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Volumn 7, Issue 7, 2012, Pages

Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex - the Squalius alburnoides

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA; SMALL RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

EID: 84864001526     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041158     Document Type: Article
Times cited : (19)

References (35)
  • 1
    • 0035544488 scopus 로고    scopus 로고
    • Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review
    • Alves MJ, Coelho MM, Collares-Pereira MJ, (2001) Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review. Genetica 111: 375-385.
    • (2001) Genetica , vol.111 , pp. 375-385
    • Alves, M.J.1    Coelho, M.M.2    Collares-Pereira, M.J.3
  • 2
    • 0001322806 scopus 로고    scopus 로고
    • Diversity in the reproductive modes of females of the Rutilus alburnoides complex (Teleostei, Cyprinidae): a way to avoid the genetic constraints of uniparentalism
    • Alves MJ, Coelho MM, Collares-Pereira MJ, (1998) Diversity in the reproductive modes of females of the Rutilus alburnoides complex (Teleostei, Cyprinidae): a way to avoid the genetic constraints of uniparentalism. Molecular Biology and Evolution 15: 1233-1242.
    • (1998) Molecular Biology and Evolution , vol.15 , pp. 1233-1242
    • Alves, M.J.1    Coelho, M.M.2    Collares-Pereira, M.J.3
  • 3
    • 33749985440 scopus 로고    scopus 로고
    • Modes of reproduction of the hybridogenetic fish Squalius alburnoides in the Tejo and Guadiana rivers: an approach with microsatellites
    • Crespo-López ME, Duarte T, Dowling T, Coelho MM, (2006) Modes of reproduction of the hybridogenetic fish Squalius alburnoides in the Tejo and Guadiana rivers: an approach with microsatellites. Zoology 109: 277-286.
    • (2006) Zoology , vol.109 , pp. 277-286
    • Crespo-López, M.E.1    Duarte, T.2    Dowling, T.3    Coelho, M.M.4
  • 4
    • 50849097543 scopus 로고    scopus 로고
    • Dosage compensation by gene copy silencing in a triploid hybrid fish
    • Pala I, Coelho MM, Schartl M, (2008) Dosage compensation by gene copy silencing in a triploid hybrid fish. Curr Biol. 18: 1344-1348.
    • (2008) Curr Biol , vol.18 , pp. 1344-1348
    • Pala, I.1    Coelho, M.M.2    Schartl, M.3
  • 5
    • 78149245728 scopus 로고    scopus 로고
    • Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex
    • Pala I, Schartl M, Brito M, Malta-Vacas J, Coelho MM, (2010) Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex. Proc. R. Soc. B 277: 3519-3525.
    • (2010) Proc. R. Soc. B , vol.277 , pp. 3519-3525
    • Pala, I.1    Schartl, M.2    Brito, M.3    Malta-Vacas, J.4    Coelho, M.M.5
  • 6
    • 82655189433 scopus 로고    scopus 로고
    • Ploidy mosaicism and gene expression in the allopolyploid Squalius alburnoides
    • Matos I, Sucena E, Machado M, Inácio A, Gardner R, et al. (2011) Ploidy mosaicism and gene expression in the allopolyploid Squalius alburnoides. BMC Genetics 12: 101.
    • (2011) BMC Genetics , vol.12 , pp. 101
    • Matos, I.1    Sucena, E.2    Machado, M.3    Inácio, A.4    Gardner, R.5
  • 7
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • Bartel PD, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, P.D.1
  • 8
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of miRNAs and siRNAs
    • Carthew RW, Sontheimer EJ, (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 9
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNA
    • Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNA. Cell 136: 669-687.
    • (2009) Cell , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 10
    • 77955902024 scopus 로고    scopus 로고
    • The widespread regulation of microRNA biogenesis, function and decay
    • Krol J, LoedigeI, Filipowicz W, (2010) The widespread regulation of microRNA biogenesis, function and decay. Nature Rev Genet 11: 597-610.
    • (2010) Nature Rev Genet , vol.11 , pp. 597-610
    • Krol, J.1    Loedige, I.2    Filipowicz, W.3
  • 11
    • 21244449997 scopus 로고    scopus 로고
    • Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation
    • Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, et al. (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol 14: 2493-2510.
    • (2005) Mol Ecol , vol.14 , pp. 2493-2510
