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2016
J. J. Wang, Lu, X. K., Yin, Z. J., Mu, M., Zhao, X. J., Wang, D. L., Wang, S., Fan, W. L., Guo, L. X., Ye, W. W., Yu, S. X., Wang, J. J., Lu, X. K., Yin, Z. J., Mu, M., Zhao, X. J., Wang, D. L., Wang, S., Fan, W. L., Guo, L. X., Ye, W. W., and Yu, S. X., Genome-wide identification and expression analysis of CIPK genes in diploid cottons, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSWe would like to thank Dr. Cairui Lu for help in data analysis. Research supported by grants from the National High-tech R&D Program (“863” Program) (Grant #2011AA10A102). REFERENCESAlbrecht V, Ritz O, Linder S, Harter K, et al (2001). The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. EMBO J. 20: 1051-1063. http://dx.doi.org/10.1093/emboj/20.5.1051 Assmann SM, Wang XQ, et al (2001). From milliseconds to millions of years: guard cells and environmental responses. Curr. Opin. Plant Biol. 4: 421-428. http://dx.doi.org/10.1016/S1369-5266(00)00195-3 Carra A, Gambino G, Schubert A, et al (2007). A cetyltrimethylammonium bromide-based method to extract low-molecular-weight RNA from polysaccharide-rich plant tissues. Anal. Biochem. 360: 318-320. http://dx.doi.org/10.1016/j.ab.2006.09.022 Chae MJ, Lee JS, Nam MH, Cho K, et al (2007). A rice dehydration-inducible SNF1-related protein kinase 2 phosphorylates an abscisic acid responsive element-binding factor and associates with ABA signaling. Plant Mol. Biol. 63: 151-169. http://dx.doi.org/10.1007/s11103-006-9079-x Chen L, Ren F, Zhou L, Wang QQ, et al (2012). The Brassica napus calcineurin B-Like 1/CBL-interacting protein kinase 6 (CBL1/CIPK6) component is involved in the plant response to abiotic stress and ABA signalling. J. Exp. Bot. 63: 6211-6222. http://dx.doi.org/10.1093/jxb/ers273 Chen L, Wang QQ, Zhou L, Ren F, et al (2013). Arabidopsis CBL-interacting protein kinase (CIPK6) is involved in plant response to salt/osmotic stress and ABA. Mol. Biol. Rep. 40: 4759-4767. http://dx.doi.org/10.1007/s11033-013-2572-9 Chen X, Gu Z, Xin D, Hao L, et al (2011). Identification and characterization of putative CIPK genes in maize. J. Genet. Genomics 38: 77-87. http://dx.doi.org/10.1016/j.jcg.2011.01.005 Chothia C, Gough J, Vogel C, Teichmann SA, et al (2003). Evolution of the protein repertoire. Science 300: 1701-1703. http://dx.doi.org/10.1126/science.1085371 Flagel LE, Wendel JF, et al (2009). Gene duplication and evolutionary novelty in plants. New Phytol. 183: 557-564. http://dx.doi.org/10.1111/j.1469-8137.2009.02923.x Halfter U, Ishitani M, Zhu JK, et al (2000). The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3. Proc. Natl. Acad. Sci. USA 97: 3735-3740. http://dx.doi.org/10.1073/pnas.97.7.3735 Harper JF, et al (2001). Dissecting calcium oscillators in plant cells. Trends Plant Sci. 6: 395-397. http://dx.doi.org/10.1016/S1360-1385(01)02023-4 He DH, Lei ZP, Tang BS, Xing HY, et al (2015). Identification and analysis of the TIFY gene family in Gossypium raimondii. Genet. Mol. Res. 14: 10119-10138. http://dx.doi.org/10.4238/2015.August.21.19 He L, Yang X, Wang L, Zhu L, et al (2013). Molecular cloning and functional characterization of a novel cotton CBL-interacting protein kinase gene (GhCIPK6) reveals its involvement in multiple abiotic stress tolerance in transgenic plants. Biochem. Biophys. Res. Commun. 