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Volumn 5, Issue 8, 2015, Pages 1585-1592

The Wukong terminal-repeat retrotransposon in miniature (TRIM) elements in diverse maize germplasm

Author keywords

Insertion polymorphism; Maize (Zea mays); NGS; Retrotransposon; TRIM

Indexed keywords

MESSENGER RNA; MOLECULAR MARKER; PLANT DNA; RETROPOSON;

EID: 84938828965     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.115.018317     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 33645415035 scopus 로고    scopus 로고
    • TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports
    • Antonius-Klemola, K., R. Kalendar, and A. H. Schulman, 2006 TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor. Appl. Genet. 112: 999-1008.
    • (2006) Theor. Appl. Genet. , vol.112 , pp. 999-1008
    • Antonius-Klemola, K.1    Kalendar, R.2    Schulman, A.H.3
  • 2
    • 33749387064 scopus 로고    scopus 로고
    • Uneven chromosome contraction and expansion in the maize genome
    • Bruggmann, R., A. K. Bharti, H. Gundlach, J. Lai, S. Young et al., 2006 Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16: 1241-1251.
    • (2006) Genome Res. , vol.16 , pp. 1241-1251
    • Bruggmann, R.1    Bharti, A.K.2    Gundlach, H.3    Lai, J.4    Young, S.5
  • 3
    • 0037225254 scopus 로고    scopus 로고
    • Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs
    • Cheng, C., R. Motohashi, S. Tsuchimoto, Y. Fukuta, H. Ohtsubo et al., 2003 Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol. Biol. Evol. 20: 67-75.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 67-75
    • Cheng, C.1    Motohashi, R.2    Tsuchimoto, S.3    Fukuta, Y.4    Ohtsubo, H.5
  • 4
    • 84863007735 scopus 로고    scopus 로고
    • Maize HapMap2 identifies extant variation from a genome in flux
    • Chia, J. M., C. Song, P. J. Bradbury, D. Costich, N. de Leon et al., 2012 Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44: 803-807.
    • (2012) Nat. Genet. , vol.44 , pp. 803-807
    • Chia, J.M.1    Song, C.2    Bradbury, P.J.3    Costich, D.4    de Leon, N.5
  • 5
    • 84884916694 scopus 로고    scopus 로고
    • Detecting Alu insertions from high-throughput sequencing data
    • David, M., H. Mustafa, and M. Brudno, 2013 Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Res. 41: e169.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e169
    • David, M.1    Mustafa, H.2    Brudno, M.3
  • 6
    • 0041353551 scopus 로고    scopus 로고
    • LINE-mediated retrotransposition of marked Alu sequences
    • Dewannieux, M., C. Esnault, and T. Heidmann, 2003 LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35: 41-48.
    • (2003) Nat. Genet. , vol.35 , pp. 41-48
    • Dewannieux, M.1    Esnault, C.2    Heidmann, T.3
  • 7
    • 79957933956 scopus 로고    scopus 로고
    • Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
    • Ewing, A. D., and H. H. Kazazian, Jr., 2011 Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res. 21: 985-990.
    • (2011) Genome Res. , vol.21 , pp. 985-990
    • Ewing, A.D.1    Kazazian, H.H.2
  • 8
    • 0026544795 scopus 로고
    • Retroelements in higher plants
    • Grandbastien, M. A., 1992 Retroelements in higher plants. Trends Genet. 8: 103-108.
    • (1992) Trends Genet. , vol.8 , pp. 103-108
    • Grandbastien, M.A.1
  • 9
    • 77954205450 scopus 로고    scopus 로고
    • Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
    • Hormozdiari, F., I. Hajirasouliha, P. Dao, F. Hach, D. Yorukoglu et al., 2010 Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26: i350-i357.
    • (2010) Bioinformatics , vol.26 , pp. i350-i357
    • Hormozdiari, F.1    Hajirasouliha, I.2    Dao, P.3    Hach, F.4    Yorukoglu, D.5
  • 11
    • 84862993359 scopus 로고    scopus 로고
    • Comparative population genomics of maize domestication and improvement
    • Hufford, M. B., X. Xu, J. van Heerwaarden, T. Pyhajarvi, J. M. Chia et al., 2012 Comparative population genomics of maize domestication and improvement. Nat. Genet. 44: 808-811.
    • (2012) Nat. Genet. , vol.44 , pp. 808-811
    • Hufford, M.B.1    Xu, X.2    van Heerwaarden, J.3    Pyhajarvi, T.4    Chia, J.M.5
  • 12
    • 0036021406 scopus 로고    scopus 로고
    • Dasheng: A recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice
    • Jiang,N., Z. Bao, S. Temnykh, Z. Cheng, J. Jiang et al., 2002 Dasheng: A recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305.
    • (2002) Genetics , vol.161 , pp. 1293-1305
    • Jiang, N.1    Bao, Z.2    Temnykh, S.3    Cheng, Z.4    Jiang, J.5
