메뉴 건너뛰기




Volumn 16, Issue 6, 2006, Pages 796-803

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling

(48)  Morin, Ryan D a   Chang, Elbert a   Petrescu, Anca a   Liao, Nancy a   Griffith, Malachi a   Kirkpatrick, Robert a   Butterfield, Yaron S a   Young, Alice C c   Stott, Jeffrey a   Barber, Sarah a   Babakaiff, Ryan a   Dickson, Mark C b   Matsuo, Corey a   Wong, David a   Yang, George S a   Smailus, Duane E a   Wetherby, Keith D c   Kwong, Peggy N c   Grimwood, Jane b   Brinkley III, Charles P c   more..


Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

EID: 33744807179     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4871006     Document Type: Article
Times cited : (66)

References (37)
  • 1
    • 14744277777 scopus 로고    scopus 로고
    • Polyploidy and genome evolution in plants
    • Adams, K.L. and Wendel, J.F. 2005. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8: 135-141.
    • (2005) Curr. Opin. Plant Biol. , vol.8 , pp. 135-141
    • Adams, K.L.1    Wendel, J.F.2
  • 5
    • 0030681260 scopus 로고    scopus 로고
    • The significance of digital gene expression profiles
    • Audic, S. and Claverie, J.M. 1997. The significance of digital gene expression profiles. Genome Res. 7: 986-995.
    • (1997) Genome Res. , vol.7 , pp. 986-995
    • Audic, S.1    Claverie, J.M.2
  • 9
    • 0025286650 scopus 로고
    • Phylogenetic relationships of the pipid frogs Xenopus and Silurana: An integration of ribosomal DNA morphology
    • De Sa, R.O. and Hillis, D.M. 1990. Phylogenetic relationships of the pipid frogs Xenopus and Silurana: An integration of ribosomal DNA morphology. Mol. Biol. Evol. 7: 365-376.
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 365-376
    • De Sa, R.O.1    Hillis, D.M.2
  • 10
    • 4344713315 scopus 로고    scopus 로고
    • A mitochondrial DNA phylogeny of African clawed frogs: Phylogeography and implications for polyploid evolution
    • Evans, B.J., Kelley, D.B., Tinsley, R.C., Melnick, D.J., and Cannatella, D.C. 2004. A mitochondrial DNA phylogeny of African clawed frogs: Phylogeography and implications for polyploid evolution. Mol. Phylogenet. Evol. 33: 197-213.
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 197-213
    • Evans, B.J.1    Kelley, D.B.2    Tinsley, R.C.3    Melnick, D.J.4    Cannatella, D.C.5
  • 11
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using Phred. II. Error probabilities
    • Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 12
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y., and Postlethwait, J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3    Amores, A.4    Yan, Y.5    Postlethwait, J.6
  • 14
    • 3042540826 scopus 로고    scopus 로고
    • Defining a large set of full-length clones from a Xenopus tropicalis EST project
    • Gilchrist, M.J., Zorn, A.M., Voigt, J., Smith, J.C., Papalopulu, N., and Amaya, E. 2004. Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev. Biol. 271: 498-516.
    • (2004) Dev. Biol. , vol.271 , pp. 498-516
    • Gilchrist, M.J.1    Zorn, A.M.2    Voigt, J.3    Smith, J.C.4    Papalopulu, N.5    Amaya, E.6
  • 15
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
    • (1998) Genome Res. , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 16
    • 0026272190 scopus 로고
    • Genetics of Xenopus laevis
    • Graf, J. and Kobel, H. 1991. Genetics of Xenopus laevis. Methods Cell Biol. 36: 663-669.
    • (1991) Methods Cell Biol. , vol.36 , pp. 663-669
    • Graf, J.1    Kobel, H.2
  • 17
    • 0036895152 scopus 로고    scopus 로고
    • Xenopus, the next generation: X. tropicalis genetics and genomics
    • Hirsch, N., Zimmerman, L., and Grainger, R. 2002. Xenopus, the next generation: X. tropicalis genetics and genomics. Dev. Dyn. 225: 422-433.
    • (2002) Dev. Dyn. , vol.225 , pp. 422-433
    • Hirsch, N.1    Zimmerman, L.2    Grainger, R.3
  • 18
    • 0027423610 scopus 로고
    • Evolution of duplicate genes in a tetraploid animal, Xenopus laevis
    • Hughes, M.K. and Hughes, A.L. 1993. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10: 1360-1369.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1360-1369
