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Volumn 13, Issue 3, 2015, Pages 421-434

microRNA evolution and expression analysis in polyploidized cotton genome

Author keywords

Cotton; Evolution; Gene duplication; Gene regulation; MicroRNA

Indexed keywords

GOSSYPIUM HIRSUTUM;

EID: 84926407562     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/pbi.12295     Document Type: Article
Times cited : (41)

References (47)
  • 1
    • 24644457076 scopus 로고    scopus 로고
    • Novel patterns of gene expression in polyploid plants
    • Adams, K.L. and Wendel, J.F. (2005) Novel patterns of gene expression in polyploid plants. Trends Genet. 21, 539-543.
    • (2005) Trends Genet. , vol.21 , pp. 539-543
    • Adams, K.L.1    Wendel, J.F.2
  • 2
    • 58049220318 scopus 로고    scopus 로고
    • CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
    • Addo-Quaye, C., Miller, W. and Axtell, M.J. (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25, 130-131.
    • (2009) Bioinformatics , vol.25 , pp. 130-131
    • Addo-Quaye, C.1    Miller, W.2    Axtell, M.J.3
  • 3
    • 9644272448 scopus 로고    scopus 로고
    • Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana
    • Allen, E., Xie, Z., Gustafson, A.M., Sung, G.H., Spatafora, J.W. and Carrington, J.C. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 36, 1282-1290.
    • (2004) Nat. Genet. , vol.36 , pp. 1282-1290
    • Allen, E.1    Xie, Z.2    Gustafson, A.M.3    Sung, G.H.4    Spatafora, J.W.5    Carrington, J.C.6
  • 4
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • Ambros, V. (2004) The functions of animal microRNAs. Nature 431, 350-355.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 5
    • 0242361521 scopus 로고    scopus 로고
    • Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes
    • Aukerman, M.J. and Sakai, H. (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell, 15, 2730-2741.
    • (2003) Plant Cell , vol.15 , pp. 2730-2741
    • Aukerman, M.J.1    Sakai, H.2
  • 6
    • 22144457368 scopus 로고    scopus 로고
    • Antiquity of microRNAs and their targets in land plants
    • Axtell, M.J. and Bartel, D.P. (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell, 17, 1658-1673.
    • (2005) Plant Cell , vol.17 , pp. 1658-1673
    • Axtell, M.J.1    Bartel, D.P.2
  • 7
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 8
    • 84949179889 scopus 로고    scopus 로고
    • Genetic Consequences of Polyploidy in Plants.
    • Birchler, J.A. (2012) Genetic Consequences of Polyploidy in Plants. 21-32.
    • (2012) , pp. 21-32
    • Birchler, J.A.1
  • 9
    • 0033789617 scopus 로고    scopus 로고
    • Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids
    • Comai, L., Tyagi, A.P., Winter, K., Holmes-Davis, R., Reynolds, S.H., Stevens, Y. and Byers, B. (2000) Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell, 12, 1551-1568.
    • (2000) Plant Cell , vol.12 , pp. 1551-1568
    • Comai, L.1    Tyagi, A.P.2    Winter, K.3    Holmes-Davis, R.4    Reynolds, S.H.5    Stevens, Y.6    Byers, B.7
  • 10
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., Navon, R., Steinfeld, I., Lipson, D. and Yakhini, Z. (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10, 48.
    • (2009) BMC Bioinformatics , vol.10 , pp. 48
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 11
    • 84898939935 scopus 로고    scopus 로고
    • Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice
    • Fang, Y., Xie, K. and Xiong, L. (2014) Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J. Exp. Bot. 65, 2119-2135.
    • (2014) J. Exp. Bot. , vol.65 , pp. 2119-2135
    • Fang, Y.1    Xie, K.2    Xiong, L.3
  • 12
    • 84895557335 scopus 로고    scopus 로고
    • The target gene of tae-miR164, a novel NAC transcription factor from the NAM subfamily, negatively regulates resistance of wheat to stripe rust