  • 13
    • 0036849412 scopus 로고    scopus 로고
    • LINEs mobilize SINEs in the eel through a shared 39 sequence
    • Kajikawa, M., and N. Okada, 2002 LINEs mobilize SINEs in the eel through a shared 39 sequence. Cell 111: 433-444.
    • (2002) Cell , vol.111 , pp. 433-444
    • Kajikawa, M.1    Okada, N.2
  • 15
    • 1942421723 scopus 로고    scopus 로고
    • Large retrotransposon derivatives: Abundant, conserved but nonautonomous retroelements of barley and related genomes
    • Kalendar, R., C. M. Vicient, O. Peleg, K. Anamthawat-Jonsson, A. Bolshoy et al., 2004 Large retrotransposon derivatives: Abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166: 1437-1450.
    • (2004) Genetics , vol.166 , pp. 1437-1450
    • Kalendar, R.1    Vicient, C.M.2    Peleg, O.3    Anamthawat-Jonsson, K.4    Bolshoy, A.5
  • 16
    • 35348988679 scopus 로고    scopus 로고
    • Paired-end mapping reveals extensive structural variation in the human genome
    • Korbel, J. O., A. E. Urban, J. P. Affourtit, B. Godwin, F. Grubert et al., 2007 Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426.
    • (2007) Science , vol.318 , pp. 420-426
    • Korbel, J.O.1    Urban, A.E.2    Affourtit, J.P.3    Godwin, B.4    Grubert, F.5
  • 18
    • 3342927934 scopus 로고    scopus 로고
    • Role of transposable elements in heterochromatin and epigenetic control
    • Lippman, Z., A. V. Gendrel, M. Black, M. W. Vaughn, N. Dedhia et al., 2004 Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
    • (2004) Nature , vol.430 , pp. 471-476
    • Lippman, Z.1    Gendrel, A.V.2    Black, M.3    Vaughn, M.W.4    Dedhia, N.5
  • 19
    • 4344616881 scopus 로고    scopus 로고
    • Rapid recent growth and divergence of rice nuclear genomes
    • Ma, J., and J. L. Bennetzen, 2004 Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101: 12404-12410.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12404-12410
    • Ma, J.1    Bennetzen, J.L.2
  • 21
    • 72749127435 scopus 로고
    • The origin and behavior of mutable loci in maize
    • McClintock, B., 1950 The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. USA 36: 344-355.
    • (1950) Proc. Natl. Acad. Sci. USA , vol.36 , pp. 344-355
    • McClintock, B.1
  • 22
    • 68449094455 scopus 로고    scopus 로고
    • Genetic properties of the maize nested association mapping population
    • McMullen, M. D., S. Kresovich, H. S. Villeda, P. Bradbury, H. Li et al., 2009 Genetic properties of the maize nested association mapping population. Science 325: 737-740.
    • (2009) Science , vol.325 , pp. 737-740
    • McMullen, M.D.1    Kresovich, S.2    Villeda, H.S.3    Bradbury, P.4    Li, H.5
  • 23
    • 70350515004 scopus 로고    scopus 로고
    • Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
    • Naito, K., F. Zhang, T. Tsukiyama, H. Saito, C. N. Hancock et al., 2009 Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134.
    • (2009) Nature , vol.461 , pp. 1130-1134
    • Naito, K.1    Zhang, F.2    Tsukiyama, T.3    Saito, H.4    Hancock, C.N.5
  • 24
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song, 2011 Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443-451.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 25
    • 58449137410 scopus 로고    scopus 로고
    • The Sorghum bicolor genome and the diversification of grasses
    • Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood et al., 2009 The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
    • (2009) Nature , vol.457 , pp. 551-556
    • Paterson, A.H.1    Bowers, J.E.2    Bruggmann, R.3    Dubchak, I.4    Grimwood, J.5
  • 26
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 27
    • 0036121338 scopus 로고    scopus 로고
    • Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome
    • Rizzon, C., G. Marais, M. Gouy, and C. Biemont, 2002 Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res. 12: 400-407.
    • (2002) Genome Res. , vol.12 , pp. 400-407
    • Rizzon, C.1    Marais, G.2    Gouy, M.3    Biemont, C.4
  • 28
    • 1342331102 scopus 로고    scopus 로고
    • DISTRUCT: a program for the graphical display of population structure
    • Rosenberg, N. A., 2004 DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4: 137-138.
    • (2004) Mol. Ecol. Notes , vol.4 , pp. 137-138
    • Rosenberg, N.A.1
  • 30
    • 74549221016 scopus 로고    scopus 로고
    • Genome sequence of the palaeopolyploid soybean
    • Schmutz, J., S. B. Cannon, J. Schlueter, J. Ma, T. Mitros et al., 2010 Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
