics , vol.50 , pp. 1-19
    • Mukai, T.1
  • 29
    • 0021022685 scopus 로고
    • Evolution of a large population under gene conversion
    • Nagylaki, T., 1983 Evolution of a large population under gene conversion. Proc. Natl. Acad. Sci. USA 80: 5941-5945.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 5941-5945
    • Nagylaki, T.1
  • 30
    • 74849090833 scopus 로고    scopus 로고
    • The rate andmolecular spectrum of spontaneous mutations in Arabidopsis thaliana
    • Ossowski, S., K. Schneeberger, J. I. Lucas-Lledó, N. Warthmann, R. M. Clark et al., 2010 The rate andmolecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
    • (2010) Science , vol.327 , pp. 92-94
    • Ossowski, S.1    Schneeberger, K.2    Lucas-Lledó, J.I.3    Warthmann, N.4    Clark, R.M.5
  • 31
    • 84900500340 scopus 로고    scopus 로고
    • Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data
    • Rödelsperger, C., R. A. Neher, A. M. Weller, G. Eberhardt, H. Witte et al., 2014 Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics 196: 1153-1166.
    • (2014) Genetics , vol.196 , pp. 1153-1166
    • Rödelsperger, C.1    Neher, R.A.2    Weller, A.M.3    Eberhardt, G.4    Witte, H.5
  • 32
    • 45849121794 scopus 로고    scopus 로고
    • The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex
    • Seyfert, A. L., M. E. A. Cristescu, L. Frisse, S. Schaack, W. K. Thomas et al., 2008 The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178: 2113-2121.
    • (2008) Genetics , vol.178 , pp. 2113-2121
    • Seyfert, A.L.1    Cristescu, M.E.A.2    Frisse, L.3    Schaack, S.4    Thomas, W.K.5
  • 33
    • 67349243011 scopus 로고    scopus 로고
    • The future of evo-devo: Model systems and evolutionary theory
    • Sommer, R. J., 2009 The future of evo-devo: model systems and evolutionary theory. Nat. Rev. Genet. 10: 416-422.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 416-422
    • Sommer, R.J.1
  • 35
    • 0023726166 scopus 로고
    • The repairability of oxidative free radical mediated damage to DNA: A review
    • Teebor, G. W., R. J. Boorstein, and J. Cadet, 1988 The repairability of oxidative free radical mediated damage to DNA: a review. Int. J. Radiat. Biol. 54: 131-150.
    • (1988) Int. J. Radiat. Biol. , vol.54 , pp. 131-150
    • Teebor, G.W.1    Boorstein, R.J.2    Cadet, J.3
  • 37
    • 0021092250 scopus 로고
    • Role of biased gene conversion in one-locus neutral theory and genome evolution
    • Walsh, J. B., 1983 Role of biased gene conversion in one-locus neutral theory and genome evolution. Genetics 105: 461-468.
    • (1983) Genetics , vol.105 , pp. 461-468
    • Walsh, J.B.1
  • 38
    • 77953830894 scopus 로고    scopus 로고
    • Quantitative assessment of the nematode fauna present on Geotrupes dung beetles reveals species-rich communities with a heterogeneous distribution
    • Weller, A. M., W. E. Mayer, R. Rae, andR. J. Sommer, 2010 Quantitative assessment of the nematode fauna present on Geotrupes dung beetles reveals species-rich communities with a heterogeneous distribution. J. Parasitol. 96: 525-531.
    • (2010) J. Parasitol. , vol.96 , pp. 525-531
    • Weller, A.M.1    Mayer, W.E.2    Rae, R.3    Sommer, R.J.4
  • 39
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 40
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang, Z., and J. P. Bielawski, 2000 Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15: 496-503.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.