Alves M, Dadalto S, Gonçalves A, De Souza G, Barros V, Fietto L. Plant bZIP transcription factors responsive to pathogens: a review. Int J Mol Sci. 2013;14(4):7815–28.
Article
PubMed
PubMed Central
Google Scholar
Kaur S, Iquebal MA, Jaiswal S, Tandon G, Sundaram RM, Gautam RK, Suresh KP, Rai A, Kumar D. A meta-analysis of potential candidate genes associated with salinity stress tolerance in rice. Agri Gene. 2016;1:126–34.
Article
Google Scholar
Theißen G, Melzer R, Rümpler F. MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution. Development. 2016;143(18):3259–71.
Article
PubMed
Google Scholar
Peng J, Carol P, Richards DE, King KE, Cowling RJ, Murphy GP, Harberd NP. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 1997;11(23):3194.
Article
CAS
PubMed
PubMed Central
Google Scholar
Silverstone AL, Ciampaglio CN, Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell. 1998;10(2):155–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Di LL, Wysockadiller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, Hahn MG, Feldmann KA, Benfey PN. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 1996;86(3):423–33.
Article
Google Scholar
Zhang D, Iyer LM, Aravind L. Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics. 2012;28(19):2407–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu W, Chen Z, Ahmed N, Han B, Cui Q, Liu A. Genome-wide identification, evolutionary analysis, and stress responses of the GRAS gene family in Castor beans. Int J Mol Sci. 2016;17(7):1004.
Article
PubMed Central
Google Scholar
Tian C, Wan P, Sun S, Li J, Chen M. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol. 2004;54(4):519–32.
Article
CAS
PubMed
Google Scholar
Chen YQ, Tai SS, Wang DW, Ding AM, Sun TT, Wang WF, Sun YH. Homology-based analysis of the GRAS gene family in tobacco. Genet Mol Res. 2015;14(4):15188–200.
Article
CAS
PubMed
Google Scholar
Liu X, Widmer A. Genome-wide comparative analysis of the GRAS gene family in Populus, Arabidopsis and Rice. Plant Mol Biol Report. 2014;32(6):1129–45.
Article
CAS
Google Scholar
Song X-M, Liu T-K, Duan W-K, Ma Q-H, Ren J, Wang Z, Li Y, Hou X-L. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics. 2014;103(1):135–46.
Article
CAS
PubMed
Google Scholar
Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and functional analysis of the GRAS gene family in grapevine indicates a role of GRAS proteins in the control of development and stress responses. Front Plant Sci. 2016;7:353.
Article
PubMed
PubMed Central
Google Scholar
Guo Y, Wu H, Li X, Li Q, Zhao X, Duan X, An Y, Lv W, An H. Identification and expression of GRAS family genes in maize (Zea mays L.). PLoS One. 2017;12(9):e0185418.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Shi S, Zhou Y, Zhou Y, Yang J, Tang X. Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera). PeerJ. 2016;4:e2388.
Article
PubMed
PubMed Central
Google Scholar
Mayrose M, Ekengren SK, Melech-Bonfil S, Martin GB, Sessa G. A novel link between tomato GRAS genes, plant disease resistance and mechanical stress response. Mol Plant Pathol. 2006;7(6):593–604.
Article
CAS
PubMed
Google Scholar
Bolle C. The role of GRAS proteins in plant signal transduction and development. Planta. 2004;218(5):683–92.
Article
CAS
PubMed
Google Scholar
Stuurman J, Jäggi F, Kuhlemeier C. Shoot meristem maintenance is controlled by a GRAS-gene mediated signal from differentiating cells. Genes Dev. 2002;16(17):2213–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science (New York, NY). 2007;316(5823):421–5.
