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Volumn 4, Issue 4, 2012, Pages 575-585

Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats

Author keywords

Chiroptera; Survey sequencing; Transposon

Indexed keywords

CHIROPTERA; MAMMALIA; MYOTIS; MYOTIS LUCIFUGUS; PHYLLOSTOMIDAE; VESPERTILIONIDAE;

EID: 84864081575     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs038     Document Type: Conference Paper
Times cited : (34)

References (57)
  • 1
    • 65549101705 scopus 로고    scopus 로고
    • TEclass - A tool for automated classification of unknown eukaryotic transposable elements
    • Abrusän G, Grundmann N, DeMester L, Makalowski W. 2009. TEclass - a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25(10):1329-1330.
    • (2009) Bioinformatics , vol.25 , Issue.10 , pp. 1329-1330
    • Abrusän, G.1    Grundmann, N.2    De Mester, L.3    Makalowski, W.4
  • 2
    • 52049098967 scopus 로고    scopus 로고
    • A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice
    • Aravin AA, et al. 2008. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell. 31(6):785-799.
    • (2008) Mol Cell. , vol.31 , Issue.6 , pp. 785-799
    • Aravin, A.A.1
  • 3
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • DOI 10.1093/nar/27.2.573
    • Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27(2):573-580. (Pubitemid 29210025)
    • (1999) Nucleic Acids Research , vol.27 , Issue.2 , pp. 573-580
    • Benson, G.1
  • 4
    • 13144255696 scopus 로고    scopus 로고
    • The ecology of the genome - Mobile DNA elements and their hosts
    • DOI 10.1038/nrg1524
    • Brookfield JF. 2005. The ecology of the genome - mobile DNA elements and their hosts. Nat Rev Genet. 6(2):128-136. (Pubitemid 40179535)
    • (2005) Nature Reviews Genetics , vol.6 , Issue.2 , pp. 128-136
    • Brookfield, J.F.Y.1
  • 7
    • 79960892350 scopus 로고    scopus 로고
    • Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing
    • Castoe TA, et al. 2011. Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing. Genome Biol Evol. 3:641-653.
    • (2011) Genome Biol Evol. , vol.3 , pp. 641-653
    • Castoe, T.A.1
  • 8
    • 4444358450 scopus 로고    scopus 로고
    • Retrotransposition of Alu elements: How many sources?
    • DOI 10.1016/j.tig.2004.07.012, PII S0168952504002124
    • Cordaux R, Hedges DJ, Batzer MA. 2004. Retrotransposition of Alu elements: how many sources? Trends Genet. 20(10):464-467. (Pubitemid 39201063)
    • (2004) Trends in Genetics , vol.20 , Issue.10 , pp. 464-467
    • Cordaux, R.1    Hedges, D.J.2    Batzer, M.A.3
  • 9
    • 77952960668 scopus 로고    scopus 로고
    • Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia)
    • Datzmann T, von Helversen O, Mayer F. 2010. Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia). BMC Evol Biol. 10(1):165.
    • (2010) BMC Evol Biol. , vol.10 , Issue.1 , pp. 165
    • Datzmann, T.1    Von Helversen, O.2    Mayer, F.3
  • 12
    • 79958278227 scopus 로고    scopus 로고
    • Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System
    • Dong H, et al. 2011. Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System. Acta Biochim Biophys Sin. 43(6):496-500.
    • (2011) Acta Biochim Biophys Sin. , vol.43 , Issue.6 , pp. 496-500
    • Dong, H.1
  • 13
    • 1842684068 scopus 로고    scopus 로고
    • Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    • Gibbs RA, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493-521.
    • (2004) Nature , vol.428 , Issue.6982 , pp. 493-521
    • Gibbs, R.A.1
  • 14
    • 77951778552 scopus 로고    scopus 로고
    • A role for host-parasite interactions in the horizontal transfer of transposons across phyla
    • Gilbert C, Schaack S, Pace Ii JK, Brindley PJ, Feschotte C. 2010. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464(7293):1347-1350.
