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Volumn 538, Issue 7625, 2016, Pages 336-343

Genome evolution in the allotetraploid frog Xenopus laevis

(74)  Session, Adam M a,b   Uno, Yoshinobu c   Kwon, Taejoon d,e   Chapman, Jarrod A b   Toyoda, Atsushi f   Takahashi, Shuji g   Fukui, Akimasa h   Hikosaka, Akira i   Suzuki, Atsushi g   Kondo, Mariko j   Van Heeringen, Simon J k   Quigley, Ian l   Heinz, Sven l   Ogino, Hajime m   Ochi, Haruki n   Hellsten, Uffe b   Lyons, Jessica B a   Simakov, Oleg o   Putnam, Nicholas p   Stites, Jonathan p   more..


Author keywords

[No Author keywords available]

Indexed keywords

DNA; MITOCHONDRIAL PROTEIN; PROTEIN; TRANSPOSON;

EID: 84992376574     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature19840     Document Type: Article
Times cited : (717)

References (57)
  • 1
    • 70349325524 scopus 로고    scopus 로고
    • The evolutionary significance of ancient genome duplications
    • Van de Peer, Y., Maere, S., Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725-732 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 725-732
    • Van De Peer, Y.1    Maere, S.2    Meyer, A.3
  • 3
    • 0001732966 scopus 로고
    • Why polyploidy is rarer in animals than in plants
    • Muller, H. J. Why polyploidy is rarer in animals than in plants. Am. Nat. 59, 346-353 (1925).
    • (1925) Am. Nat. , vol.59 , pp. 346-353
    • Muller, H.J.1
  • 4
    • 0000986896 scopus 로고
    • 'Why polyploidy is rarer in animals than in plants' revisited
    • Orr, H. A. 'Why polyploidy is rarer in animals than in plants' revisited. Am. Nat. 136, 759-770 (1990).
    • (1990) Am. Nat. , vol.136 , pp. 759-770
    • Orr, H.A.1
  • 5
    • 84899099281 scopus 로고    scopus 로고
    • The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates
    • Berthelot, C. et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat. Commun. 5, 3657 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 3657
    • Berthelot, C.1
  • 6
    • 24344440632 scopus 로고    scopus 로고
    • The zebrafish gene map defines ancestral vertebrate chromosomes
    • Woods, I. G. et al. The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res. 15, 1307-1314 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1307-1314
    • Woods, I.G.1
  • 7
    • 84922482278 scopus 로고    scopus 로고
    • Whole-genome duplication in teleost fishes and its evolutionary consequences
    • Glasauer, S. M. K., Neuhauss, S. C. F. Whole-genome duplication in teleost fishes and its evolutionary consequences. Mol. Genet. Genomics 289, 1045-1060 (2014).
    • (2014) Mol. Genet. Genomics , vol.289 , pp. 1045-1060
    • Glasauer, S.M.K.1    Neuhauss, S.C.F.2
  • 8
    • 35548954250 scopus 로고    scopus 로고
    • The evolutionary consequences of polyploidy
    • Otto, S. P. The evolutionary consequences of polyploidy. Cell 131, 452-462 (2007).
    • (2007) Cell , vol.131 , pp. 452-462
    • Otto, S.P.1
  • 10
    • 46149136123 scopus 로고
    • Genetics of polyploid Xenopus
    • Kobel, H. R., Du Pasquier, L. Genetics of polyploid Xenopus. Trends Genet. 2, 310-315 (1986).
    • (1986) Trends Genet. , vol.2 , pp. 310-315
    • Kobel, H.R.1    Du Pasquier, L.2
  • 11
    • 81055157765 scopus 로고    scopus 로고
    • Xenopus research: Metamorphosed by genetics and genomics
    • Harland, R. M., Grainger, R. M. Xenopus research: metamorphosed by genetics and genomics. Trends Genet. 27, 507-515 (2011).
    • (2011) Trends Genet. , vol.27 , pp. 507-515
    • Harland, R.M.1    Grainger, R.M.2
  • 12
    • 0001832110 scopus 로고
    • A list of chromosome numbers of anuran amphibians
    • Kuramoto, M. A list of chromosome numbers of anuran amphibians. Bull. Fukuoka Univ. Educ. 39, 83-127 (1990).
    • (1990) Bull. Fukuoka Univ. Educ. , vol.39 , pp. 83-127
    • Kuramoto, M.1
  • 14
    • 84886101769 scopus 로고    scopus 로고
    • Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication
    • Uno, Y., Nishida, C., Takagi, C., Ueno, N., Matsuda, Y. Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication. Heredity 111, 430-436 (2013).
    • (2013) Heredity , vol.111 , pp. 430-436
    • Uno, Y.1    Nishida, C.2    Takagi, C.3    Ueno, N.4    Matsuda, Y.5
  • 15