435: 209-215. http://dx.doi.org/10.1016/j.bbrc.2013.04.080 Huang C, Ding S, Zhang H, Du H, et al (2011). CIPK7 is involved in cold response by interacting with CBL1 in Arabidopsis thaliana. Plant Sci. 181: 57-64. http://dx.doi.org/10.1016/j.plantsci.2011.03.011 Huertas R, Olías R, Eljakaoui Z, Gálvez FJ, et al (2012). Overexpression of SlSOS2 (SlCIPK24) confers salt tolerance to transgenic tomato. Plant Cell Environ. 35: 1467-1482. http://dx.doi.org/10.1111/j.1365-3040.2012.02504.x Iqbal K, Azhar FM, Khan IA, et al, Ehsan-Ullah (2011). Variability for Drought Tolerance in Cotton (Gossypium hirsutum) and its Genetic Basis. Int. J. Agric. Biol. 13: 61-66. Kolukisaoglu U, Weinl S, Blazevic D, Batistic O, et al (2004). Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol. 134: 43-58. http://dx.doi.org/10.1104/pp.103.033068 Lecharny A, Boudet N, Gy I, Aubourg S, et al (2003). Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. J. Struct. Funct. Genomics 3: 111-116. http://dx.doi.org/10.1023/A:1022614001371 Li F, Fan G, Wang K, Sun F, et al (2014). Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46: 567-572. http://dx.doi.org/10.1038/ng.2987 Li LB, Zhang YR, Liu KC, Ni ZF, et al (2010). Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum. Agric. Sci. China 9: 19-30. http://dx.doi.org/10.1016/S1671-2927(09)60063-8 Long M, Rosenberg C, Gilbert W, et al (1995). Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92: 12495-12499. http://dx.doi.org/10.1073/pnas.92.26.12495 Mahajan S, Sopory SK, Tuteja N, et al (2006). Cloning and characterization of CBL-CIPK signalling components from a legume (Pisum sativum). FEBS J. 273: 907-925. http://dx.doi.org/10.1111/j.1742-4658.2006.05111.x Mortazavi A, Williams BA, McCue K, Schaeffer L, et al (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. http://dx.doi.org/10.1038/nmeth.1226 Pandey GK, Cheong YH, Kim BG, Grant JJ, et al (2007). CIPK9: a calcium sensor-interacting protein kinase required for low-potassium tolerance in Arabidopsis. Cell Res. 17: 411-421. http://dx.doi.org/10.1038/cr.2007.39 Paterson AH, Wendel JF, Gundlach H, Guo H, et al (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423-427. http://dx.doi.org/10.1038/nature11798 Roy SJ, Huang W, Wang XJ, Evrard A, et al (2013). A novel protein kinase involved in Na(+) exclusion revealed from positional cloning. Plant Cell Environ. 36: 553-568. http://dx.doi.org/10.1111/j.1365-3040.2012.02595.x Sanders D, Pelloux J, Brownlee C, Harper JF, et al (2002). Calcium at the crossroads of signaling. Plant Cell 14 (Suppl): S401-S417. Schauser L, Wieloch W, Stougaard J, et al (2005). Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus. J. Mol. Evol. 60: 229-237. http://dx.doi.org/10.1007/s00239-004-0144-2 Schwachtje J, Minchin PEH, Jahnke S, van Dongen JT, et al (2006). SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots. Proc. Natl. Acad. Sci. USA 103: 12935-12940. http://dx.doi.org/10.1073/pnas.0602316103 Tang RJ, Liu H, Bao Y, Lv QD, et al (2010). The woody plant poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress. Plant Mol. Biol. 74: 367-380. http://dx.doi.org/10.1007/s11103-010-9680-x Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D, et al (2009). CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. Plant J. 58: 778-790. http://dx.doi.org/10.1111/j.1365-313X.2009.03812.x Wang K, Wang Z, Li F, Ye W, et al (2012). The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44: 1098-1103. http://dx.doi.org/10.1038/ng.2371 Wang QQ, Liu F, Chen XS, Ma XJ, et al (2010). Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96: 369-376. http://dx.doi.org/10.1016/j.ygeno.2010.08.009 Wei KF, Wang YM, Xie DX, et al (2014). Identification and expression profile analysis of the protein kinase gene superfamily in maize development. Mol. Breed. 33: 155-172. http://dx.doi.org/10.1007/s11032-013-9941-x Weinl S, Kudla J, et al (2009). The CBL-CIPK Ca(2+)-decoding signaling network: function and perspectives. New Phytol. 184: 517-528. http://dx.doi.org/10.1111/j.1469-8137.2009.02938.x Xiang Y, Huang Y, Xiong L, et al (2007). Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol. 144: 1416-1428. http://dx.doi.org/10.1104/pp.107.101295 Xu J, Li HD, Chen LQ, Wang Y, et al (2006). A protein kinase, interacting with two calcineurin B-like proteins, regulates K+ transporter AKT1 in Arabidopsis. Cell 125: 1347-1360. http://dx.doi.org/10.1016/j.cell.2006.06.011 Yin Z, Wang J, Wang D, Fan W, et al (2013). The MAPKKK gene family in Gossypium raimondii: genome-wide identification, classification and expression analysis. Int. J. Mol. Sci. 14: 18740-18757. http://dx.doi.org/10.3390/ijms140918740  
J. J. Wang, Lu, X. K., Yin, Z. J., Mu, M., Zhao, X. J., Wang, D. L., Wang, S., Fan, W. L., Guo, L. X., Ye, W. W., Yu, S. X., Wang, J. J., Lu, X. K., Yin, Z. J., Mu, M., Zhao, X. J., Wang, D. L., Wang, S., Fan, W. L., Guo, L. X., Ye, W. W., and Yu, S. X., Genome-wide identification and expression analysis of CIPK genes in diploid cottons, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSWe would like to thank Dr. Cairui Lu for help in data analysis. Research supported by grants from the National High-tech R&D Program (“863” Program) (Grant #2011AA10A102). REFERENCESAlbrecht V, Ritz O, Linder S, Harter K, et al (2001). The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. EMBO J. 20: 1051-1063. http://dx.doi.org/10.1093/emboj/20.5.1051 Assmann SM, Wang XQ, et al (2001). From milliseconds to millions of years: guard cells and environmental responses. Curr. Opin. Plant Biol. 4: 421-428. http://dx.doi.org/10.1016/S1369-5266(00)00195-3 Carra A, Gambino G, Schubert A, et al (2007). A cetyltrimethylammonium bromide-based method to extract low-molecular-weight RNA from polysaccharide-rich plant tissues. Anal. Biochem. 360: 318-320. http://dx.doi.org/10.1016/j.ab.2006.09.022 Chae MJ, Lee JS, Nam MH, Cho K, et al (2007). A rice dehydration-inducible SNF1-related protein kinase 2 phosphorylates an abscisic acid responsive element-binding factor and associates with ABA signaling. Plant Mol. Biol. 63: 151-169. http://dx.doi.org/10.1007/s11103-006-9079-x Chen L, Ren F, Zhou L, Wang QQ, et al (2012). The Brassica napus calcineurin B-Like 1/CBL-interacting protein kinase 6 (CBL1/CIPK6) component is involved in the plant response to abiotic stress and ABA signalling. J. Exp. Bot. 63: 6211-6222. http://dx.doi.org/10.1093/jxb/ers273 Chen L, Wang QQ, Zhou L, Ren F, et al (2013). Arabidopsis CBL-interacting protein kinase (CIPK6) is involved in plant response to salt/osmotic stress and ABA. Mol. Biol. Rep. 40: 4759-4767. http://dx.doi.org/10.1007/s11033-013-2572-9 Chen X, Gu Z, Xin D, Hao L, et al (2011). Identification and characterization of putative CIPK genes in maize. J. Genet. Genomics 38: 77-87. http://dx.doi.org/10.1016/j.jcg.2011.01.005 Chothia C, Gough J, Vogel C, Teichmann SA, et al (2003). Evolution of the protein repertoire. Science 300: 1701-1703. http://dx.doi.org/10.1126/science.1085371 Flagel LE, Wendel JF, et al (2009). Gene duplication and evolutionary novelty in plants. New Phytol. 