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Volumn 8, Issue 2, 2016, Pages 403-410

Accurate transposable element annotation is vital when analyzing new genome assemblies

Author keywords

Genome annotation; Heliconius melpomene; Heterocephalus glaber; Microtus ochrogaster; Transposable elements

Indexed keywords

TRANSPOSON;

EID: 85007197691     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw009     Document Type: Article
Times cited : (88)

References (43)
  • 1
    • 65549101705 scopus 로고    scopus 로고
    • TEclass-A tool for automated classification of unknown eukaryotic transposable elements
    • Abrusán G, Grundmann N, DeMester L, Makalowski W. 2009. TEclass-A tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25:1329-1330.
    • (2009) Bioinformatics , vol.25 , pp. 1329-1330
    • Abrusán, G.1    Grundmann, N.2    DeMester, L.3    Makalowski, W.4
  • 2
    • 0037355121 scopus 로고    scopus 로고
    • Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes
    • Adkins RM, Walton AH, Honeycutt RL. 2003. Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol Phylogenet Evol. 26:409-420.
    • (2003) Mol Phylogenet Evol. , vol.26 , pp. 409-420
    • Adkins, R.M.1    Walton, A.H.2    Honeycutt, R.L.3
  • 3
    • 80053359585 scopus 로고    scopus 로고
    • The genome of the green anole lizard and a comparative analysis with birds and mammals
    • Alfoldi J, et al. 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587-591.
    • (2011) Nature , vol.477 , pp. 587-591
    • Alfoldi, J.1
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 5
    • 0029749096 scopus 로고    scopus 로고
    • Parallel race formation and the evolution of mimicry in Heliconius butterflies: A phylogenetic hypothesis from mitochondrial DNA sequences
    • Brower AVZ. 1996. Parallel race formation and the evolution of mimicry in Heliconius butterflies: A phylogenetic hypothesis from mitochondrial DNA sequences. Evolution 50:195-221.
    • (1996) Evolution , vol.50 , pp. 195-221
    • Brower, A.V.Z.1
  • 8
    • 71749089142 scopus 로고    scopus 로고
    • Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes
    • Feschotte C, Keswani U, Ranganathan N, Guibotsy ML, Levine D. 2009. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biol Evol. 1:205-220.
    • (2009) Genome Biol Evol. , vol.1 , pp. 205-220
    • Feschotte, C.1    Keswani, U.2    Ranganathan, N.3    Guibotsy, M.L.4    Levine, D.5
  • 9
    • 84875474477 scopus 로고    scopus 로고
    • Transposable element annotation in completely sequenced eukaryote genomes
    • Grandbastien MA, Casacuberta JM, editors. Berlin Heidelberg (Germany/publisher-loc): Springer
    • Flutre T, Permal E, Quesneville H. 2012. Transposable element annotation in completely sequenced eukaryote genomes. In: Grandbastien MA, Casacuberta JM, editors. Plant transposable elements. Berlin Heidelberg (Germany/publisher-loc): Springer. p. 17-39.
    • (2012) Plant Transposable Elements , pp. 17-39
    • Flutre, T.1    Permal, E.2    Quesneville, H.3
  • 10
    • 0348048755 scopus 로고    scopus 로고
    • L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish
    • Furano AV, Duvernell DD, Boissinot S. 2004. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet. 20:9-14.
    • (2004) Trends Genet. , vol.20 , pp. 9-14
    • Furano, A.V.1    Duvernell, D.D.2    Boissinot, S.3
  • 11
    • 0036094818 scopus 로고    scopus 로고
    • An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks
    • Gaunt MW,Miles MA. 2002. An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol. 19:748-761.
    • (2002) Mol Biol Evol. , vol.19 , pp. 748-761
    • Gaunt, M.W.1    Miles, M.A.2
  • 12
    • 84878718523 scopus 로고    scopus 로고
    • Draft genome sequence of the Tibetan antelope
    • Ge RL, et al. 2013. Draft genome sequence of the Tibetan antelope. Nat Commun. 4:1858
    • (2013) Nat Commun. , vol.4 , pp. 1858
    • Ge, R.L.1
  • 13
    • 84917697073 scopus 로고    scopus 로고
    • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
    • Green RE, et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449.
    • (2014) Science , vol.346 , pp. 1254449
    • Green, R.E.1