    • 84871723836 scopus 로고    scopus 로고
    • Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping
    • Uno, Y. et al. Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLoS One 7, e53027 (2012).
    • (2012) PLoS One , vol.7 , pp. e53027
    • Uno, Y.1
  • 16
    • 84941941730 scopus 로고    scopus 로고
    • A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis
    • Matsuda, Y. et al. A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis. Cytogenet. Genome Res. 145, 187-191 (2015).
    • (2015) Cytogenet. Genome Res. , vol.145 , pp. 187-191
    • Matsuda, Y.1
  • 17
    • 40649100327 scopus 로고    scopus 로고
    • A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis
    • Yoshimoto, S. et al. A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis. Proc. Natl Acad. Sci. USA 105, 2469-2474 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 2469-2474
    • Yoshimoto, S.1
  • 18
    • 0035940510 scopus 로고    scopus 로고
    • P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases
    • Zhang, X. et al. P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl Acad. Sci. USA 98, 12572-12577 (2001).
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 12572-12577
    • Zhang, X.1
  • 19
    • 0035940397 scopus 로고    scopus 로고
    • PIFs meet Tourists and Harbingers: A superfamily reunion
    • Jurka, J., Kapitonov, V. V. PIFs meet Tourists and Harbingers: a superfamily reunion. Proc. Natl Acad. Sci. USA 98, 12315-12316 (2001).
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 12315-12316
    • Jurka, J.1    Kapitonov, V.V.2
  • 20
    • 58049200248 scopus 로고    scopus 로고
    • MMTS a new subfamily of Tc1-like transposons
    • Ahn, S. J., Kim, M.-S., Jang, J. H., Lim, S. U., Lee, H. H. MMTS, a new subfamily of Tc1-like transposons. Mol. Cells 26, 387-395 (2008).
    • (2008) Mol. Cells , vol.26 , pp. 387-395
    • Ahn, S.J.1    Kim, M.-S.2    Jang, J.H.3    Lim, S.U.4    Lee, H.H.5
  • 21
    • 33744807179 scopus 로고    scopus 로고
    • Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
    • Morin, R. D. et al. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 16, 796-803 (2006).
    • (2006) Genome Res. , vol.16 , pp. 796-803
    • Morin, R.D.1
  • 22
    • 34548171771 scopus 로고    scopus 로고
    • Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis
    • Hellsten, U. et al. Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. BMC Biol. 5, 31 (2007).
    • (2007) BMC Biol. , vol.5 , pp. 31
    • Hellsten, U.1
  • 24
    • 84941944238 scopus 로고    scopus 로고
    • Xenopus in space and time: Fossils, node calibrations, tip-dating, and paleobiogeography
    • Cannatella, D. Xenopus in space and time: fossils, node calibrations, tip-dating, and paleobiogeography. Cytogenet. Genome Res. 145, 283-301 (2015).
    • (2015) Cytogenet. Genome Res. , vol.145 , pp. 283-301
    • Cannatella, D.1
  • 25
    • 80051566443 scopus 로고    scopus 로고
    • Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
    • Voss, S. R. et al. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res. 21, 1306-1312 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1306-1312
    • Voss, S.R.1
  • 27
    • 1542338594 scopus 로고    scopus 로고
    • Genomic duplication, fractionation and the origin of regulatory novelty
    • Langham, R. J. et al. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166, 935-945 (2004).
    • (2004) Genetics , vol.166 , pp. 935-945
    • Langham, R.J.1
  • 28
    • 0002281363 scopus 로고
    • The part played by recurrent mutation in evolution
    • Haldane, J. B. S. The part played by recurrent mutation in evolution. Am. Nat. 67, 5-19 (1933).
    • (1933) Am. Nat. , vol.67 , pp. 5-19
    • Haldane, J.B.S.1
  • 29
    • 84866294456 scopus 로고    scopus 로고
    • Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines
    • Birchler, J. A., Veitia, R. A. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc. Natl Acad. Sci. USA 109, 14746-14753 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 14746-14753
    • Birchler, J.A.1    Veitia, R.A.2
  • 30
    • 79952744855 scopus 로고    scopus 로고
    • Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
