메뉴 건너뛰기




Volumn 6, Issue 7, 2014, Pages 1818-1829

Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders

Author keywords

Age distribution; Cryptobranchus; Genome size evolution; Indels; Phylogeny; Transposable element

Indexed keywords

RETROPOSON;

EID: 84924558000     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu143     Document Type: Article
Times cited : (49)

References (52)
  • 1
    • 14044251790 scopus 로고    scopus 로고
    • [Internet]. Berkeley (CA): AmphibiaWeb;[cited 2014 Apr 5]. Available from
    • AmphibiaWeb: information on amphibian biology and conservation [Internet]. Berkeley (CA): AmphibiaWeb;2014) [cited 2014 Apr 5]. Available from: http: //amphibiaweb.org/.
    • (2014) Amphibia Web: Information on Amphibian Biology and Conservation
  • 2
    • 24344505990 scopus 로고    scopus 로고
    • Microdeletions and microinsertions causing human genetic disease: Common mechanisms of mutagenesis and the role of local dna sequence complexity
    • Ball EV, et al (2005) Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat. 26: 205-213.
    • (2005) Hum Mutat. , vol.26 , pp. 205-213
    • Ball, E.V.1
  • 3
    • 0029066087 scopus 로고
    • A tandemly repeated dna family originated from sine-related elements in the european plethodontid salamanders (amphibia, urodela
    • Batistoni R, Pesole G,Marracci S, Nardi I (1995) A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Amphibia, Urodela). J Mol Evol. 40: 608-615.
    • (1995) J Mol Evol. , vol.40 , pp. 608-615
    • Batistoni, R.1    Pesole, G.2    Marracci, S.3    Nardi, I.4
  • 5
    • 3042666256 scopus 로고    scopus 로고
    • Muscle: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 6
    • 70350294348 scopus 로고    scopus 로고
    • Systematic artifacts in metagenomes from complex microbial communities
    • Gomez-Alvarez V, Teal TK, Schmidt TM (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3: 1314-1317.
    • (2009) ISME J. , vol.3 , pp. 1314-1317
    • Gomez-Alvarez, V.1    Teal, T.K.2    Schmidt, T.M.3
  • 7
    • 0007811230 scopus 로고
    • Supernumerary chromosomes in amphibians
    • In: Green DM, Sessions SK, editors San Diego (CA): Academic Press, Inc
    • Green DM 1991) Supernumerary chromosomes in amphibians. In: Green DM, Sessions SK, editors. Amphibian cytogenetics and evolution. San Diego (CA): Academic Press, Inc. p. 333-355.
    • (1991) Amphibian Cytogenetics and Evolution , pp. 333-355
    • Green, D.M.1
  • 8
    • 0346158529 scopus 로고    scopus 로고
    • Insertion-deletion biases and the evolution of genome size
    • Gregory TR (2004) Insertion-deletion biases and the evolution of genome size. Gene 324: 15-34.
    • (2004) Gene , vol.324 , pp. 15-34
    • Gregory, T.R.1
  • 10
    • 0003535927 scopus 로고    scopus 로고
    • [Internet] [cited 2014 April 5]. Available from
    • Gregory TR (2014) Animal Genome Size Database. [Internet] [cited 2014 April 5]. Available from: http: //www.genomesize.com.
    • (2014) Animal Genome Size Database
    • Gregory, T.R.1
  • 11
    • 46649114729 scopus 로고    scopus 로고
    • Identification of repeat structure in large genomes using repeat probability clouds
    • Gu W, Castoe TA, Hedges DJ, Batzer MA, Pollock DD (2008) Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem. 380: 77-83.
    • (2008) Anal Biochem. , vol.380 , pp. 77-83
    • Gu, W.1    Castoe, T.A.2    Hedges, D.J.3    Batzer, M.A.4    Pollock, D.D.5
  • 12
    • 0027133373 scopus 로고
    • Miniaturization of body size: Organismal consequences and evolutionary significance
    • Hanken J, Wake DB (1993) Miniaturization of body size: organismal consequences and evolutionary significance. Annu Rev Ecol Syst. 24: 501-519.
    • (1993) Annu Rev Ecol Syst. , vol.24 , pp. 501-519
    • Hanken, J.1    Wake, D.B.2
  • 13
    • 79955468851 scopus 로고    scopus 로고
    • The arabidopsis lyrata genome sequence and the basis of rapid genome size change
    • Hu TT, et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 43: 476-481.
    • (2011) Nat Genet. , vol.43 , pp. 476-481
    • Hu, T.T.1
  • 14
    • 0030910563 scopus 로고    scopus 로고
    • An evolutionary correlate of genome size change in plethodontid salamanders
