메뉴 건너뛰기




Volumn 9, Issue 5, 2014, Pages

Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PLANT DNA; TRANSPOSON;

EID: 84901479316     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0097189     Document Type: Article
Times cited : (16)

References (42)
  • 1
    • 84861405834 scopus 로고    scopus 로고
    • Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence
    • Lepesant JM, Cosseau C, Boissier J, Freitag M, Portela J, et al. (2012) Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence. Genome Biol 13: 14-28.
    • (2012) Genome Biol , vol.13 , pp. 14-28
    • Lepesant, J.M.1    Cosseau, C.2    Boissier, J.3    Freitag, M.4    Portela, J.5
  • 2
    • 85047686163 scopus 로고    scopus 로고
    • Dioecious plants. A key to the early events of sex chromosome evolution
    • DOI 10.1104/pp.127.4.1418
    • Negrutiu İ, Vyskot B, Barbacar N, Georgiev S, Moneger F (2001) Dioecious plants. A key to the early events of sex chromosome evolution. Plant Physiol 127: 1418-1424. (Pubitemid 34050009)
    • (2001) Plant Physiology , vol.127 , Issue.4 , pp. 1418-1424
    • Negrutiu, I.1    Vyskot, B.2    Barbacar, N.3    Georgiev, S.4    Moneger, F.5
  • 3
    • 58749097041 scopus 로고    scopus 로고
    • The evolution of restricted recombination in sex chromosomes
    • Bergero R, Charlesworth D (2009) The evolution of restricted recombination in sex chromosomes. Trends Ecol Evol 24: 94-102.
    • (2009) Trends Ecol Evol , vol.24 , pp. 94-102
    • Bergero, R.1    Charlesworth, D.2
  • 4
    • 84872318678 scopus 로고    scopus 로고
    • Plant sex chromosome evolution
    • Charlesworth D (2013) Plant sex chromosome evolution. J Exp Bot 64: 405-420.
    • (2013) J Exp Bot , vol.64 , pp. 405-420
    • Charlesworth, D.1
  • 6
    • 23644455954 scopus 로고    scopus 로고
    • Steps in the evolution of heteromorphic sex chromosomes
    • DOI 10.1038/sj.hdy.6800697
    • Charlesworth D, Charlesworth B, Marais G (2005) Steps in the evolution of heteromorphic sex chromosomes. Heredity 95: 118-128. (Pubitemid 41133194)
    • (2005) Heredity , vol.95 , Issue.2 , pp. 118-128
    • Charlesworth, D.1    Charlesworth, B.2    Marais, G.3
  • 7
    • 0029668422 scopus 로고    scopus 로고
    • Sexually antagonistic male adaptation triggered by experimental arrest of female evolution
    • Rice WR (1996) Sexually antagonistic male adaptation triggered by experimental arrest of female evolution. Nature 381: 232-234.
    • (1996) Nature , vol.381 , pp. 232-234
    • Rice, W.R.1
  • 8
    • 55149110544 scopus 로고    scopus 로고
    • Survey of repetitive sequence in Silene latifolia with respect to their distribution on sex chromosome
    • Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, et al. (2008) Survey of repetitive sequence in Silene latifolia with respect to their distribution on sex chromosome. Chromosome Res 16: 961-976.
    • (2008) Chromosome Res , vol.16 , pp. 961-976
    • Cermak, T.1    Kubat, Z.2    Hobza, R.3    Koblizkova, A.4    Widmer, A.5
  • 10
    • 51249171246 scopus 로고
    • Nuclear DNA content of some important plant species
    • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218.
    • (1991) Plant Mol Biol Rep , vol.9 , pp. 208-218
    • Arumuganathan, K.1    Earle, E.D.2
  • 11
    • 0000684928 scopus 로고
    • Asparagus breeding
    • Bassett MJ, editor. AVI, Westport
    • Ellison JH (1986) Asparagus breeding. In: Bassett MJ, editor. Breeding Vegetable Crops, AVI, Westport. 523-568.
    • (1986) Breeding Vegetable Crops , pp. 523-568
    • Ellison, J.H.1
  • 12
    • 0038680931 scopus 로고
    • Determination of sex in Asparagus officinalis L
    • Rick CM, Hanna GC (1943) Determination of sex in Asparagus officinalis L. Am J Bot 30: 711-714.
