Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development
Abstract
1. Introduction
2. Materials and Methods
2.1. Gene Identification Procedures
2.2. Phylogenetic Analysis of the EIL/EIN3 Protein Family
2.3. Analysis of Cis-Acting Regulatory Elements and miRNA Targets
2.4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of EIL/EIN3 Genes
2.5. Protein Interaction Networks of EIL/EIN3 Genes
2.6. Plant Material, RNA-seq, and Data Analysis
3. Results and Discussion
3.1. Gene Identification Procedures
3.2. Gene Structure Analysis and Conserved Motif Analysis of EIL/EIN3 Genes
3.3. Phylogeny of EIL/EIN3 Members
3.4. Cis-Regulatory Element Analysis
3.5. GO and KEGG Pathway Analysis of EIL/EIN3 Genes
3.6. Protein–Protein Interaction Networks of EIL/EIN3 Genes
3.7. Expression Level Analysis of Cotton EIL/EIN3 Genes
3.8. Prediction of miRNA Targets in Cotton EIL/EIN3 Genes during Cotton Fiber Development
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Availability of Materials and Data
References
- Lata, C.; Prasad, M. Role of DREBs in regulation of abiotic stress responses in plants. J. Exp. Bot. 2011, 62, 4731–4748. [Google Scholar] [CrossRef]
- Corbineau, F.; Xia, Q.; Bailly, C.; El-Maarouf-Bouteau, H. Ethylene, a key factor in the regulation of seed dormancy. Front. Plant Sci. 2014, 5, 539. [Google Scholar] [CrossRef] [PubMed]
- Cheng, X.; Ruyter-Spira, C.; Bouwmeester, H. The interaction between strigolactones and other plant hormones in the regulation of plant development. Front. Plant Sci. 2013. [Google Scholar] [CrossRef] [PubMed]
- Fahad, S.; Hussain, S.; Matloob, A.; Khan, F.A.; Khaliq, A.; Saud, S.; Hassan, S.; Shan, D.; Khan, F.; Ullah, N.; et al. Phytohormones and plant responses to salinity stress: A review. Plant Growth Regul. 2015, 75, 391–404. [Google Scholar] [CrossRef]
- Chen, Y.-F.; Etheridge, N.; Schaller, G.E. Ethylene Signal Transduction. Ann. Bot. 2005, 95, 901–915. [Google Scholar] [CrossRef] [PubMed]
- Hyun, S.C.; Kieber, J.J. Eto Brute? Role of ACS turnover in regulating ethylene biosynthesis. Trends Plant Sci. 2005, 10, 291–296. [Google Scholar]
- Cara, B.; Giovannoni, J.J. Molecular biology of ethylene during tomato fruit development and maturation. Plant Sci. 2008, 175, 106–113. [Google Scholar] [CrossRef]
- An, F.; Zhang, X.; Zhu, Z.; Ji, Y.; He, W.; Jiang, Z.; Li, M.; Guo, H. Coordinated regulation of apical hook development by gibberellins and ethylene in etiolated Arabidopsis seedlings. Cell Res. 2012, 22, 915–927. [Google Scholar] [CrossRef] [PubMed]
- Ju, C.; Chang, C. Mechanistic Insights in Ethylene Perception and Signal Transduction. Plant Physiol. 2015. [Google Scholar] [CrossRef]
- Hall, B.P.; Shakeel, S.N.; Schaller, G.E. Ethylene receptors: Ethylene perception and signal transduction. J. Plant Growth Regul. 2007, 26, 118–130. [Google Scholar] [CrossRef]
- Fang, L.; Wang, Q.; Hu, Y.; Jia, Y.; Chen, J.; Liu, B.; Zhang, Z.; Guan, X.; Chen, S.; Zhou, B.; et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat. Genet. 2017, 49, 1089–1098. [Google Scholar] [CrossRef] [PubMed]