    • Jockusch EL (1997) An evolutionary correlate of genome size change in plethodontid salamanders. Proc R Soc Lond B Biol Sci. 264: 597.
    • (1997) Proc R Soc Lond B Biol Sci. , vol.264 , pp. 597
    • Jockusch, E.L.1
  • 15
    • 67650087600 scopus 로고    scopus 로고
    • Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
    • Kvikstad EM, Chiaromonte F, Makova KD (2009) Ride the wavelet: a multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Res. 19: 1153-1164.
    • (2009) Genome Res. , vol.19 , pp. 1153-1164
    • Kvikstad, E.M.1    Chiaromonte, F.2    Makova, K.D.3
  • 16
  • 17
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 19
    • 0034917751 scopus 로고    scopus 로고
    • Phylogenetic analysis of ribonuclease h domains suggests a late, chimeric origin of ltr retrotransposable elements and retroviruses
    • Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11: 1187-1197.
    • (2001) Genome Res. , vol.11 , pp. 1187-1197
    • Malik, H.S.1    Eickbush, T.H.2
  • 20
    • 34249739745 scopus 로고    scopus 로고
    • Fossils, molecules, divergence times, and the origin of lissamphibians
    • MarjanovićD, Laurin M (2007) Fossils, molecules, divergence times, and the origin of lissamphibians. Syst Biol. 56: 369-388.
    • (2007) Syst Biol. , vol.56 , pp. 369-388
    • Marjanovic, D.1    Laurin, M.2
  • 21
    • 0030443143 scopus 로고    scopus 로고
    • Gypsy/ty3-like elements in the genome of the terrestrial salamander hydromantes (amphibia, urodela
    • Marracci S, Batistoni R, Pesole G, Citti L, Nardi I (1996) Gypsy/Ty3-like elements in the genome of the terrestrial salamander Hydromantes (Amphibia, Urodela). J Mol Evol. 43: 584-593.
    • (1996) J Mol Evol. , vol.43 , pp. 584-593
    • Marracci, S.1    Batistoni, R.2    Pesole, G.3    Citti, L.4    Nardi, I.5
  • 22
    • 34548337129 scopus 로고    scopus 로고
    • Themajority of recent short dna insertions in the human genome are tandem duplications
    • Messer PW, Arndt PF (2007) Themajority of recent short DNA insertions in the human genome are tandem duplications. Mol Biol Evol. 24: 1190-1197.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1190-1197
    • Messer, P.W.1    Arndt, P.F.2
  • 23
    • 84920001686 scopus 로고    scopus 로고
    • Accommodating the load: The transposable element content of very large genomes
    • Metcalfe CJ, Casane D (2013) Accommodating the load: The transposable element content of very large genomes. Mob Genet Elements. 3: e24775.
    • (2013) Mob Genet Elements. , vol.3
    • Metcalfe, C.J.1    Casane, D.2
  • 24
    • 84867761085 scopus 로고    scopus 로고
    • Evolution of the australian lungfish (neoceratodus forsteri) genome: A major role for cr1 and l2 line elements
    • Metcalfe CJ, Filee J, Germon I, Joss J, Casane D (2012) Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements. Mol Biol Evol. 29: 3529-3539.
    • (2012) Mol Biol Evol. , vol.29 , pp. 3529-3539
    • Metcalfe, C.J.1    Filee, J.2    Germon, I.3    Joss, J.4    Casane, D.5
  • 25
    • 33744997660 scopus 로고    scopus 로고
    • Evolutionary rates, divergence dates, and the performance of mitochondrial genes in bayesian phylogenetic analysis
    • Mueller RL (2006) Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst Biol. 55: 289.
    • (2006) Syst Biol. , vol.55 , pp. 289
    • Mueller, R.L.1
  • 26
    • 44949234786 scopus 로고    scopus 로고
    • Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders
    • Mueller RL, Gregory TR, Gregory SM, Hsieh A, Boore JL (2008) Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. Zoology 111: 218-230.
    • (2008) Zoology , vol.111 , pp. 218-230
    • Mueller, R.L.1    Gregory, T.R.2    Gregory, S.M.3    Hsieh, A.4    Boore, J.L.5
  • 27
    • 84863642420 scopus 로고    scopus 로고
    • Recombination drives vertebrate genome contraction
    • Nam K, Ellegren H (2012) Recombination drives vertebrate genome contraction. PLoS Genet. 8: e1002680.
    • (2012) PLoS Genet. , vol.8
    • Nam, K.1    Ellegren, H.2
  • 28
    • 77950645212 scopus 로고    scopus 로고
    • Artificial and natural duplicates in pyrosequencing reads of metagenomic data
    • Niu B, Fu L, Sun S, Li W (2010) Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11: 187.