    • Feng, H., Duan, X., Zhang, Q., Li, X., Wang, B., Huang, L., Wang, X. and Kang, Z. (2014) The target gene of tae-miR164, a novel NAC transcription factor from the NAM subfamily, negatively regulates resistance of wheat to stripe rust. Mol. Plant Pathol. 15, 284-296.
    • (2014) Mol. Plant Pathol. , vol.15 , pp. 284-296
    • Feng, H.1    Duan, X.2    Zhang, Q.3    Li, X.4    Wang, B.5    Huang, L.6    Wang, X.7    Kang, Z.8
  • 13
    • 77950531313 scopus 로고    scopus 로고
    • Over-expression of osa-MIR396c decreases salt and alkali stress tolerance
    • Gao, P., Bai, X., Yang, L., Lv, D., Li, Y., Cai, H., Ji, W., Guo, D. and Zhu, Y. (2010) Over-expression of osa-MIR396c decreases salt and alkali stress tolerance. Planta, 231, 991-1001.
    • (2010) Planta , vol.231 , pp. 991-1001
    • Gao, P.1    Bai, X.2    Yang, L.3    Lv, D.4    Li, Y.5    Cai, H.6    Ji, W.7    Guo, D.8    Zhu, Y.9
  • 14
    • 84892526727 scopus 로고    scopus 로고
    • Composition and expression of conserved MicroRNA genes in diploid cotton (Gossypium) species
    • Gong, L., Kakrana, A., Arikit, S., Meyers, B.C. and Wendel, J.F. (2013) Composition and expression of conserved MicroRNA genes in diploid cotton (Gossypium) species. Genome Biol. Evol. 5, 2449-2459.
    • (2013) Genome Biol. Evol. , vol.5 , pp. 2449-2459
    • Gong, L.1    Kakrana, A.2    Arikit, S.3    Meyers, B.C.4    Wendel, J.F.5
  • 16
    • 24944510549 scopus 로고    scopus 로고
    • MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development
    • Guo, H.S., Xie, Q., Fei, J.F. and Chua, N.H. (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell, 17, 1376-1386.
    • (2005) Plant Cell , vol.17 , pp. 1376-1386
    • Guo, H.S.1    Xie, Q.2    Fei, J.F.3    Chua, N.H.4
  • 17
    • 84871436735 scopus 로고    scopus 로고
    • Cotton fiber: a powerful single-cell model for cell wall and cellulose research
    • Haigler, C.H., Betancur, L., Stiff, M.R. and Tuttle, J.R. (2012) Cotton fiber: a powerful single-cell model for cell wall and cellulose research. Front Plant Sci. 3, 104.
    • (2012) Front Plant Sci. , vol.3 , pp. 104
    • Haigler, C.H.1    Betancur, L.2    Stiff, M.R.3    Tuttle, J.R.4
  • 18
    • 33747161960 scopus 로고    scopus 로고
    • Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication
    • Hegarty, M.J., Barker, G.L., Wilson, I.D., Abbott, R.J., Edwards, K.J. and Hiscock, S.J. (2006) Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Current Biol. 16, 1652-1659.
    • (2006) Current 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    Hiscock, S.J.6
  • 19
    • 84878349247 scopus 로고    scopus 로고
    • Transcription factor OsAP21 gene increases salt/drought tolerance in transgenic Arabidopsis thaliana
    • Jin, X., Xue, Y., Wang, R., Xu, R., Bian, L., Zhu, B., Han, H., Peng, R. and Yao, Q. (2013) Transcription factor OsAP21 gene increases salt/drought tolerance in transgenic Arabidopsis thaliana. Mol. Biol. Rep. 40, 1743-1752.
    • (2013) Mol. Biol. Rep. , vol.40 , pp. 1743-1752
    • Jin, X.1    Xue, Y.2    Wang, R.3    Xu, R.4    Bian, L.5    Zhu, B.6    Han, H.7    Peng, R.8    Yao, Q.9
  • 20
    • 84881462705 scopus 로고    scopus 로고
    • The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis
    • Kang, N.Y., Lee, H.W. and Kim, J. (2013) The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis. Plant Cell Physiol. 54, 1326-1334.
    • (2013) Plant Cell Physiol. , vol.54 , pp. 1326-1334
    • Kang, N.Y.1    Lee, H.W.2    Kim, J.3
  • 21
    • 79955780739 scopus 로고    scopus 로고
    • Domestication of transposable elements into MicroRNA genes in plants
    • Li, Y., Li, C., Xia, J. and Jin, Y. (2011) Domestication of transposable elements into MicroRNA genes in plants. PLoS One, 6, e19212.