- An, F.; Zhao, Q.; Ji, Y.; Li, W.; Jiang, Z.; Yu, X.; Zhang, C.; Han, Y.; He, W.; Liu, Y.; et al. Ethylene-Induced Stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 Is Mediated by Proteasomal Degradation of EIN3 Binding F-Box 1 and 2 That Requires EIN2 in Arabidopsis. Plant Cell Online 2010. [Google Scholar] [CrossRef]
- Shinshi, H. Ethylene-regulated transcription and crosstalk with jasmonic acid. Plant Sci. 2008, 175, 18–23. [Google Scholar] [CrossRef]
- Zhu, Z.; An, F.; Feng, Y.; Li, P.; Xue, L.; Mu, A.; Jiang, Z.; Kim, J.-M.; To, T.K.; Li, W.; et al. Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis. Proc. Natl. Acad. Sci. USA 2011, 108, 12539–12544. [Google Scholar] [CrossRef] [PubMed]
- Yamasaki, K.; Kigawa, T.; Inoue, M.; Yamasaki, T.; Yabuki, T.; Aoki, M.; Seki, E.; Matsuda, T.; Tomo, Y.; Terada, T.; et al. Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3. J. Mol. Biol. 2005, 348, 253–264. [Google Scholar] [CrossRef] [PubMed]
- Chao, Q.; Rothenberg, M.; Solano, R.; Roman, G.; Terzaghi, W.; Ecker, J.R. Activation of the ethylene gas response pathway in arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell 1997, 89, 1133–1144. [Google Scholar] [CrossRef]
- Solano, R.; Stepanova, A.; Chao, Q.; Ecker, J.R. Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 1998, 12, 3703–3714. [Google Scholar] [CrossRef]
- Wawrzyńska, A.; Lewandowska, M.; Sirko, A. Nicotiana tabacum EIL2 directly regulates expression of at least one tobacco gene induced by sulphur starvation. J. Exp. Bot. 2010, 61, 889–900. [Google Scholar] [CrossRef]
- Li, J.; Li, Z.; Tang, L.; Yang, Y.; Zouine, M.; Bouzayen, M. A conserved phosphorylation site regulates the transcriptional function of ETHYLENE-INSENSITIVE3-like1 in tomato. J. Exp. Bot. 2012, 63, 427–439. [Google Scholar] [CrossRef][Green Version]
- Liu, S.; Xu, L.; Jia, Z.; Xu, Y.; Yang, Q.; Fei, Z.; Lu, X.; Chen, H.; Huang, S. Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.). Appl. Genet. 2008, 117, 927–933. [Google Scholar] [CrossRef]
- Bie, B.B.; Pan, J.S.; He, H.L.; Yang, X.Q.; Zhao, J.L.; Cai, R. Molecular cloning and expression analysis of the ethylene insensitive3 (EIN3) gene in cucumber (Cucumis sativus). Genet. Mol. Res. 2013, 12, 4179–4191. [Google Scholar] [CrossRef] [PubMed]
- Jin, X.; Qin, Z.; Wu, T.; Zhou, X. Identification of Ethylene-Responsive Genes in Ethrel-Treated Shoot Apices of Cucumber by Suppression Subtractive Hybridization. Plant Mol. Biol. Rep. 2011, 29, 875–884. [Google Scholar] [CrossRef]
- Yang, C.; Ma, B.; He, S.-J.; Xiong, Q.; Duan, K.-X.; Yin, C.-C.; Chen, H.; Lu, X.; Chen, S.-Y.; Zhang, J.-S. MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice. Plant Physiol. 2015, 169, 148–165. [Google Scholar] [CrossRef] [PubMed]
- Maruyama-Nakashita, A.; Nakamura, Y.; Tohge, T.; Saito, K.; Takahashi, H. Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell 2006, 18, 3235–3251. [Google Scholar] [CrossRef]
- Zhong, S.; Zhao, M.; Shi, T.; Shi, H.; An, F.; Zhao, Q.; Guo, H. EIN3/EIL1 cooperate with PIF1 to prevent photo-oxidation and to promote greening of Arabidopsis seedlings. Proc. Natl. Acad. Sci. USA 2009, 106, 21431–21436. [Google Scholar] [CrossRef]
- Shi, H.; Lyu, M.; Luo, Y.; Liu, S.; Li, Y.; He, H.; Wei, N.; Deng, X.W.; Zhong, S. Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors. Proc. Natl. Acad. Sci. USA 2018, 115, 6482–6487. [Google Scholar] [CrossRef]