    • Hegarty, M.J.1    Jones, J.M.2    Wilson, I.D.3    Barker, G.L.4    Coghill, J.A.5
  • 12
    • 33747161960 scopus 로고    scopus 로고
    • Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication
    • Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, et al. (2006) Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr Biol 16: 1652-1659.
    • (2006) Curr Biol , vol.16 , pp. 1652-1659
    • Hegarty, M.J.1    Barker, G.L.2    Wilson, I.D.3    Abbott, R.J.4    Edwards, K.J.5
  • 13
    • 33644762929 scopus 로고    scopus 로고
    • Genome wide nonadditive gene regulation in Arabidopsis allotetraploids
    • Wang J, Tian L, Lee HS, Wei NE, Jiang H, et al. (2006) Genome wide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507-517.
    • (2006) Genetics , vol.172 , pp. 507-517
    • Wang, J.1    Tian, L.2    Lee, H.S.3    Wei, N.E.4    Jiang, H.5
  • 14
    • 70449588694 scopus 로고    scopus 로고
    • Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis inter-specific hybrids and allopolyploids
    • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, et al. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis inter-specific hybrids and allopolyploids. Proc Natl Acad Sci USA 106: 17835-17840.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 17835-17840
    • Ha, M.1    Lu, J.2    Tian, L.3    Ramachandran, V.4    Kasschau, K.D.5
  • 15
    • 78751477191 scopus 로고    scopus 로고
    • Gene silencing by microRNAs: contributions of translational repression and mRNA decay
    • Huntzinger E, Izaurralde E, (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12: 99-110.
    • (2011) Nat Rev Genet , vol.12 , pp. 99-110
    • Huntzinger, E.1    Izaurralde, E.2
  • 17
    • 0035966319 scopus 로고    scopus 로고
    • microRNAs: Tiny Regulators with Great Potential
    • Ambros V, (2001) microRNAs: Tiny Regulators with Great Potential. Cell 107: 823-826.
    • (2001) Cell , vol.107 , pp. 823-826
    • Ambros, V.1
  • 18
    • 68149156103 scopus 로고    scopus 로고
    • Sex Determination in the Squalius alburnoides Complex: An Initial Characterization of Sex Cascade Elements in the Context of a Hybrid Polyploid Genome
    • doi:10.1371
    • Pala I, Schartl M, Thorsteinsdo S, Coelho MM, (2009) Sex Determination in the Squalius alburnoides Complex: An Initial Characterization of Sex Cascade Elements in the Context of a Hybrid Polyploid Genome. PLoS ONE 4: e6401 doi:10.1371.
    • (2009) PLoS ONE , vol.4
    • Pala, I.1    Schartl, M.2    Thorsteinsdo, S.3    Coelho, M.M.4
  • 19
    • 33947641602 scopus 로고    scopus 로고
    • Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world's smallest vertebrate
    • doi:10.1186/1471-2148-7-38
    • Rüber L, Kottelat M, Tan HH, KL Ng P, Britz R, (2007) Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world's smallest vertebrate. BMC Evolutionary Biology 7: 38 doi:10.1186/1471-2148-7-38.
    • (2007) BMC Evolutionary Biology , vol.7 , pp. 38
    • Rüber, L.1    Kottelat, M.2    Tan, H.H.3    Ng, P.4    Britz, R.5
  • 20
    • 0037697476 scopus 로고    scopus 로고
    • Growth and reproductive traits of diploid and triploids forms of the Squalius alburnoides cyprinid complex in a tributary of the Guadiana River, Portugal
    • Ribeiro F, Cowx IG, Tiago P, Filipe AF, Moreira da Costa L, et al. (2003) Growth and reproductive traits of diploid and triploids forms of the Squalius alburnoides cyprinid complex in a tributary of the Guadiana River, Portugal. Arch. Hydrobiol. 156: 451-84.
    • (2003) Arch. Hydrobiol , vol.156 , pp. 451-484
    • Ribeiro, F.1    Cowx, I.G.2    Tiago, P.3    Filipe, A.F.4    Moreira da Costa, L.5
  • 21
    • 33644681986 scopus 로고    scopus 로고
    • Advantages and disadvantages of polyploidy
    • Comai L, (2005) Advantages and disadvantages of polyploidy. Nature Reviews Genetics 6: 836-846.
    • (2005) Nature Reviews Genetics , vol.6 , pp. 836-846
    • Comai, L.1
  • 22
    • 0030003670 scopus 로고    scopus 로고
    • Dosage effects on gene expression in a maize ploidy series
    • Guo M, Davis D, Birchler JA, (1996) Dosage effects on gene expression in a maize ploidy series. 142: 1349-1355.
    • (1996) , vol.142 , pp. 1349-1355
    • Guo, M.1    Davis, D.2    Birchler, J.A.3
  • 23
    • 55049138084 scopus 로고    scopus 로고
    • Interspecies regulation of microRNAs and their targets