    • (2011) PLoS One , vol.6 , pp. e19212
    • Li, Y.1    Li, C.2    Xia, J.3    Jin, Y.4
  • 23
    • 77956297226 scopus 로고    scopus 로고
    • Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis
    • Liang, C., Zhang, X., Zou, J., Xu, D., Su, F. and Ye, N. (2010) Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One, 5, e10698.
    • (2010) PLoS One , vol.5 , pp. e10698
    • Liang, C.1    Zhang, X.2    Zou, J.3    Xu, D.4    Su, F.5    Ye, N.6
  • 24
    • 78650271190 scopus 로고    scopus 로고
    • Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera
    • Licausi, F., Giorgi, F.M., Zenoni, S., Osti, F., Pezzotti, M. and Perata, P. (2010) Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genom. 11, 719.
    • (2010) BMC Genom. , vol.11 , pp. 719
    • Licausi, F.1    Giorgi, F.M.2    Zenoni, S.3    Osti, F.4    Pezzotti, M.5    Perata, P.6
  • 25
    • 33645509923 scopus 로고    scopus 로고
    • Evolution of Arabidopsis microRNA families through duplication events
    • Maher, C., Stein, L. and Ware, D. (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 16, 510-519.
    • (2006) Genome Res. , vol.16 , pp. 510-519
    • Maher, C.1    Stein, L.2    Ware, D.3
  • 26
    • 2942697259 scopus 로고    scopus 로고
    • MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs
    • Mallory, A.C., Dugas, D.V., Bartel, D.P. and Bartel, B. (2004) MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Current Biol. 14, 1035-1046.
    • (2004) Current Biol. , vol.14 , pp. 1035-1046
    • Mallory, A.C.1    Dugas, D.V.2    Bartel, D.P.3    Bartel, B.4
  • 28
    • 33746776849 scopus 로고    scopus 로고
    • Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana
    • Mlotshwa, S., Yang, Z., Kim, Y. and Chen, X. (2006) Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana. Plant Mol. Biol. 61, 781-793.
    • (2006) Plant Mol. Biol. , vol.61 , pp. 781-793
    • Mlotshwa, S.1    Yang, Z.2    Kim, Y.3    Chen, X.4
  • 29
    • 76249125348 scopus 로고    scopus 로고
    • Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)
    • Pang, M., Woodward, A.W., Agarwal, V., Guan, X., Ha, M., Ramachandran, V., Chen, X., Triplett, B.A., Stelly, D.M. and Chen, Z.J. (2009) Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol. 10, R122.
    • (2009) Genome Biol. , vol.10 , pp. R122
    • Pang, M.1    Woodward, A.W.2    Agarwal, V.3    Guan, X.4    Ha, M.5    Ramachandran, V.6    Chen, X.7    Triplett, B.A.8    Stelly, D.M.9    Chen, Z.J.10
  • 31
    • 42449099982 scopus 로고    scopus 로고
    • Dual coding of siRNAs and miRNAs by plant transposable elements
    • Piriyapongsa, J. and Jordan, I.K. (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA, 14, 814-821.
    • (2008) RNA , vol.14 , pp. 814-821
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 32
    • 78751591032 scopus 로고    scopus 로고
    • How cotton fibers elongate: a tale of linear cell-growth mode
    • Qin, Y.M. and Zhu, Y.X. (2011) How cotton fibers elongate: a tale of linear cell-growth mode. Curr. Opin. Plant Biol. 14, 106-111.
    • (2011) Curr. Opin. Plant Biol. , vol.14 , pp. 106-111
    • Qin, Y.M.1    Zhu, Y.X.2
  • 33
    • 0031845074 scopus 로고    scopus 로고
    • The AP2/EREBP family of plant transcription factors
    • Riechmann, J.L. and Meyerowitz, E.M. (1998) The AP2/EREBP family of plant transcription factors. Biol. Chem. 379, 633-646.
    • (1998) Biol. Chem. , vol.379 , pp. 633-646
    • Riechmann, J.L.1    Meyerowitz, E.M.2
  • 34
    • 84901254233 scopus 로고    scopus 로고
    • Genome-wide transcriptome profiling revealed cotton fuzz fiber development having a similar molecular model as Arabidopsis trichome