Article
CAS
Google Scholar
Heo JO, Estelle M. Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root. Proc Natl Acad Sci U S A. 2011;108(5):2166.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greb T, Clarenz O, Schafer E, Muller D, Herrero R, Schmitz G, Theres K. Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation. Genes Dev. 2003;17(9):1175–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Mai YX, Zhang YC, Luo Q, Yang HQ. MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis. Mol Plant. 2010;3(5):794–806.
Article
PubMed
Google Scholar
Cui H. Killing two birds with one stone: transcriptional regulators coordinate development and stress responses in plants. Plant Signal Behav. 2012;7(6):701–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fode B, Siemsen T, Thurow C, Weigel R, Gatz C. The Arabidopsis GRAS protein SCL14 interacts with class II TGA transcription factors and is essential for the activation of stress-inducible promoters. The Plant Cell Online. 2008;20(11):3122–35.
Article
CAS
Google Scholar
Ma H-S, Liang D, Shuai P, Xia X-L, Yin W-L. The salt- and drought-inducible poplar GRAS protein SCL7 confers salt and drought tolerance in Arabidopsis thaliana. J Exp Bot. 2010;61(14):4011–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kai X, Chen S, Li T, Ma X, Liang X, Ding X, Liu H, Luo L. OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes. BMC Plant Biol. 2015;15(1):141.
Article
Google Scholar
Yuan Y, Fang L, Karungo SK, Zhang L, Gao Y, Li S, Xin H. Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis. Plant Cell Rep. 2016;35(3):655–66.
Article
CAS
PubMed
Google Scholar
Huang J, Pang C, Fan S, Song M, Yu J, Wei H, Ma Q, Li L, Zhang C, Yu S. Genome-wide analysis of the family 1 glycosyltransferases in cotton. Mol Gen Genomics. 2015;290(5):1805–18.
Article
CAS
Google Scholar
Heo JO, Chang KS, Kim IA, Lee MH, Lee SA, Song SK, Lee MM, Lim J. Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root. Proc Natl Acad Sci U S A. 2011;108(5):2166.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Mu C, Du M, Chen Y, Tian X, Zhang M, Li Z. The effect of mepiquat chloride on elongation of cotton (Gossypium hirsutum L.) internode is associated with low concentration of gibberellic acid. Plant Sci. 2014;225(8):15.
Article
CAS
PubMed
Google Scholar
Shi G, Guo X, Guo J, Liu L, Hua J. Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of upland cotton (Gossypium hirsutum L.). Plant Cell Rep. 2015;34(6):1005–23.
Article
CAS
PubMed
Google Scholar
Ma Z, Hu X, Cai W, Huang W, Zhou X, Luo Q, Yang H, Wang J, Huang J. Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet. 2014;10:e1004519.
Article
PubMed
PubMed Central
Google Scholar
Wang Q, Liu N, Yang X, Tu L, Zhang X. Small RNA-mediated responses to low- and high-temperature stresses in cotton. Sci Rep. 2016;6(1):35558.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol. 2015;33(5):531–7.
Article
CAS
PubMed
Google Scholar
Cenci A, Rouard M. Evolutionary analyses of GRAS transcription factors in angiosperms. Front Plant Sci. 2017;8:273.
Article
PubMed
PubMed Central
Google Scholar
Wu ZY, Wu PZ, Chen YP, Li MR, Wu GJ, Jiang HW. Genome-wide analysis of the GRAS gene family in physic nut (Jatropha curcas L.). Genet Mol Res. 2015;14(4):19211–24.
Article
CAS
PubMed
Google Scholar
Roy SW. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet. 2006;7(3):211.
PubMed
Google Scholar
Roy SW, Penny D. A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Molecular Biology & Evolution. 2007;24(7):1447.
Article
CAS
Google Scholar
Roy SW, Gilbert W. Complex early genes. Proc Natl Acad Sci U S A. 2005;102(6):1986–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Owamoto M, Maekawa M, Saito A, Higo H, Higo K. Evolutionary relationship of plant catalase genes inferred from exon-intron structures: isozyme divergence after the separation of monocots and dicots. Theoretical & Applied Genetics. 1998;97(1–2):9–19.