    • (2010) Nature , vol.463 , pp. 178-183
    • Schmutz, J.1    Cannon, S.B.2    Schlueter, J.3    Ma, J.4    Mitros, T.5
  • 31
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: complexity, diversity, and dynamics
    • Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei et al., 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3    Stein, J.C.4    Wei, F.5
  • 32
    • 0042307299 scopus 로고    scopus 로고
    • Gene expression of a gene family in maize based on noncollinear haplotypes
    • Song, R., and J. Messing, 2003 Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. USA 100: 9055-9060.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9055-9060
    • Song, R.1    Messing, J.2
  • 33
    • 5144234363 scopus 로고    scopus 로고
    • Close split of sorghum and maize genome progenitors
    • Swigonova, Z., J. Lai, J. Ma, W. Ramakrishna, V. Llaca et al., 2004 Close split of sorghum and maize genome progenitors. Genome Res. 14: 1916-1923.
    • (2004) Genome Res. , vol.14 , pp. 1916-1923
    • Swigonova, Z.1    Lai, J.2    Ma, J.3    Ramakrishna, W.4    Llaca, V.5
  • 34
    • 85017792236 scopus 로고    scopus 로고
    • PAUP*: phylogenetic analysis using parsimony, version 4.0b10 (and other methods)
    • Swofford, D. L., 2002 PAUP*: phylogenetic analysis using parsimony, version 4.0b10 (and other methods). Genome Res. 14: 1188-1190.
    • (2002) Genome Res. , vol.14 , pp. 1188-1190
    • Swofford, D.L.1
  • 35
    • 84871856746 scopus 로고    scopus 로고
    • Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean
    • Tian, Z., M. Zhao, M. She, J. Du, S. B. Cannon et al., 2012 Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24: 4422-4436.
    • (2012) Plant Cell , vol.24 , pp. 4422-4436
    • Tian, Z.1    Zhao, M.2    She, M.3    Du, J.4    Cannon, S.B.5
  • 36
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • Wicker, T., F. Sabot, A. Hua-Van, J. L. Bennetzen, P. Capy et al., 2007 A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8: 973-982.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 973-982
    • Wicker, T.1    Sabot, F.2    Hua-Van, A.3    Bennetzen, J.L.4    Capy, P.5
  • 37
    • 0035923510 scopus 로고    scopus 로고
    • Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes
    • Witte, C. P., Q. H. Le, T. Bureau, and A. Kumar, 2001 Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc. Natl. Acad. Sci. USA 98: 13778-13783.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 13778-13783
    • Witte, C.P.1    Le, Q.H.2    Bureau, T.3    Kumar, A.4
  • 38
    • 33344469072 scopus 로고    scopus 로고
    • A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement
    • Yamasaki, M., M. I. Tenaillon, I. V. Bi, S. G. Schroeder, H. Sanchez-Villeda et al., 2005 A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17: 2859-2872.
    • (2005) Plant Cell , vol.17 , pp. 2859-2872
    • Yamasaki, M.1    Tenaillon, M.I.2    Bi, I.V.3    Schroeder, S.G.4    Sanchez-Villeda, H.5
  • 39
    • 70249087648 scopus 로고    scopus 로고
    • Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE
    • Yang, G., D. H. Nagel, C. Feschotte, C. N. Hancock, and S. R. Wessler, 2009 Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 325: 1391-1394.
    • (2009) Science , vol.325 , pp. 1391-1394
    • Yang, G.1    Nagel, D.H.2    Feschotte, C.3    Hancock, C.N.4    Wessler, S.R.5
  • 40
    • 33846794768 scopus 로고    scopus 로고
    • Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives
    • Yang, T. J., S. J. Kwon, B. S. Choi, J. S. Kim, M. Jin et al., 2007 Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theor. Appl. Genet. 114: 627-636.
    • (2007) Theor. Appl. Genet. , vol.114 , pp. 627-636
    • Yang, T.J.1    Kwon, S.J.2    Choi, B.S.3    Kim, J.S.4    Jin, M.5
  • 41
    • 84902997341 scopus 로고    scopus 로고
    • Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.)
    • Yin, H., J. Du, L. Li, C. Jin, L. Fan et al., 2014 Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). Genome Biol. Evol. 6: 1423-1436.
    • (2014) Genome Biol. Evol. , vol.6 , pp. 1423-1436
    • Yin, H.1    Du, J.2    Li, L.3    Jin, C.4    Fan, L.5
  • 42
    • 84871704864 scopus 로고    scopus 로고
    • A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus
    • Zhou, Y., and S. H. Cahan, 2012 A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus. PLoS ONE 7: e53401.
    • (2012) PLoS ONE , vol.7 , pp. e53401
    • Zhou, Y.1    Cahan, S.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.