  • 14
    • 84885086234 scopus 로고    scopus 로고
    • Identification and evolution of the silkworm helitrons and their contribution to transcripts
    • Han MJ, et al. 2013. Identification and evolution of the silkworm helitrons and their contribution to transcripts. DNA Res. 20:471-484.
    • (2013) DNA Res. , vol.20 , pp. 471-484
    • Han, M.J.1
  • 15
    • 80054760378 scopus 로고    scopus 로고
    • Variation in the mutation rate across mammalian genomes
    • Hodgkinson A, Eyre-Walker A. 2011. Variation in the mutation rate across mammalian genomes. Nat Rev Genet. 12:756-766.
    • (2011) Nat Rev Genet. , vol.12 , pp. 756-766
    • Hodgkinson, A.1    Eyre-Walker, A.2
  • 16
    • 84938573693 scopus 로고    scopus 로고
    • A call for benchmarking transposable element annotation methods
    • Hoen DR, et al. 2015. A call for benchmarking transposable element annotation methods. Mobile DNA 6:1-9.
    • (2015) Mobile DNA , vol.6 , pp. 1-9
    • Hoen, D.R.1
  • 17
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: A web server for clustering and comparing biological sequences
    • Huang Y, Niu B, Gao Y, Fu L, Li W. 2010. CD-HIT Suite: A web server for clustering and comparing biological sequences. Bioinformatics 26:680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 18
    • 34250627653 scopus 로고    scopus 로고
    • Multiple molecular evidences for a living mammalian fossil
    • Huchon D, et al. 2007. Multiple molecular evidences for a living mammalian fossil. Proc Natl Acad Sci U S A. 104:7495-7499.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 7495-7499
    • Huchon, D.1
  • 19
    • 85007202097 scopus 로고    scopus 로고
    • Long terminal repeats from rabbit
    • Jurka J. 2009a. Long terminal repeats from rabbit. Repbase Rep. 9:2900.
    • (2009) Repbase Rep. , vol.9 , pp. 2900
    • Jurka, J.1
  • 20
    • 85007202085 scopus 로고    scopus 로고
    • Long terminal repeats from the American Pika
    • Jurka J. 2009b. Long terminal repeats from the American Pika. Repbase Rep. 9:2205.
    • (2009) Repbase Rep. , vol.9 , pp. 2205
    • Jurka, J.1
  • 21
    • 0033288597 scopus 로고    scopus 로고
    • Molecular paleontology of transposable elements from Arabidopsis thaliana
    • Kapitonov V, Jurka J. 1999. Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107:27-37.
    • (1999) Genetica , vol.107 , pp. 27-37
    • Kapitonov, V.1    Jurka, J.2
  • 22
    • 0037975554 scopus 로고    scopus 로고
    • Molecular paleontology of transposable elements in the Drosophila melanogaster genome
    • Kapitonov VV, Jurka J. 2003. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 100:6569-6574.
    • (2003) Proc Natl Acad Sci U S A. , vol.100 , pp. 6569-6574
    • Kapitonov, V.V.1    Jurka, J.2
  • 23
    • 1542513556 scopus 로고    scopus 로고
    • Mobile elements: Drivers of genome evolution
    • Kazazian HH. 2004. Mobile elements: drivers of genome evolution. Science 303:1626-1632.
    • (2004) Science , vol.303 , pp. 1626-1632
    • Kazazian, H.H.1
  • 24
    • 0035105221 scopus 로고    scopus 로고
    • Perspective: Transposable elements, parasitic DNA, and genome evolution
    • Kidwell MG, Lisch DR. 2001. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55:1-24.
    • (2001) Evolution , vol.55 , pp. 1-24
    • Kidwell, M.G.1    Lisch, D.R.2
  • 25
    • 80855165387 scopus 로고    scopus 로고
    • Genome sequencing reveals insights into physiology and longevity of the naked mole rat
    • Kim EB, et al. 2011. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479:223-227.
    • (2011) Nature , vol.479 , pp. 223-227
    • Kim, E.B.1
  • 26
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120.
    • (1980) J Mol Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 28
    • 84884748768 scopus 로고    scopus 로고
    • Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera
    • Lavoie C, Platt R, Novick P, Counterman B, Ray D. 2013. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mobile DNA 4:21
    • (2013) Mobile DNA , vol.4 , pp. 21
    • Lavoie, C.1    Platt, R.2    Novick, P.3    Counterman, B.4    Ray, D.5
  • 29
    • 25144488228 scopus 로고    scopus 로고