183: 557-564. http://dx.doi.org/10.1111/j.1469-8137.2009.02923.x Halfter U, Ishitani M, Zhu JK, et al (2000). The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3. Proc. Natl. Acad. Sci. USA 97: 3735-3740. http://dx.doi.org/10.1073/pnas.97.7.3735 Harper JF, et al (2001). Dissecting calcium oscillators in plant cells. Trends Plant Sci. 6: 395-397. http://dx.doi.org/10.1016/S1360-1385(01)02023-4 He DH, Lei ZP, Tang BS, Xing HY, et al (2015). Identification and analysis of the TIFY gene family in Gossypium raimondii. Genet. Mol. Res. 14: 10119-10138. http://dx.doi.org/10.4238/2015.August.21.19 He L, Yang X, Wang L, Zhu L, et al (2013). Molecular cloning and functional characterization of a novel cotton CBL-interacting protein kinase gene (GhCIPK6) reveals its involvement in multiple abiotic stress tolerance in transgenic plants. Biochem. Biophys. Res. Commun. 435: 209-215. http://dx.doi.org/10.1016/j.bbrc.2013.04.080 Huang C, Ding S, Zhang H, Du H, et al (2011). CIPK7 is involved in cold response by interacting with CBL1 in Arabidopsis thaliana. Plant Sci. 181: 57-64. http://dx.doi.org/10.1016/j.plantsci.2011.03.011 Huertas R, Olías R, Eljakaoui Z, Gálvez FJ, et al (2012). Overexpression of SlSOS2 (SlCIPK24) confers salt tolerance to transgenic tomato. Plant Cell Environ. 35: 1467-1482. http://dx.doi.org/10.1111/j.1365-3040.2012.02504.x Iqbal K, Azhar FM, Khan IA, et al, Ehsan-Ullah (2011). Variability for Drought Tolerance in Cotton (Gossypium hirsutum) and its Genetic Basis. Int. J. Agric. Biol. 13: 61-66. Kolukisaoglu U, Weinl S, Blazevic D, Batistic O, et al (2004). Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol. 134: 43-58. http://dx.doi.org/10.1104/pp.103.033068 Lecharny A, Boudet N, Gy I, Aubourg S, et al (2003). Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. J. Struct. Funct. Genomics 3: 111-116. http://dx.doi.org/10.1023/A:1022614001371 Li F, Fan G, Wang K, Sun F, et al (2014). Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46: 567-572. http://dx.doi.org/10.1038/ng.2987 Li LB, Zhang YR, Liu KC, Ni ZF, et al (2010). Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum. Agric. Sci. China 9: 19-30. http://dx.doi.org/10.1016/S1671-2927(09)60063-8 Long M, Rosenberg C, Gilbert W, et al (1995). Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92: 12495-12499. http://dx.doi.org/10.1073/pnas.92.26.12495 Mahajan S, Sopory SK, Tuteja N, et al (2006). Cloning and characterization of CBL-CIPK signalling components from a legume (Pisum sativum). FEBS J. 273: 907-925. http://dx.doi.org/10.1111/j.1742-4658.2006.05111.x Mortazavi A, Williams BA, McCue K, Schaeffer L, et al (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. http://dx.doi.org/10.1038/nmeth.1226 Pandey GK, Cheong YH, Kim BG, Grant JJ, et al (2007). CIPK9: a calcium sensor-interacting protein kinase required for low-potassium tolerance in Arabidopsis. Cell Res. 17: 411-421. http://dx.doi.org/10.1038/cr.2007.39 Paterson AH, Wendel JF, Gundlach H, Guo H, et al (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423-427. http://dx.doi.org/10.1038/nature11798 Roy SJ, Huang W, Wang XJ, Evrard A, et al (2013). A novel protein kinase involved in Na(+) exclusion revealed from positional cloning. Plant Cell Environ. 