    • Schnable, J. C., Springer, N. M., Freeling, M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl Acad. Sci. USA 108, 4069-4074 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 4069-4074
    • Schnable, J.C.1    Springer, N.M.2    Freeling, M.3
  • 31
    • 84859919827 scopus 로고    scopus 로고
    • A model for biased fractionation after whole genome duplication
    • Sankoff, D., Zheng, C., Wang, B. A model for biased fractionation after whole genome duplication. BMC Genomics 13 (Suppl. 1), S8 (2012).
    • (2012) BMC Genomics , vol.13 , pp. S8
    • Sankoff, D.1    Zheng, C.2    Wang, B.3
  • 32
    • 84893062974 scopus 로고    scopus 로고
    • Two evolutionarily distinct classes of paleopolyploidy
    • Garsmeur, O. et al. Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol. 31, 448-454 (2014).
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 448-454
    • Garsmeur, O.1
  • 33
    • 46149123448 scopus 로고    scopus 로고
    • Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis
    • Sémon, M., Wolfe, K. H. Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. Proc. Natl Acad. Sci. USA 105, 8333-8338 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 8333-8338
    • Sémon, M.1    Wolfe, K.H.2
  • 34
    • 83155191058 scopus 로고    scopus 로고
    • The odds of duplicate gene persistence after polyploidization
    • Chain, F. J. J., Dushoff, J., Evans, B. J. The odds of duplicate gene persistence after polyploidization. BMC Genomics 12, 599 (2011).
    • (2011) BMC Genomics , vol.12 , pp. 599
    • Chain, F.J.J.1    Dushoff, J.2    Evans, B.J.3
  • 35
    • 79952163548 scopus 로고    scopus 로고
    • Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
    • Lee, A. P., Kerk, S. Y., Tan, Y. Y., Brenner, S., Venkatesh, B. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol. Biol. Evol. 28, 1205-1215 (2011).
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 1205-1215
    • Lee, A.P.1    Kerk, S.Y.2    Tan, Y.Y.3    Brenner, S.4    Venkatesh, B.5
  • 36
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545 (1999).
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1
  • 37
    • 70349668982 scopus 로고    scopus 로고
    • Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals
    • Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., Springer, M. S. Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet. 5, e1000634 (2009).
    • (2009) PLoS Genet. , vol.5 , pp. e1000634
    • Meredith, R.W.1    Gatesy, J.2    Murphy, W.J.3    Ryder, O.A.4    Springer, M.S.5
  • 38
    • 2942744316 scopus 로고    scopus 로고
    • A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications
    • Kondrashov, F. A., Koonin, E. V. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20, 287-290 (2004).
    • (2004) Trends Genet. , vol.20 , pp. 287-290
    • Kondrashov, F.A.1    Koonin, E.V.2
  • 39
    • 33750858684 scopus 로고    scopus 로고
    • Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
    • Aury, J.-M. et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444, 171-178 (2006).
    • (2006) Nature , vol.444 , pp. 171-178
    • Aury, J.-M.1
  • 40
    • 77953212314 scopus 로고    scopus 로고
    • The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
    • Paramecium Post-Genomics Consortium
    • Gout, J.-F., Kahn, D., Duret, L., Paramecium Post-Genomics Consortium. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet. 6, e1000944 (2010).
    • (2010) PLoS Genet. , vol.6 , pp. e1000944
    • Gout, J.-F.1    Kahn, D.2    Duret, L.3
  • 41
    • 79954452308 scopus 로고    scopus 로고
    • Mapping gene expression in two Xenopus species: Evolutionary constraints and developmental flexibility
    • Yanai, I., Peshkin, L., Jorgensen, P., Kirschner, M. W. Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Dev. Cell 20, 483-496 (2011).
    • (2011) Dev. Cell , vol.20 , pp. 483-496
    • Yanai, I.1    Peshkin, L.2    Jorgensen, P.3    Kirschner, M.W.4
  • 42
    • 84908093872 scopus 로고    scopus 로고
    • New insights into the maternal to zygotic transition
    • Langley, A. R., Smith, J. C., Stemple, D. L., Harvey, S. A. New insights into the maternal to zygotic transition. Development 141, 3834-3841 (2014).
    • (2014) Development , vol.141 , pp. 3834-3841