    • (2010) BMC Bioinformatics , vol.11 , pp. 187
    • Niu, B.1    Fu, L.2    Sun, S.3    Li, W.4
  • 29
    • 84875056107 scopus 로고    scopus 로고
    • Deep metazoan phylogeny: When different genes tell different stories
    • Nosenko T, et al (2013) Deep metazoan phylogeny: when different genes tell different stories. Mol Phylogenet Evol. 67: 223-233.
    • (2013) Mol Phylogenet Evol. , vol.67 , pp. 223-233
    • Nosenko, T.1
  • 30
    • 79952274187 scopus 로고    scopus 로고
    • The evolution and diversity of dna transposons in the genome of the lizard anolis carolinensis
    • Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S (2010) The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biol Evol. 3: 1-14.
    • (2010) Genome Biol Evol. , vol.3 , pp. 1-14
    • Novick, P.A.1    Smith, J.D.2    Floumanhaft, M.3    Ray, D.A.4    Boissinot, S.5
  • 31
    • 0029856377 scopus 로고    scopus 로고
    • High intrinsic rate of dna loss in drosophila
    • Petrov DA, Lozovskaya ER, Hartl DL (1996) High intrinsic rate of DNA loss in Drosophila. Nature 384: 346-349.
    • (1996) Nature , vol.384 , pp. 346-349
    • Petrov, D.A.1    Lozovskaya, E.R.2    Hartl, D.L.3
  • 32
    • 8744242187 scopus 로고    scopus 로고
    • Whole-genome analysis of alu repeat elements reveals complex evolutionary history
    • Price AL, Eskin E, Pevzner PA (2004) Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 14: 2245-2252.
    • (2004) Genome Res. , vol.14 , pp. 2245-2252
    • Price, A.L.1    Eskin, E.2    Pevzner, P.A.3
  • 33
    • 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(S1): i351-i358.
    • (2005) Bioinformatics , vol.21 , Issue.S1
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 34
    • 80052717965 scopus 로고    scopus 로고
    • A large-scale phylogeny of amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
    • Pyron AR, Wiens JJ (2011) A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol. 61: 543-583.
    • (2011) Mol Phylogenet Evol. , vol.61 , pp. 543-583
    • Pyron, A.R.1    Wiens, J.J.2
  • 35
    • 79959381301 scopus 로고    scopus 로고
    • Divergence time estimation using fossils as terminal taxa and the origins of lissamphibia
    • Pyron RA (2011) Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol. 60: 466-481.
    • (2011) Syst Biol. , vol.60 , pp. 466-481
    • Pyron, R.A.1
  • 36
    • 0028276789 scopus 로고
    • Cell size predicts morphological complexity in the brains of frogs and salamanders
    • Roth G, Blanke J, Wake DB (1994) Cell size predicts morphological complexity in the brains of frogs and salamanders. Proc Natl Acad Sci U S A. 91: 4796-4800.
    • (1994) Proc Natl Acad Sci U S A. , vol.91 , pp. 4796-4800
    • Roth, G.1    Blanke, J.2    Wake, D.B.3
  • 37
    • 0031184378 scopus 로고    scopus 로고
    • Genome size, secondary simplification, and the evolution of the brain in salamanders
    • Roth G, Nishikawa KC, Wake DB (1997) Genome size, secondary simplification, and the evolution of the brain in salamanders. Brain Behav Evol. 50: 50-59.
    • (1997) Brain Behav Evol. , vol.50 , pp. 50-59
    • Roth, G.1    Nishikawa, K.C.2    Wake, D.B.3
  • 38
    • 0343326695 scopus 로고
    • Evolutionary cytogenetics of bolitoglossine salamanders (family plethodontidae
    • In: Green DM, Sessions SK, editors San Diego (CA): Academic Press, Inc
    • Sessions SK, Kezer J (1991) Evolutionary cytogenetics of bolitoglossine salamanders (family Plethodontidae). In: Green DM, Sessions SK, editors. Amphibian cytogenetics and evolution. San Diego (CA): Academic Press, Inc. p. 89-130.
    • (1991) Amphibian Cytogenetics and Evolution , pp. 89-130
    • Sessions, S.K.1    Kezer, J.2
  • 39
    • 0000335620 scopus 로고
    • Developmental correlates of genome size in plethodontid salamanders and their implications for genome evolution
    • Sessions SK, Larson A (1987) Developmental correlates of genome size in plethodontid salamanders and their implications for genome evolution. Evolution 41: 1239-1251.
    • (1987) Evolution , vol.41 , pp. 1239-1251
    • Sessions, S.K.1    Larson, A.2
  • 40
    • 29544440896 scopus 로고    scopus 로고