36: 553-568. http://dx.doi.org/10.1111/j.1365-3040.2012.02595.x Sanders D, Pelloux J, Brownlee C, Harper JF, et al (2002). Calcium at the crossroads of signaling. Plant Cell 14 (Suppl): S401-S417. Schauser L, Wieloch W, Stougaard J, et al (2005). Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus. J. Mol. Evol. 60: 229-237. http://dx.doi.org/10.1007/s00239-004-0144-2 Schwachtje J, Minchin PEH, Jahnke S, van Dongen JT, et al (2006). SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots. Proc. Natl. Acad. Sci. USA 103: 12935-12940. http://dx.doi.org/10.1073/pnas.0602316103 Tang RJ, Liu H, Bao Y, Lv QD, et al (2010). The woody plant poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress. Plant Mol. Biol. 74: 367-380. http://dx.doi.org/10.1007/s11103-010-9680-x Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D, et al (2009). CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. Plant J. 58: 778-790. http://dx.doi.org/10.1111/j.1365-313X.2009.03812.x Wang K, Wang Z, Li F, Ye W, et al (2012). The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44: 1098-1103. http://dx.doi.org/10.1038/ng.2371 Wang QQ, Liu F, Chen XS, Ma XJ, et al (2010). Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96: 369-376. http://dx.doi.org/10.1016/j.ygeno.2010.08.009 Wei KF, Wang YM, Xie DX, et al (2014). Identification and expression profile analysis of the protein kinase gene superfamily in maize development. Mol. Breed. 33: 155-172. http://dx.doi.org/10.1007/s11032-013-9941-x Weinl S, Kudla J, et al (2009). The CBL-CIPK Ca(2+)-decoding signaling network: function and perspectives. New Phytol. 184: 517-528. http://dx.doi.org/10.1111/j.1469-8137.2009.02938.x Xiang Y, Huang Y, Xiong L, et al (2007). Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol. 144: 1416-1428. http://dx.doi.org/10.1104/pp.107.101295 Xu J, Li HD, Chen LQ, Wang Y, et al (2006). A protein kinase, interacting with two calcineurin B-like proteins, regulates K+ transporter AKT1 in Arabidopsis. Cell 125: 1347-1360. http://dx.doi.org/10.1016/j.cell.2006.06.011 Yin Z, Wang J, Wang D, Fan W, et al (2013). The MAPKKK gene family in Gossypium raimondii: genome-wide identification, classification and expression analysis. Int. J. Mol. Sci. 14: 18740-18757. http://dx.doi.org/10.3390/ijms140918740  
Y. L. Zhao, Wang, H. M., Shao, B. X., Chen, W., Guo, Z. J., Gong, H. Y., Sang, X. H., Wang, J. J., Ye, W. W., Zhao, Y. L., Wang, H. M., Shao, B. X., Chen, W., Guo, Z. J., Gong, H. Y., Sang, X. H., Wang, J. J., and Ye, W. W., SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.), vol. 15, p. -, 2016.
Y. L. Zhao, Wang, H. M., Shao, B. X., Chen, W., Guo, Z. J., Gong, H. Y., Sang, X. H., Wang, J. J., Ye, W. W., Zhao, Y. L., Wang, H. M., Shao, B. X., Chen, W., Guo, Z. J., Gong, H. Y., Sang, X. H., Wang, J. J., and Ye, W. W., SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.), vol. 15, p. -, 2016.