    • (2010) Nature , vol.464 , Issue.7293 , pp. 1347-1350
    • Gilbert, C.1    Schaack, S.2    Pace II, J.K.3    Brindley, P.J.4    Feschotte, C.5
  • 15
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • Harismendy O, et al. 2009. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10(3):R32.
    • (2009) Genome Biol. , vol.10 , Issue.3
    • Harismendy, O.1
  • 16
    • 1142290091 scopus 로고    scopus 로고
    • Molecular phylogenetics of the chiropteran family Vespertilionidae
    • Molecular phylogenetics of the chiropteran family Vespertilionidae
    • Hoofer SR, Van Den Bussche RA. 2003. Molecular phylogenetics of the chiropteran family Vespertilionidae. Acta Chiropt. 5(Suppl):1-63. (Pubitemid 38211291)
    • (2003) Acta Chiropterologica , vol.5 , Issue.SUPPL. , pp. 1-63
    • Hoofer, S.R.1    Van Den Bussche, R.A.2
  • 17
    • 80052854314 scopus 로고    scopus 로고
    • Families of transposable elements, population structure, and the origin of species
    • Jurka J, Bao W, Kojima KK. 2011. Families of transposable elements, population structure, and the origin of species. Biol Direct. 6(44):1-16.
    • (2011) Biol Direct. , vol.6 , Issue.44 , pp. 1-16
    • Jurka, J.1    Bao, W.2    Kojima, K.K.3
  • 19
    • 2342458877 scopus 로고    scopus 로고
    • Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate
    • Kim T-M, Hong S-J, Rhyu M-G. 2004. Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate. J Korean Med Sci. 19(2):177-185. (Pubitemid 38591789)
    • (2004) Journal of Korean Medical Science , vol.19 , Issue.2 , pp. 177-185
    • Kim, T.-M.1    Hong, S.-J.2    Rhyu, M.-G.3
  • 21
    • 78650438634 scopus 로고    scopus 로고
    • Identifying the confounding factors in resolving phylogenetic relationships in Vespertilionidae
    • Lack JB, Van Den Bussche RA. 2010. Identifying the confounding factors in resolving phylogenetic relationships in Vespertilionidae. J Mammal. 91(6):1435-1448.
    • (2010) J Mammal. , vol.91 , Issue.6 , pp. 1435-1448
    • Lack, J.B.1    Van Den Bussche, R.A.2
  • 23
    • 33750461976 scopus 로고    scopus 로고
    • Population genetics models of competition between transposable element subfamilies
    • DOI 10.1534/genetics.105.052241
    • Le Rouzic A, Capy P. 2006. Population genetics models of competition between transposable element subfamilies. Genetics 174(2):785-793. (Pubitemid 44656467)
    • (2006) Genetics , vol.174 , Issue.2 , pp. 785-793
    • Le Rouzic, A.1    Capy, P.2
  • 25
    • 79251553493 scopus 로고    scopus 로고
    • Comparative and demographic analysis of orangutan genomes
    • Locke DP, et al. 2011. Comparative and demographic analysis of orangutan genomes. Nature 469(7331):529-533.
    • (2011) Nature , vol.469 , Issue.7331 , pp. 529-533
    • Locke, D.P.1
  • 26
    • 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, Navratilova 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    Navratilova, A.3
  • 27
    • 84866434527 scopus 로고
    • A review of bats as carriers of organisms which are capable of infecting man or domestic animals
    • Marinkelle CJ, Grose ES. 1972. A review of bats as carriers of organisms which are capable of infecting man or domestic animals. Mitt Inst Colombo-Aleman Invest Cient. 6:31-51.
    • (1972) Mitt Inst Colombo-aleman Invest Cient. , vol.6 , pp. 31-51
    • Marinkelle, C.J.1    Grose, E.S.2
  • 28
    • 80051695708 scopus 로고    scopus 로고
    • Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae
    • McCulloch ES, Stevens RD. 2011. Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae. Mol Ecol Resour. 11(5):903-913.
    • (2011) Mol Ecol Resour. , vol.11 , Issue.5 , pp. 903-913
    • McCulloch, E.S.1    Stevens, R.D.2
  • 29
    • 84155180868 scopus 로고    scopus 로고
    • Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera
    • Meganathan PR, Pagan HJT, McCulloch ES, Stevens RD, Ray DA. 2012. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene 492(1):121-129.
    • (2012) Gene , vol.492 , Issue.1 , pp. 121-129
    • Meganathan, P.R.1    Pagan, H.J.T.2    McCulloch, E.S.3    Stevens, R.D.4    Ray, D.A.5
  • 32
    • 77954854627 scopus 로고    scopus 로고
    • Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
    • Novak P, Neumann P, Macas J. 2010. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11(1):378.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 378
    • Novak, P.1    Neumann, P.2    Macas, J.3
  • 33
    • 33947731008 scopus 로고    scopus 로고
    • Mighty Piwis Defend the Germline against Genome Intruders
    • DOI 10.1016/j.cell.2007.03.028, PII S0092867407003960
    • O'Donnell KA, Boeke JD. 2007. Mighty Piwis defend the germline against genome intruders. Cell 129(1):37-44. (Pubitemid 46507597)
    • (2007) Cell , vol.129 , Issue.1 , pp. 37-44
    • O'Donnell, K.A.1    Boeke, J.D.2
  • 35
    • 80053266481 scopus 로고    scopus 로고
    • Mobile DNA and the TE-Thrust hypothesis: Supporting evidence from the primates
    • Oliver K, Greene W. 2011. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA. 2(1):1-17.
    • (2011) Mob DNA , vol.2 , Issue.1 , pp. 1-17
    • Oliver, K.1    Greene, W.2
  • 36
    • 70349339300 scopus 로고    scopus 로고
    • Transposable elements: Powerful facilitators of evolution
    • Oliver KR, Greene WK. 2009. Transposable elements: powerful facilitators of evolution. Bioessays 31(7):703-714.
    • (2009) Bioessays , vol.31 , Issue.7 , pp. 703-714
    • Oliver, K.R.1    Greene, W.K.2
  • 37
    • 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. Evolution 105(44):17023-17028.
    • (2008) Evolution , vol.105 , Issue.44 , pp. 17023-17028
    • Pace, J.K.1    Gilbert, C.2    Clark, M.S.3    Feschotte, C.4
  • 38
    • 77958455491 scopus 로고    scopus 로고
    • PiggyBacing on a primate genome: Novel elements, recent activity and horizontal transfer
    • Pagan HJT, Smith JD, Hubley RM, Ray DA. 2010. PiggyBacing on a primate genome: novel elements, recent activity and horizontal transfer. Genome Biol Evol. 2(0):293-303.
    • (2010) Genome Biol Evol. , vol.2 , pp. 293-303
    • Pagan, H.J.T.1    Smith, J.D.2    Hubley, R.M.3    Ray, D.A.4
  • 40
    • 0037123606 scopus 로고    scopus 로고
    • RNA silencing: The Genome's immune system
    • DOI 10.1126/science.1072148
    • Plasterk RHA. 2002. RNA silencing: the genome's immune system. Science 296(5571):1263-1265. (Pubitemid 34522772)
    • (2002) Science , vol.296 , Issue.5571 , pp. 1263-1265
    • Plasterk, R.H.A.1
  • 41
    • 43149113564 scopus 로고    scopus 로고
    • Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus
    • Pritham EJ, Feschotte C. 2007. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci U S A. 17(4):422-432.
    • (2007) Proc Natl Acad Sci U S A , vol.17 , Issue.4 , pp. 422-432
    • Pritham, E.J.1    Feschotte, C.2
  • 42
    • 33847633354 scopus 로고    scopus 로고
    • Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis
    • DOI 10.1093/molbev/msl192
    • Ray DA, Pagan HJT, Thompson ML, Stevens RD. 2007. Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol. 24:632-639. (Pubitemid 46355788)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.3 , pp. 632-639
    • Ray, D.A.1    Pagan, H.J.T.2    Thompson, M.L.3    Stevens, R.D.4
  • 44
    • 77952487819 scopus 로고    scopus 로고
    • Jumping genes and epigenetics: Towards new species
    • Rebollo R, Horard B, Hubert B, Vieira C. 2010. Jumping genes and epigenetics: towards new species. Gene 454(1-2):1-7.
    • (2010) Gene , vol.454 , Issue.1-2 , pp. 1-7
    • Rebollo, R.1    Horard, B.2    Hubert, B.3    Vieira, C.4
  • 45
    • 0345306117 scopus 로고    scopus 로고
    • Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi
    • DOI 10.1038/nature02107
    • Sijen T, Plasterk RHA. 2003. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426(6964):310-314. (Pubitemid 37463152)
    • (2003) Nature , vol.426 , Issue.6964 , pp. 310-314
    • Sijen, T.1    Plasterk, R.H.A.2
  • 46
    • 33845965438 scopus 로고    scopus 로고
    • Order chiroptera
    • Wilson DE, Reeder DM, editors Baltimore (MD): The Johns Hopkins University Press
    • Simmons NB. 2005. Order Chiroptera. In: Wilson DE, Reeder DM, editors. Mammal species of the world: a taxonomic and geographic reference. Baltimore (MD): The Johns Hopkins University Press. p. 312-529.
    • (2005) Mammal Species of the World: A Taxonomic and Geographic Reference , pp. 312-529
    • Simmons, N.B.1
  • 47
    • 80155157561 scopus 로고    scopus 로고
    • Expedited batch processing and analysis of transposon insertions
    • Smith J, Ray D. 2011. Expedited batch processing and analysis of transposon insertions. BMC Res Notes. 4(1):482.
    • (2011) BMC Res Notes , vol.4 , Issue.1 , pp. 482
    • Smith, J.1    Ray, D.2
  • 48
    • 32144444851 scopus 로고    scopus 로고
    • TRAP: Automated classification, quantification and annotation of tandemly repeated sequences
    • DOI 10.1093/bioinformatics/bti809
    • Sobreira TJP, Durham AM, Gruber A. 2006. TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics 22(3):361-362. (Pubitemid 43205386)
    • (2006) Bioinformatics , vol.22 , Issue.3 , pp. 361-362
    • Sobreira, T.J.P.1    Durham, A.M.2    Gruber, A.3
  • 49
    • 0029654258 scopus 로고
    • A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis
    • Sonnhammer EL, Durbin R. 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167(1-2): GC1-GC10. (Pubitemid 126731667)
    • (1995) Gene , vol.167 , Issue.1-2
    • Durbin, R.1
  • 50
    • 33947591101 scopus 로고    scopus 로고
    • Molecular phylogeny of New World Myotis (Chiroptera, Vespertilionidae) inferred from mitochondrial and nuclear DNA genes
    • DOI 10.1016/j.ympev.2006.06.019, PII S1055790306002648
    • Stadelmann B, Lin LK, Kunz TH, Ruedi M. 2007. Molecular phylogeny of New World Myotis (Chiroptera, Vespertilionidae) inferred from mito-chondrial and nuclear DNA genes. Mol Phylogenet Evol. 43(1):32-48. (Pubitemid 46484343)
    • (2007) Molecular Phylogenetics and Evolution , vol.43 , Issue.1 , pp. 32-48
    • Stadelmann, B.1    Lin, L.-K.2    Kunz, T.H.3    Ruedi, M.4
  • 51
    • 84865806641 scopus 로고    scopus 로고
    • LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders
    • Sun C, et al. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol. 4(2):168-183.
    • (2012) Genome Biol Evol. , vol.4 , Issue.2 , pp. 168-183
    • Sun, C.1
  • 52
    • 79952006291 scopus 로고    scopus 로고
    • The limited distribution of Helitrons to vesper bats supports horizontal transfer
    • Thomas J, Sorourian M, Ray D, Baker RJ, Pritham EJ. 2011. The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 474(1-2):52-58.
    • (2011) Gene , vol.474 , Issue.1-2 , pp. 52-58
    • Thomas, J.1    Sorourian, M.2    Ray, D.3    Baker, R.J.4    Pritham, E.J.5
  • 56
    • 69149101693 scopus 로고    scopus 로고
    • Structure-based discovery and description of plant and animal Helitrons
    • Yang L, Bennetzen JL. 2009. Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci U S A. 106(31): 12832-12837.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.31 , pp. 12832-12837
    • Yang, L.1    Bennetzen, J.L.2
  • 57
    • 70349323106 scopus 로고    scopus 로고
    • Transposable elements and an epigenetic basis for punctuated equilibria
    • Zeh DW, Zeh JA, Ishida Y. 2009. Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays 31(7):715-726.
    • (2009) Bioessays , vol.31 , Issue.7 , pp. 715-726
    • Zeh, D.W.1    Zeh, J.A.2    Ishida, Y.3


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