    • Sal-site: Integrating new and existing ambystomatid salamander research and informational resources
    • Smith J, et al (2005) Sal-Site: integrating new and existing ambystomatid salamander research and informational resources. BMC Genomics 6: 181.
    • (2005) BMC Genomics , vol.6 , pp. 181
    • Smith, J.1
  • 41
    • 60849108658 scopus 로고    scopus 로고
    • Genic regions of a large salamander genome contain long introns and novel genes
    • Smith J, et al (2009) Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10: 19.
    • (2009) BMC Genomics , vol.10 , pp. 19
    • Smith, J.1
  • 42
    • 84876525108 scopus 로고    scopus 로고
    • Slow dna loss in the gigantic genomes of salamanders
    • Sun C, Arriaza JRL, Mueller RL (2012) Slow DNA loss in the gigantic genomes of salamanders. Genome Biol Evol. 4: 1340-1348.
    • (2012) Genome Biol Evol. , vol.4 , pp. 1340-1348
    • Sun, C.1    Arriaza, J.R.L.2    Mueller, R.L.3
  • 43
    • 84865806641 scopus 로고    scopus 로고
    • Ltr retrotransposons contribute to genomic gigantism in plethodontid salamanders
    • Sun C, Shepard DB, et al (2012) LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol. 4: 168-183.
    • (2012) Genome Biol Evol. , vol.4 , pp. 168-183
    • Sun, C.1    Shepard, D.B.2
  • 44
    • 79957613599 scopus 로고    scopus 로고
    • Mega5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28: 2731-2739.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 45
    • 43549095247 scopus 로고    scopus 로고
    • Sequence context affects the rate of short insertions and deletions in flies and primates
    • Tanay A, Siggia ED (2008) Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 9: R37.
    • (2008) Genome Biol. , vol.9
    • Tanay, A.1    Siggia, E.D.2
  • 46
    • 0000784294 scopus 로고
    • Chicken erythrocytes as an internal reference for analysis of dna content by flow cytometry in grass carp
    • Tiersch TR, Chandler RW (1989) Chicken erythrocytes as an internal reference for analysis of DNA content by flow cytometry in grass carp. Trans Am Fish Soc. 118: 713-717.
    • (1989) Trans Am Fish Soc. , vol.118 , pp. 713-717
    • Tiersch, T.R.1    Chandler, R.W.2
  • 47
    • 80051566443 scopus 로고    scopus 로고
    • Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
    • Voss SR, et al (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res. 21: 1306-1312.
    • (2011) Genome Res. , vol.21 , pp. 1306-1312
    • Voss, S.R.1
  • 48
    • 84890859934 scopus 로고    scopus 로고
    • Salamander hox clusters contain repetitive dna and expanded non-coding regions: A typical hox structure for non-mammalian tetrapod vertebrates?
    • Voss SR, et al (2013) Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates? Hum Genomics. 7: 9.
    • (2013) Hum Genomics. , vol.7 , pp. 9
    • Voss, S.R.1
  • 49
    • 77951714105 scopus 로고    scopus 로고
    • What salamanders have taught us about evolution
    • Wake DB (2009) What salamanders have taught us about evolution. Annu Rev Ecol Evol Syst. 40: 333-352.
    • (2009) Annu Rev Ecol Evol Syst. , vol.40 , pp. 333-352
    • Wake, D.B.1
  • 50
    • 34547681631 scopus 로고    scopus 로고
    • Global patterns of diversification and species richness in amphibians
    • Wiens JJ (2007) Global patterns of diversification and species richness in amphibians. Am Nat. 170: S86-S106.
    • (2007) Am Nat. , vol.170
    • Wiens, J.J.1
  • 51
    • 0000533013 scopus 로고
    • Anatomy, neurophysiology and functional aspects of the nucleus isthmi in salamanders of the family plethodontidae
    • Wiggers W, Roth G (1991) Anatomy, neurophysiology and functional aspects of the nucleus isthmi in salamanders of the family Plethodontidae. J Comp Physiol A (169: 165-176.
    • (1991) J Comp Physiol A , vol.169 , pp. 165-176
    • Wiggers, W.1    Roth, G.2
  • 52
    • 84866619376 scopus 로고    scopus 로고
    • Retrotransposon long interspersed nucleotide element-1 (line-1) is activated during salamander limb regeneration
    • Zhu W, et al (2012) Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Dev Growth Differ. 54: 673-685.
    • (2012) Dev Growth Differ. , vol.54 , pp. 673-685
    • Zhu, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.