    • Wan, Q., Zhang, H., Ye, W., Wu, H. and Zhang, T. (2014) Genome-wide transcriptome profiling revealed cotton fuzz fiber development having a similar molecular model as Arabidopsis trichome. PLoS One, 9, e97313.
    • (2014) PLoS One , vol.9 , pp. e97313
    • Wan, Q.1    Zhang, H.2    Ye, W.3    Wu, H.4    Zhang, T.5
  • 37
    • 78449293356 scopus 로고    scopus 로고
    • Target-align: a tool for plant microRNA target identification
    • Xie, F. and Zhang, B. (2010) Target-align: a tool for plant microRNA target identification. Bioinformatics, 26, 3002-3003.
    • (2010) Bioinformatics , vol.26 , pp. 3002-3003
    • Xie, F.1    Zhang, B.2
  • 38
    • 80555154263 scopus 로고    scopus 로고
    • Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database
    • Xie, F., Sun, G., Stiller, J.W. and Zhang, B. (2011) Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database. PLoS One, 6, e26980.
    • (2011) PLoS One , vol.6 , pp. e26980
    • Xie, F.1    Sun, G.2    Stiller, J.W.3    Zhang, B.4
  • 39
    • 84865407608 scopus 로고    scopus 로고
    • miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs
    • Xie, F., Xiao, P., Chen, D., Xu, L. and Zhang, B. (2012) miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol. Biol.. 80, 75-84.
    • (2012) Plant Mol. Biol. , vol.80 , pp. 75-84
    • Xie, F.1    Xiao, P.2    Chen, D.3    Xu, L.4    Zhang, B.5
  • 40
    • 84926419766 scopus 로고    scopus 로고
    • Small RNA sequencing identifies miRNA roles in ovule and fiber development
    • Xie, F.L., Jones, D.C., Wang, Q.L., Sun, R.R. and Zhang, B.H. (2015) Small RNA sequencing identifies miRNA roles in ovule and fiber development. Plant Biotechnol. J. doi: 10.1111/pbj.12296.
    • (2015) Plant Biotechnol. J.
    • Xie, F.L.1    Jones, D.C.2    Wang, Q.L.3    Sun, R.R.4    Zhang, B.H.5
  • 41
    • 84910073298 scopus 로고    scopus 로고
    • MicroRNA-based Biotechnology for Plant Improvement
    • Zhang, B.H. and Wang, Q.L. (2015) MicroRNA-based Biotechnology for Plant Improvement. J. Cell. Physiol. 230, 1-15.
    • (2015) J. Cell. Physiol. , vol.230 , pp. 1-15
    • Zhang, B.H.1    Wang, Q.L.2
  • 42
    • 33845601726 scopus 로고    scopus 로고
    • MicroRNAs and their regulatory roles in animals and plants
    • Zhang, B.H., Wang, Q.H. and Pan, X.P. (2007) MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol. 210, 279-289.
    • (2007) J. Cell. Physiol. , vol.210 , pp. 279-289
    • Zhang, B.H.1    Wang, Q.H.2    Pan, X.P.3
  • 45
    • 83355173057 scopus 로고    scopus 로고
    • Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model
    • Zhang, Y., Jiang, W.K. and Gao, L.Z. (2011) Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model. PLoS One, 6, e28073.
    • (2011) PLoS One , vol.6 , pp. e28073
    • Zhang, Y.1    Jiang, W.K.2    Gao, L.Z.3
  • 46
    • 34249093687 scopus 로고    scopus 로고
    • A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
    • Zhao, T., Li, G., Mi, S., Li, S., Hannon, G.J., Wang, X.J. and Qi, Y. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev. 21, 1190-1203.
    • (2007) Genes Dev. , vol.21 , pp. 1190-1203
    • Zhao, T.1    Li, G.2    Mi, S.3    Li, S.4    Hannon, G.J.5    Wang, X.J.6    Qi, Y.7
  • 47
    • 84885966708 scopus 로고    scopus 로고
    • Overexpression of a cotton gene that encodes a putative transcription factor of AP2/EREBP family in Arabidopsis affects growth and development of transgenic plants
    • Zhou, Y., Xia, H., Li, X.J., Hu, R., Chen, Y. and Li, X.B. (2013) Overexpression of a cotton gene that encodes a putative transcription factor of AP2/EREBP family in Arabidopsis affects growth and development of transgenic plants. PLoS One, 8, e78635.
    • (2013) PLoS One , vol.8 , pp. e78635
    • Zhou, Y.1    Xia, H.2    Li, X.J.3    Hu, R.4    Chen, Y.5    Li, X.B.6


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