- Guo, X.; Zhang, Y.; Tu, Y.; Wang, Y.; Cheng, W.; Yang, Y. Overexpression of an EIN3-binding F-box protein2-like gene caused elongated fruit shape and delayed fruit development and ripening in tomato. Plant Sci. 2018, 272, 131–141. [Google Scholar] [CrossRef]
- Shi, Y.H.; Zhu, S.W.; Mao, X.Z.; Feng, J.X.; Qin, Y.M.; Zhang, L.; Cheng, J.; Wei, L.P.; Wang, Z.Y.; Zhu, Y.X. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 2006, 8, 651–664. [Google Scholar] [CrossRef]
- Cao, Y.; Han, Y.; Meng, D.; Li, D.; Jin, Q.; Lin, Y.; Cai, Y. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae. PEER J. 2017, 5, e3400. [Google Scholar] [CrossRef]
- Li, M.; Wang, R.; Liang, Z.; Wu, X.; Wang, J. Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization. BMC Plant Biol. 2019, 19, 1–16. [Google Scholar] [CrossRef]
- Thyssen, G.N.; Fang, D.D.; Turley, R.B.; Florane, C.; Li, P.; Naoumkina, M. Next generation genetic mapping of the Ligon-lintless-2 (Li₂) locus in upland cotton (Gossypium hirsutum L.). Appl. Genet. 2014, 127, 2183–2192. [Google Scholar] [CrossRef]
- Naoumkina, M.; Thyssen, G.N.; Fang, D.D. RNA-seq analysis of short fiber mutants Ligon-lintless-1 (Li 1) and-2 (Li 2) revealed important role of aquaporins in cotton (Gossypium hirsutum L.) fiber elongation. BMC Plant Biol. 2015, 15, 65. [Google Scholar] [CrossRef] [PubMed]
- Salih, H.; Gong, W.; He, S.; Xia, W.; Odongo, M.R.; Du, X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genom. 2019, 1–16. [Google Scholar] [CrossRef]
- Salih, H.; Gong, W.; He, S.; Mustafa, N.S.; Du, X. Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development. Mol. Genet. Genom. 2018, 294, 23–34. [Google Scholar] [CrossRef]
- Dai, X.; Zhao, P.X. PsRNATarget: A plant small RNA target analysis server. Nucleic Acids Res. 2011, 39, W155–W159. [Google Scholar] [CrossRef] [PubMed]
- Szklarczyk, D.; Franceschini, A.; Wyder, S.; Forslund, K.; Heller, D.; Huerta-Cepas, J.; Simonovic, M.; Roth, A.; Santos, A.; Tsafou, K.P.; et al. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015, 43, D447–D452. [Google Scholar] [CrossRef] [PubMed]
- Zhang, T.; Hu, Y.; Jiang, W.; Fang, L.; Guan, X.; Chen, J.; Zhang, J.; Saski, C.A.; Scheffler, B.E.; Stelly, D.M.; et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 2015, 33, 531–537. [Google Scholar] [CrossRef]
- Salih, H.; Gong, W.; He, S.; Sun, G.; Sun, J.; Du, X. Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum. BMC Genet. 2016, 17, 129. [Google Scholar] [CrossRef]
- Filiz, E.; Vatansever, R.; Ozyigit, I.I.; Uras, M.E.; Sen, U.; Anjum, N.A.; Pereira, E. Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa). Arch. Biochem. Biophys. 2017, 627, 30–45. [Google Scholar] [CrossRef] [PubMed]
- Sanagi, M.M.; Salleh, S.; Ibrahim, W.A.W.; Naim, A.A.; Hermawan, D.; Miskam, M.; Hussain, I.; Aboul-Enein, H.Y. Molecularly imprinted polymer solid-phase extraction for the analysis of organophosphorus pesticides in fruit samples. J. Food Compos. Anal. 2013, 32, 155–161. [Google Scholar] [CrossRef]
- Chen, A.; He, S.; Li, F.; Li, Z.; Ding, M.; Liu, Q.; Rong, J. Analyses of the sucrose synthase gene family in cotton: Structure, phylogeny and expression patterns. BMC Plant Biol. 2012, 12, 85. [Google Scholar] [CrossRef] [PubMed]