    • Gene duplication and exon shuffling by helitronlike transposons generate intraspecies diversity in maize
    • Morgante M, et al. 2005. Gene duplication and exon shuffling by helitronlike transposons generate intraspecies diversity in maize. Nat Genet. 37:997-1002.
    • (2005) Nat Genet. , vol.37 , pp. 997-1002
    • Morgante, M.1
  • 31
    • 55949134735 scopus 로고    scopus 로고
    • Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods
    • Pace JK, Gilbert C, Clark MS, Feschotte C. 2008. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A. 105:17023-17028.
    • (2008) Proc Natl Acad Sci U S A. , vol.105 , pp. 17023-17028
    • Pace, J.K.1    Gilbert, C.2    Clark, M.S.3    Feschotte, C.4
  • 32
    • 49249121601 scopus 로고    scopus 로고
    • Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies
    • Papa R, et al. 2008. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. BMC Genomics 9:345
    • (2008) BMC Genomics , vol.9 , pp. 345
    • Papa, R.1
  • 33
    • 84860335554 scopus 로고    scopus 로고
    • A non-LTR retroelement extinction in Spermophilus tridecemlineatus
    • Platt RN II, Ray DA. 2012. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 500:47-53.
    • (2012) Gene , vol.500 , pp. 47-53
    • Platt, I.I.R.N.1    Ray, D.A.2
  • 34
    • 84901467575 scopus 로고    scopus 로고
    • Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats
    • Platt RN II, et al. 2014. Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mol Biol Evol. 31:1536-1545.
    • (2014) Mol Biol Evol. , vol.31 , pp. 1536-1545
    • Platt, I.I.R.N.1
  • 35
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21:i351-i358.
    • (2005) Bioinformatics , vol.21 , pp. i351-i358
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 36
    • 33846931279 scopus 로고    scopus 로고
    • Massive amplification of rolling-circle transposons in the lineage of the batMyotis lucifugus
    • Pritham EJ, Feschotte C. 2007. Massive amplification of rolling-circle transposons in the lineage of the batMyotis lucifugus. Proc Natl Acad Sci U S A. 104:1895-1900.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 1895-1900
    • Pritham, E.J.1    Feschotte, C.2
  • 38
    • 84939468193 scopus 로고    scopus 로고
    • The specific requirements for CR1 retrotransposition explain the scarcity of retrogenes in birds
    • Suh A. 2015. The specific requirements for CR1 retrotransposition explain the scarcity of retrogenes in birds. J Mol Evol. 81:18-20.
    • (2015) J Mol Evol. , vol.81 , pp. 18-20
    • Suh, A.1
  • 39
    • 77955273950 scopus 로고    scopus 로고
    • A triptych of the evolution of plant transposable elements
    • Tenaillon MI, Hollister JD, Gaut BS. 2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15:471-478.
    • (2010) Trends Plant Sci. , vol.15 , pp. 471-478
    • Tenaillon, M.I.1    Hollister, J.D.2    Gaut, B.S.3
  • 40
    • 84929996202 scopus 로고    scopus 로고
    • Rolling-circle transposons catalyze genomic innovation in a mammalian lineage
    • Thomas J, Phillips CD, Baker RJ, Pritham EJ. 2014. Rolling-circle transposons catalyze genomic innovation in a mammalian lineage. Genome Biol Evol. 6:2595-2610.
    • (2014) Genome Biol Evol. , vol.6 , pp. 2595-2610
    • Thomas, J.1    Phillips, C.D.2    Baker, R.J.3    Pritham, E.J.4
  • 41
    • 24344509193 scopus 로고    scopus 로고
    • Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates
    • van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL. 2005. Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res. 15:1243-1249.
    • (2005) Genome Res. , vol.15 , pp. 1243-1249
    • Van De Lagemaat, L.N.1    Gagnier, L.2    Medstrand, P.3    Mager, D.L.4
  • 42
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • Wicker T, 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
  • 43
    • 34547592867 scopus 로고    scopus 로고
    • LTR-FINDER: An efficient tool for the prediction of full-length LTR retrotransposons
    • Xu Z, Wang H. 2007. LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35:W265-W268.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W265-W268
    • Xu, Z.1    Wang, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.