    • (1943) Am J Bot , vol.30 , pp. 711-714
    • Rick, C.M.1    Hanna, G.C.2
  • 13
    • 4143061437 scopus 로고    scopus 로고
    • Gender in plants: Sex chromosomes are emerging from the fog
    • DOI 10.1016/j.tig.2004.06.006, PII S0168952504001568
    • Vyskot B, Hobza R (2004) Gender in plants: sex chromosomes are emerging from the fog. Trends Genet 20: 432-438. (Pubitemid 39094572)
    • (2004) Trends in Genetics , vol.20 , Issue.9 , pp. 432-438
    • Vyskot, B.1    Hobza, R.2
  • 14
    • 84883233155 scopus 로고    scopus 로고
    • Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes
    • Vitte C, Estep MC, Leebens-Mack J Bennetzen JL (2013) Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann Bot 112: 881-889.
    • (2013) Ann Bot , vol.112 , pp. 881-889
    • Vitte, C.1    Estep, M.C.2    Leebens-Mack, J.3    Bennetzen, J.L.4
  • 15
    • 84887499114 scopus 로고    scopus 로고
    • Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales
    • Hertweck KL (2013) Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Genome 56: 487-494.
    • (2013) Genome , vol.56 , pp. 487-494
    • Hertweck, K.L.1
  • 16
    • 23944504276 scopus 로고    scopus 로고
    • Synergy between sequence and size in large-scale genomics
    • Gregory TR (2005) Synergy between sequence and size in large-scale genomics. Nat Rev Genet 6: 699-708.
    • (2005) Nat Rev Genet , vol.6 , pp. 699-708
    • Gregory, T.R.1
  • 17
    • 77954251724 scopus 로고    scopus 로고
    • Use of illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize
    • Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, et al. (2010) Use of illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63: 167-177.
    • (2010) Plant J , vol.63 , pp. 167-177
    • Williams-Carrier, R.1    Stiffler, N.2    Belcher, S.3    Kroeger, T.4    Stern, D.B.5
  • 18
    • 38349101340 scopus 로고    scopus 로고
    • Repetitive DNA in the pea (Pisum sativum L.) genome: Comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
    • Macas J, Neumann P, Navrátilová A (2007) Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 8: 427.
    • (2007) BMC Genomics , vol.8 , pp. 427
    • Macas, J.1    Neumann, P.2    Navrátilová, A.3
  • 19
    • 84871856746 scopus 로고    scopus 로고
    • Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean
    • Tian Z, Zhao M, She M, Du J, Cannon SB, et al. (2012) Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24: 1-15.
    • (2012) Plant Cell , vol.24 , pp. 1-15
    • Tian, Z.1    Zhao, M.2    She, M.3    Du, J.4    Cannon, S.B.5
  • 20
    • 0002594984 scopus 로고
    • A rapid DNA isolation procedure for small quantities of fresh leaf tissue
    • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
    • (1987) Phytochem Bull , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 22
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 24
    • 0346494835 scopus 로고    scopus 로고
    • The TIGR Plant Repeat Databases: A collective resource for the identification of repetitive sequences in plants
    • Ouyang S, Buell CR (2004) The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 32: D360-363. (Pubitemid 38081677)
    • (2004) Nucleic Acids Research , vol.32 , Issue.DATABASE ISS.
    • Ouyang, S.1    Buell, C.R.2
  • 25
    • 0036250001 scopus 로고    scopus 로고
    • Plant transposable elements: Where genetics meets genomics
    • DOI 10.1038/nrg793
    • Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3: 329-341. (Pubitemid 34506715)
    • (2002) Nature Reviews Genetics , vol.3 , Issue.5 , pp. 329-341
    • Feschotte, C.1    Jiang, N.2    Wessler, S.R.3
  • 26
    • 0033367409 scopus 로고    scopus 로고
    • Plant retrotransposons
    • DOI 10.1146/annurev.genet.33.1.479
    • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532. (Pubitemid 30083131)
    • (1999) Annual Review of Genetics , vol.33 , pp. 479-532
    • Kumar, A.1    Bennetzen, J.L.2
  • 27
    • 0034485669 scopus 로고    scopus 로고
    • Retrotransposons: Central players in the structure, evolution and function of plant genomes
    • DOI 10.1016/S1360-1385(00)01760-X
    • Kumar A, Bennetzen JL (2000) Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci 5: 509-510. (Pubitemid 32099966)
    • (2000) Trends in Plant Science , vol.5 , Issue.12 , pp. 509-510
    • Kumar, A.1    Bennetzen, J.L.2
  • 28
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 29
    • 84857524013 scopus 로고    scopus 로고
    • Assessment of metagenomic assembly using simulated next generation sequencing data
    • Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, et al. (2012) Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS One 7: e31386.
    • (2012) PLoS One , vol.7
    • Mende, D.R.1    Waller, A.S.2    Sunagawa, S.3    Järvelin, A.I.4    Chan, M.M.5
  • 30
    • 80053386792 scopus 로고    scopus 로고
    • The genome of the mesopolyploid crop species Brassica rapa
    • Wang X, Wang H, Wang J, Sun R, Wu J, et al. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43: 1035-1039.