- Li, Q.; Shen, Y.; Guo, L.; Wang, H.; Zhang, Y.; Fan, C.; Zheng, Y. The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis. Febs Open Bio 2019, 9, 629–642. [Google Scholar] [CrossRef] [PubMed]
- Sánchez-Gracia, A.; Vieira, F.G.; Almeida, F.C.; Rozas, J. Comparative Genomics of the Major Chemosensory Gene Families in Arthropods. In Encyclopedia of Life Sciences; Wiley: Hoboken, NJ, USA, 2011. [Google Scholar]
- Davies, K.T.J.; Tsagkogeorga, G.; Bennett, N.C.; Dávalos, L.M.; Faulkes, C.G.; Rossiter, S.J. Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals. Gene 2014, 549, 228–236. [Google Scholar] [CrossRef]
- Suarez, C.E.; Palmer, G.H.; Hötzel, I.; McElwain, T.F. Structure, sequence, and transcriptional analysis of the Babesia bovis rap-1 multigene locus. Mol. Biochem. Parasitol. 1998, 93, 215–224. [Google Scholar] [PubMed]
- Laloum, T.; De Mita, S.; Gamas, P.; Baudin, M.; Niebel, A. CCAAT-box binding transcription factors in plants: Y so many? Trends Plant Sci. 2013, 18, 157–166. [Google Scholar] [CrossRef] [PubMed]
- Shore, P.; Sharrocks, A.D. The MADS-Box Family of Transcription Factors. Eur. J. Biochem. 1995, 229, 1–13. [Google Scholar] [CrossRef] [PubMed]
- Ramji, D.P.; Foka, P. CCAAT/enhancer-binding proteins: Structure, function and regulation. Biochem. J. 2002, 365 Pt 3, 561–575. [Google Scholar] [CrossRef]
- Dai, Z.; An, K.; Edward, G.E.; An, G. Functional role of CAAT box element of the nopaline synthase (nos) promoter. J. Plant Biol. 1999, 42, 181–185. [Google Scholar] [CrossRef]
- Isogai, Y.; Keles, S.; Prestel, M.; Hochheimer, A.; Tjian, R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev. 2007, 21, 2936–2949. [Google Scholar] [CrossRef] [PubMed]
- Bae, S.H.; Han, H.W.; Moon, J. Functional analysis of the molecular interactions of TATA box-containing genes and essential genes. PLoS ONE 2015. [Google Scholar] [CrossRef] [PubMed]
- Walley, J.W.; Coughlan, S.; Hudson, M.E.; Covington, M.F.; Kaspi, R.; Banu, G.; Harmer, S.L.; Dehesh, K. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet. 2007. [Google Scholar] [CrossRef] [PubMed]
- Dasani, S.H.; Thaker, V.S. Role of abscisic acid in cotton fiber development. Russ. J. Plant Physiol. 2006, 53, 62–67. [Google Scholar] [CrossRef]
- Ruan, Y.L. Goldacre paper: Rapid cell expansion and cellulose synthesis regulated by plasmodesmata and sugar: Insights from the single-celled cotton fibre. Funct. Plant Biol. 2007, 34, 1–10. [Google Scholar] [CrossRef]
- Xiao, G.; Zhao, P.; Zhang, Y. A pivotal role of hormones in regulating cotton fiber development. Front. Plant Sci. 2019. [Google Scholar] [CrossRef] [PubMed]
- Liu, K.; Sun, J.; Yao, L.; Yuan, Y. Transcriptome analysis reveals critical genes and key pathways for early cotton fiber elongation in Ligon lintless-1 mutant. Genomics 2012, 100, 42–50. [Google Scholar] [CrossRef] [PubMed]
- Bray, S.J. Notch signalling: A simple pathway becomes complex. Nat. Rev. Mol. Cell Biol. 2006, 7, 678. [Google Scholar] [CrossRef]
- Hurt, C.R.; Lingappa, V.R.; Hansen, W.J. The Emergence of Small-Molecule Inhibitors of Capsid Assembly as Potential Antiviral Therapeutics. In Annual Reports in Medicinal Chemistry; Elsvier: London, UK, 2011. [Google Scholar]