    • Hughes, M.K.1    Hughes, A.L.2
  • 19
    • 0034724185 scopus 로고    scopus 로고
    • Adaptive diversification within a large family of recently duplicated, placentally expressed genes
    • Hughes, M.K., Green, J.A., Garbayo, J.M., and Roberts, R.M. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. 97: 3319-3323.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 3319-3323
    • Hughes, M.K.1    Green, J.A.2    Garbayo, J.M.3    Roberts, R.M.4
  • 20
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King, M.C. and Wilson, A.C. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 22
    • 0001841350 scopus 로고    scopus 로고
    • Allopolyploid speciation
    • eds. R.C. Tinsley and H.R. Kobel, Clarendon Press, Oxford
    • Kobel, H.R. 1996. Allopolyploid speciation. In The biology of Xenopus (eds. R.C. Tinsley and H.R. Kobel), pp. 391-401. Clarendon Press, Oxford.
    • (1996) The Biology of Xenopus , pp. 391-401
    • Kobel, H.R.1
  • 25
    • 3042855210 scopus 로고    scopus 로고
    • UniGene: A unified view of the transcriptome
    • National Center for Biotechnology Information, Bethesda, MD
    • Pontius, J.U., Wagner, L., and Schuler, G.D. 2003. UniGene: A unified view of the transcriptome. In The NCBI Handbook, pp. 857-868. National Center for Biotechnology Information, Bethesda, MD.
    • (2003) The NCBI Handbook , pp. 857-868
    • Pontius, J.U.1    Wagner, L.2    Schuler, G.D.3
  • 27
    • 0036169031 scopus 로고    scopus 로고
    • Genesis: Cluster analysis of microarray data
    • Sturn, A., Quackenbush, J., and Trajanoski, Z. 2002. Genesis: Cluster analysis of microarray data. Bioinformatics 18: 207-208.
    • (2002) Bioinformatics , vol.18 , pp. 207-208
    • Sturn, A.1    Quackenbush, J.2    Trajanoski, Z.3
  • 29
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 30
    • 0036272537 scopus 로고    scopus 로고
    • Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome
    • Thornton, K. and Long, M. 2002. Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evol. 19: 918-925.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 918-925
    • Thornton, K.1    Long, M.2
  • 31
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    • Wernersson, R. and Pedersen, A.G. 2003. RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31: 3537-3539.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 32
    • 0000465745 scopus 로고    scopus 로고
    • Fluorescence-based DNA sequencing
    • eds. B. Birren et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Wilson, R.K. and Mardis, E.R. 1997. Fluorescence-based DNA sequencing. In Genome analysis: A laboratory manual: Analyzing DNA (eds. B. Birren et al.), Vol. 1, pp. 301-395. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1997) Genome Analysis: A Laboratory Manual: Analyzing DNA , vol.1 , pp. 301-395
    • Wilson, R.K.1    Mardis, E.R.2
  • 33
    • 0030683599 scopus 로고    scopus 로고
    • PAML, a program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML, a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 34
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • _. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568-573.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 568-573
  • 36
    • 23044478689 scopus 로고    scopus 로고
    • High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
    • Zeeberg, B.R., Qin, H., Narasimhan, S., Sunshine, M., Cao, H., Kane, D.W., Reimers, M., Stephens, R.M., Bryant, D., Burt, S.K., et al. 2005. High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 6: 168.
    • (2005) BMC Bioinformatics , vol.6 , pp. 168
    • Zeeberg, B.R.1    Qin, H.2    Narasimhan, S.3    Sunshine, M.4    Cao, H.5    Kane, D.W.6    Reimers, M.7    Stephens, R.M.8    Bryant, D.9    Burt, S.K.10
  • 37
    • 0036726239 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana
    • Zhang, L., Vision, T., and Gaut, B. 2002. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19: 1464-1473.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1464-1473
    • Zhang, L.1    Vision, T.2    Gaut, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.