    • (2011) Nat Genet , vol.43 , pp. 1035-1039
    • Wang, X.1    Wang, H.2    Wang, J.3    Sun, R.4    Wu, J.5
  • 31
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 32
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE (2011) Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65.
    • (2011) Nat Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 34
    • 80052272774 scopus 로고    scopus 로고
    • The genome of the extremophile crucifer Thellungiella parvula
    • Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, et al. (2011) The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 43: 913-918.
    • (2011) Nat Genet , vol.43 , pp. 913-918
    • Dassanayake, M.1    Oh, D.H.2    Haas, J.S.3    Hernandez, A.4    Hong, H.5
  • 35
    • 33749389724 scopus 로고    scopus 로고
    • Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
    • DOI 10.1101/gr.5282906
    • Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16: 1252-1261. (Pubitemid 44506958)
    • (2006) Genome Research , vol.16 , Issue.10 , pp. 1252-1261
    • Hawkins, J.S.1    Kim, H.2    Nason, J.D.3    Wing, R.A.4    Wendel, J.F.5
  • 36
    • 35448964327 scopus 로고    scopus 로고
    • Transposable element distribution, abundance and role in genome size variation in the genus Oryza
    • Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, et al. (2007) Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol 7: 152.
    • (2007) BMC Evol Biol , vol.7 , pp. 152
    • Zuccolo, A.1    Sebastian, A.2    Talag, J.3    Yu, Y.4    Kim, H.5
  • 37
    • 79960095966 scopus 로고    scopus 로고
    • Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians
    • Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J (2011) Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol 3: 219-229.
    • (2011) Genome Biol Evol , vol.3 , pp. 219-229
    • Tenaillon, M.I.1    Hufford, M.B.2    Gaut, B.S.3    Ross-Ibarra, J.4
  • 38
    • 77956609657 scopus 로고    scopus 로고
    • Repetitive part of the banana (Musa acuminate) genome investigated by low-depth 454 sequencing
    • Hřibová E, Neumann P, Matsumoto T, Roux N, Macas J, et al. (2010) Repetitive part of the banana (Musa acuminate) genome investigated by low-depth 454 sequencing. BMC Plant Biol 10: 204.
    • (2010) BMC Plant Biol , vol.10 , pp. 204
    • Hřibová, E.1    Neumann, P.2    Matsumoto, T.3    Roux, N.4    Macas, J.5
  • 39
    • 2442657861 scopus 로고    scopus 로고
    • Evolutionary history of Oryza sativa LTR retrotransposons: A preliminary survey of the rice genome sequences
    • Gao LZ, McCarthy EM, Ganko EW, McDonald JF (2004) Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 5: 18.
    • (2004) BMC Genomics , vol.5 , pp. 18
    • Gao, L.Z.1    McCarthy, E.M.2    Ganko, E.W.3    McDonald, J.F.4
  • 40
    • 21544440440 scopus 로고    scopus 로고
    • Retrotransposon populations of Vicia species with varying genome size
    • DOI 10.1007/s00438-005-1141-x
    • Hill P, Burford D, Martin DM, Flavell AJ (2005) Retrotransposon populations of Vicia species with varying genome size. Mol Genet Genomics, 273: 371-381. (Pubitemid 40922402)
    • (2005) Molecular Genetics and Genomics , vol.273 , Issue.5 , pp. 371-381
    • Hill, P.1    Burford, D.2    Martin, D.M.A.3    Flavell, A.J.4
  • 41
    • 80655139062 scopus 로고    scopus 로고
    • Next generation sequencing-based analysis of repetitive DNA in the model dioceous plant Silene latifolia
    • Macas J, Kejnovský E, Neumann P, Novák P, Koblížková A, et al. (2011) Next generation sequencing-based analysis of repetitive DNA in the model dioceous plant Silene latifolia. PLoS One 6: e27335.
    • (2011) PLoS One , vol.6
    • Macas, J.1    Kejnovský, E.2    Neumann, P.3    Novák, P.4    Koblížková, A.5
  • 42
    • 0031971207 scopus 로고    scopus 로고
    • AFLP markers tightly linked to the sex locus in Asparagus officinalis L.
    • DOI 10.1023/A:1009650221460
    • Reamon-Büttner SM, Schondelmaier J, Jung C (1998) AFLP markers tightly linked to the sex locus in Asparagus officinalis L. Mol Breeding 4: 91-98. (Pubitemid 28209526)
    • (1998) Molecular Breeding , vol.4 , Issue.2 , pp. 91-98
    • Reamon-Buttner, S.M.1    Schondelmaier, J.2    Jung, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.