- Dreze, M.; Carvunis, A.-R.; Charloteaux, B.; Galli, M.; Pevzner, S.J.; Tasan, M.; Ahn, Y.-Y.; Balumuri, P.; Barabasi, A.-L.; Bautista, V.; et al. Evidence for Network Evolution in an Arabidopsis Interactome Map. Science 2011, 33, 601–607. [Google Scholar]
- Zhang, Y.; Gao, P.; Yuan, J. Plant Protein-Protein Interaction Network and Interactome. Curr. Genom. 2009, 11, 40–46. [Google Scholar] [CrossRef]
- Huang, Y.; Li, H.; Hutchison, C.E.; Laskey, J.; Kieber, J.J. Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis. Plant J. 2003, 33, 221–233. [Google Scholar] [CrossRef]
- Lin, W.; Li, B.; Lu, D.; Chen, S.; Zhu, N.; He, P.; Shan, L. Tyrosine phosphorylation of protein kinase complex BAK1/BIK1 mediates Arabidopsis innate immunity. Proc. Natl. Acad. Sci. USA 2014, 111, 3632–3637. [Google Scholar] [CrossRef]
- Christensen, S.K.; Dagenais, N.; Chory, J.; Weigel, D. Regulation of auxin response by the protein kinase PINOID. Cell 2000, 100, 469–478. [Google Scholar] [CrossRef]
- Gao, Z.; Chen, Y.F.; Randlett, M.D.; Zhao, X.C.; Findell, J.L.; Kieber, J.J.; Schaller, G.E. Localization of the Raf-like Kinase CTR1 to the Endoplasmic Reticulum of Arabidopsis through Participation in Ethylene Receptor Signaling Complexes. J. Biol. Chem. 2003, 278, 34725–34732. [Google Scholar] [CrossRef] [PubMed]
- Mazzucotelli, E.; Belloni, S.; Marone, D.; De Leonardis, A.; Guerra, D.; Di Fonzo, N.; Cattivelli, L.; Mastrangelo, A. The E3 Ubiquitin Ligase Gene Family in Plants: Regulation by Degradation. Curr. Genom. 2006, 7, 509–522. [Google Scholar] [CrossRef] [PubMed]
- Sharma, B.; Joshi, D.; Yadav, P.K.; Gupta, A.K.; Bhatt, T.K. Role of ubiquitin-mediated degradation system in plant biology. Front. Plant Sci. 2016. [Google Scholar] [CrossRef] [PubMed]
- Kelley, D.R.; Estelle, M. Ubiquitin-mediated control of plant hormone signaling. Plant Physiol. 2012, 160, 47–55. [Google Scholar] [CrossRef]
- Santner, A.; Estelle, M. The ubiquitin-proteasome system regulates plant hormone signaling. Plant J. 2010, 61, 1029–1040. [Google Scholar] [CrossRef]
- Scheuring, D.; Künzl, F.; Viotti, C.; Yan, M.S.W.; Jiang, L.; Schellmann, S.; Robinson, D.G.; Pimpl, P. Ubiquitin initiates sorting of Golgi and plasma membrane proteins into the vacuolar degradation pathway. BMC Plant Biol. 2012, 12, 164. [Google Scholar] [CrossRef]
- Salih, H.; Leng, X.; He, S.P.; Jia, Y.H.; Gong, W.F.; Du, X.M. Characterization of the early fiber development gene, Ligon-lintless 1 (Li1), using microarray. Plant Gene 2016, 6, 59–66. [Google Scholar] [CrossRef]
- Qin, Y.M.; Hu, C.Y.; Pang, Y.; Kastaniotis, A.J.; Hiltunen, J.K.; Zhu, Y.X. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell 2007, 19, 3692–3704. [Google Scholar] [CrossRef]
- Li, F.; Fan, G.; Lu, C.; Xiao, G.; Zou, C.; Kohel, R.J.; Ma, Z.; Shang, H.; Ma, X.; Wu, J.; et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat. Biotechnol. 2015, 33, 524–530. [Google Scholar] [CrossRef]
- Wu, G. Plant MicroRNAs and Development. J. Genet. Genom. 2013, 40, 217–230. [Google Scholar] [CrossRef] [PubMed]