Article
Google Scholar
Hu X, Worton RG. Partial gene duplication as a cause of human disease. Hum Mutat. 1992;1(1):3–12.
Article
CAS
PubMed
Google Scholar
Ariizumi T, Steber CM. Seed germination of GA-insensitive sleepy1 mutants does not require RGL2 protein disappearance in Arabidopsis. The Plant Cell Online. 2007;19(3):791–804.
Article
CAS
Google Scholar
Zhang Y, Liu Z, Liu J, Lin S, Wang J, Lin W, Xu W. GA-DELLA pathway is involved in regulation of nitrogen deficiency-induced anthocyanin accumulation. Plant Cell Rep. 2017;36(4):557–69.
Article
CAS
PubMed
Google Scholar
Qu L-J, Ma Z, Hu X, Cai W, Huang W, Zhou X, Luo Q, Yang H, Wang J, Huang J. Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet. 2014;10(8):e1004519.
Article
Google Scholar
Curaba J, Talbot M, Li Z, Helliwell C. Over-expression of microRNA171 affects phase transitions and floral meristem determinancy in barley. BMC Plant Biol. 2013;13(1):6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niu Y, Zhao T, Xu X, Li J. Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum). Peerj. 2017;5(11):e3955.
Article
PubMed
PubMed Central
Google Scholar
Czikkel BE, Maxwell DP. NtGRAS1, a novel stress-induced member of the GRAS family in tobacco, localizes to the nucleus. J Plant Physiol. 2007;164(9):1220–30.
Article
CAS
PubMed
Google Scholar
Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, Li Q, Ma Z, Lu C, Zou C, et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet. 2014;46(6):567–72.
Article
CAS
PubMed
Google Scholar
Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res. 2001;11(5):803–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wheeler TJ, Eddy SR. Nhmmer: DNA homology search with profile HMMs. Bioinformatics (Oxford, England). 2013;29(19):2487.
Article
CAS
Google Scholar
Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2015;43(Database issue):257–60.
Article
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Del Bem LE, Vincentz MG. Evolution of xyloglucan-related genes in green plants. BMC Evol Biol. 2010;10(1):341.
Article
PubMed
PubMed Central
Google Scholar
Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics (Oxford, England). 2015;31(8):1296.
Article
Google Scholar
Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee T, Jin H, Marler B, Guo H, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jia J, Zhao P, Cheng L, et al. MADS-box family genes in sheepgrass and their involvement in abiotic stress responses. BMC Plant Biol. 2018;18(1):42.
Article
PubMed
PubMed Central
Google Scholar
Zhang C, Wang J, Long M, Fan C. gKaKs: the pipeline for genome-level Ka/Ks calculation. Bioinformatics. 2013;29(5):645–6.
Article
CAS
PubMed
Google Scholar
Lu J, Zheng J, Xu Q, et al. Adaptive evolution of the vertebrate skeletal muscle sodium channel. Genetics & Molecular Biology. 2011;34(2):323.
Article
CAS
Google Scholar
Yang Z, Qian G, Qin W, Yang Z, Yuan C, Lu L, Ge X, Zhang C, Wu Z, Li F. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. BMC Plant Biol. 2017;17(1):113.
Article
PubMed
PubMed Central
Google Scholar
Deng W, Wang Y, Liu Z, Cheng H, Xue Y. HemI: a toolkit for illustrating Heatmaps. PLoS One. 2014;9(11):e111988.
Article
PubMed
PubMed Central
Google Scholar
Xu Y, Wang J, Wang S, Wang J, Chen X. Characterization of GaWRKY1, a cotton transcription factor that regulates the Sesquiterpene synthase gene (+)-δ-Cadinene synthase-a. Plant Physiol. 2004;135(1):507.
Article
CAS
PubMed
PubMed Central
Google Scholar