    • Ha MS, Pang M, Agarwal V, Chen ZJ, (2008) Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta 1779: 735-742.
    • (2008) Biochim Biophys Acta , vol.1779 , pp. 735-742
    • Ha, M.S.1    Pang, M.2    Agarwal, V.3    Chen, Z.J.4
  • 25
    • 50649089207 scopus 로고    scopus 로고
    • RNAseq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNAseq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18: 1509-1517.
    • (2008) Genome Research , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 26
    • 57149085481 scopus 로고    scopus 로고
    • Deep sequencing based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    • 't Hoen CA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, et al. (2008) Deep sequencing based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Research 36: e141.
    • (2008) Nucleic Acids Research , vol.36
    • 't Hoen, C.A.1    Ariyurek, Y.2    Thygesen, H.H.3    Vreugdenhil, E.4    Vossen, R.H.A.M.5
  • 27
    • 78649458548 scopus 로고    scopus 로고
    • RNA sequencing shows no dosage compensation of the active X-chromosome
    • Xiong Y, Chen X, Chen Z, Wang X, Shi S, et al. (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nature Genetics 42: 1043-1047.
    • (2010) Nature Genetics , vol.42 , pp. 1043-1047
    • Xiong, Y.1    Chen, X.2    Chen, Z.3    Wang, X.4    Shi, S.5
  • 28
    • 34347241740 scopus 로고    scopus 로고
    • Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
    • Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, et al. (2007) Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 8: 153.
    • (2007) BMC Genomics , vol.8 , pp. 153
    • Liu, F.1    Jenssen, T.K.2    Trimarchi, J.3    Punzo, C.4    Cepko, C.L.5
  • 29
    • 70449588694 scopus 로고    scopus 로고
    • Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis inter-specific hybrids and allopolyploids
    • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, et al. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis inter-specific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 106: 17835-17840.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 17835-17840
    • Ha, M.1    Lu, J.2    Tian, L.3    Ramachandran, V.4    Kasschau, K.D.5
  • 30
    • 79958231735 scopus 로고    scopus 로고
    • Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs
    • Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, et al. (2011) Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs. Genetics 188: 263-272.
    • (2011) Genetics , vol.188 , pp. 263-272
    • Kenan-Eichler, M.1    Leshkowitz, D.2    Tal, L.3    Noor, E.4    Melamed-Bessudo, C.5
  • 31
    • 77953931509 scopus 로고    scopus 로고
    • An easier way to characterize the genomic composition of allopolyploids: the example of the Iberian cyprinid Squalius alburnoides
    • Inácio A, Matos I, Machado M, Coelho MM, (2010) An easier way to characterize the genomic composition of allopolyploids: the example of the Iberian cyprinid Squalius alburnoides. Journal of Fish Biology 76: 1995-2001.
    • (2010) Journal of Fish Biology , vol.76 , pp. 1995-2001
    • Inácio, A.1    Matos, I.2    Machado, M.3    Coelho, M.M.4
  • 32
    • 36749013633 scopus 로고    scopus 로고
    • RNA sequence analysis defines Dicer's role in mouse embryonic stem cells
    • Calabrese J, Seila A, Yeo GW, Sharp PA, (2007) RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A 104: 18097-102.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 18097-18102
    • Calabrese, J.1    Seila, A.2    Yeo, G.W.3    Sharp, P.A.4
  • 33
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.Nucleic Acids Res. 30: 207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 34
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA, (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4: 44-57.
    • (2008) Nature Protocols , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 35
    • 84860179523 scopus 로고    scopus 로고
    • Ethanol exposure induces up-regulation of specific microRNAs in zebrafish embryos
    • Soares AR, Pereira PM, Ferreira V, Reverendo M, Simões J, et al. (2012) Ethanol exposure induces up-regulation of specific microRNAs in zebrafish embryos. Toxicol Sci 127: 18-28.
    • (2012) Toxicol Sci , vol.127 , pp. 18-28
    • Soares, A.R.1    Pereira, P.M.2    Ferreira, V.3    Reverendo, M.4    Simões, J.5


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