    • Langley, A.R.1    Smith, J.C.2    Stemple, D.L.3    Harvey, S.A.4
  • 43
    • 84940653986 scopus 로고    scopus 로고
    • Beyond the whole-genome duplication: Phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage
    • Marcet-Houben, M., Gabaldón, T. Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage. PLoS Biol. 13, e1002220 (2015).
    • (2015) PLoS Biol. , vol.13 , pp. e1002220
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 44
    • 0021715393 scopus 로고
    • The significance of responses of the genome to challenge
    • McClintock, B. The significance of responses of the genome to challenge. Science 226, 792-801 (1984).
    • (1984) Science , vol.226 , pp. 792-801
    • McClintock, B.1
  • 45
    • 80051839847 scopus 로고    scopus 로고
    • Meraculous: De novo genome assembly with short paired-end reads
    • Chapman, J. A. et al. Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6, e23501 (2011).
    • (2011) PLoS One , vol.6 , pp. e23501
    • Chapman, J.A.1
  • 46
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Chen, L. et al. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol. 30, 90-98 (2011).
    • (2011) Nat. Biotechnol. , vol.30 , pp. 90-98
    • Chen, L.1
  • 47
    • 84960380290 scopus 로고    scopus 로고
    • Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
    • Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342-350 (2016).
    • (2016) Genome Res. , vol.26 , pp. 342-350
    • Putnam, N.H.1
  • 48
    • 84961014614 scopus 로고
    • Genic control and hormonal reversal of sex differentiation in Xenopus
    • Chang, C. Y., Witschi, E. Genic control and hormonal reversal of sex differentiation in Xenopus. Proc. Soc. Exp. Biol. Med. 93, 140-144 (1956).
    • (1956) Proc. Soc. Exp. Biol. Med. , vol.93 , pp. 140-144
    • Chang, C.Y.1    Witschi, E.2
  • 49
    • 84857996686 scopus 로고    scopus 로고
    • From expression cloning to gene modeling: The development of Xenopus gene sequence resources
    • Gilchrist, M. J. From expression cloning to gene modeling: the development of Xenopus gene sequence resources. Genesis 50, 143-154 (2012).
    • (2012) Genesis , vol.50 , pp. 143-154
    • Gilchrist, M.J.1
  • 51
    • 84946074739 scopus 로고    scopus 로고
    • The InterPro protein families database: The classification resource after 15 years
    • Mitchell, A. et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213-D221 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D213-D221
    • Mitchell, A.1
  • 52
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: Back to metabolism in KEGG
    • Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D199-D205
    • Kanehisa, M.1
  • 53
    • 84979518589 scopus 로고    scopus 로고
    • MitoCarta2.0: An updated inventory of mammalian mitochondrial proteins
    • Calvo, S. E., Clauser, K. R., Mootha, V. K. MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 44, D1251-D1257 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. D1251-D1257
    • Calvo, S.E.1    Clauser, K.R.2    Mootha, V.K.3
  • 54
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder, P., Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 55
    • 16344384870 scopus 로고    scopus 로고
    • Identification of Xenopus CENP-A and an associated centromeric DNA repeat
    • Edwards, N. S., Murray, A. W. Identification of Xenopus CENP-A and an associated centromeric DNA repeat. Mol. Biol. Cell 16, 1800-1810 (2005).
    • (2005) Mol. Biol. Cell , vol.16 , pp. 1800-1810
    • Edwards, N.S.1    Murray, A.W.2
  • 56
    • 84891910353 scopus 로고    scopus 로고
    • Ohnologs are overrepresented in pathogenic copy number mutations
    • McLysaght, A. et al. Ohnologs are overrepresented in pathogenic copy number mutations. Proc. Natl. Acad. Sci. USA 111, 361-366 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 361-366
    • McLysaght, A.1
  • 57
    • 84871994580 scopus 로고    scopus 로고
    • RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
    • Tan, M. H. et al. RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res. 23, 201-216 (2013).
    • (2013) Genome Res. , vol.23 , pp. 201-216
    • Tan, M.H.1


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