- Kwak, P.; Wang, Q.; Chen, X.; Qiu, C.; Yang, Z. Enrichment of a set of microRNAs during the cotton fiber development. BMC Genom. 2009, 10, 457. [Google Scholar] [CrossRef] [PubMed]
- Xie, F.; Wang, Q.; Sun, R.; Zhang, B. Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton. J. Exp. Bot. 2015, 66, 789–804. [Google Scholar] [CrossRef] [PubMed]
- Xie, F.; Jones, D.C.; Wang, Q.; Sun, R.; Zhang, B. Small RNA sequencing identifies miRNA roles in ovule and fibre development. Plant Biotechnol. J. 2015, 13, 355–369. [Google Scholar] [CrossRef]
- Naoumkina, M.; Thyssen, G.N.; Fang, D.D.; Hinchliffe, D.J.; Florane, C.B. Small RNA sequencing and degradome analysis of developing fibers of short fiber revealed a role for miRNAs and their targets in cotton fiber elongation. BMC Genom. 2016, 1–15. [Google Scholar]
- Wu, H.J.; Ma, Y.K.; Chen, T.; Wang, M.; Wang, X.J. PsRobot: A web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res. 2012, 40. [Google Scholar] [CrossRef] [PubMed]
- Liu, N.; Tu, L.; Tang, W.; Gao, W.; Lindsey, K.; Zhang, X. Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers of Gossypium barbadense. Plant J. 2014, 80, 331–344. [Google Scholar] [CrossRef]
- Zhao, T.; Xu, X.; Wang, M.; Li, C.; Li, C.; Zhao, R.; Zhu, S.; He, Q.; Chen, J. Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application. BMC Genom. 2019, 20, 421. [Google Scholar] [CrossRef] [PubMed]
Gene ID | Protein Domain | Chro No. | Start | End | Protein Length | Isoelectric Point | Molecular Weight | Localization |
---|---|---|---|---|---|---|---|---|
Gh_A02G1256 | EIN3 | Ah02 | 74,321,882 | 74,323,399 | 505 | 5.06 | 57,338.59 | Nucleus |
Gh_A03G2063 | EIL3 | Ah03 | 76,519 | 78,363 | 603 | 5.47 | 68,277.79 | Nucleus |
Gh_A05G0554 | EIL3 | Ah05 | 5,944,064 | 5,945,875 | 603 | 5.87 | 68,073.64 | Nucleus |
Gh_A05G0871 | EIN3 | Ah05 | 8,658,831 | 8,660,669 | 612 | 5.38 | 69,300.14 | Nucleus |
Gh_A06G0989 | EIL3 | Ah06 | 47,012,156 | 47,014,682 | 690 | 5.89 | 77,907.98 | Nucleus |
Gh_A08G1750 | EIN3 | Ah08 | 97,487,518 | 97,489,359 | 613 | 5.53 | 69,551.64 | Nucleus |
Gh_A13G1864 | EIL3 | Ah13 | 78,270,382 | 78,271,984 | 363 | 9.12 | 41,004.58 | Nucleus |
Gh_A13G2005 | EIN3 | Ah13 | 79,505,190 | 79,506,980 | 596 | 5.2 | 67,093.59 | Nucleus |
Gh_D03G0396 | EIL3 | Dh03 | 5,580,925 | 5,582,439 | 504 | 4.98 | 57,282.61 | Nucleus |
Gh_D03G1810 | EIN3 | Dh03 | 45,097 | 46,944 | 615 | 5.6 | 69,643.55 | Nucleus |
Gh_D05G3883 | EIN3 | Dh05 | 159,742 | 161,580 | 612 | 5.51 | 69,328.29 | Nucleus |
Gh_D06G1178 | EIL3 | Dh06 | 29,244,232 | 29,246,749 | 686 | 5.97 | 77,587.57 | Nucleus |
Gh_D07G1670 | EIN3 | Dh07 | 34,686,430 | 34,686,759 | 109 | 6.61 | 13,052.13 | Nucleus |
Gh_D08G2099 | EIN3 | Dh08 | 59,885,901 | 59,887,745 | 614 | 5.58 | 69,713.77 | Nucleus |
Gh_D12G2800 | EIN3 | Dh12 | 93,192 | 93,557 | 121 | 4.78 | 14,486.68 | Nucleus |
Gh_D13G2252 | EIL3 | Dh13 | 58,573,978 | 58,575,579 | 363 | 9.11 | 40,835.48 | Nucleus |
Gh_D13G2404 | EIN3 | Dh13 | 60,092,959 | 60,094,743 | 594 | 5.16 | 66,776.31 | Nucleus |
Gh_Sca006457G01 | EIL3 | scaffold6457 | 4225 | 8701 | 601 | 5.58 | 67,828.14 | Nucleus |
Gorai.001G192700 | EIN3 | Chr501 | 32,645,047 | 32,645,559 | 120 | 5.03 | 15,060.47 | Nucleus |
Gorai.003G043500 | EIL3 | Chr503 | 5,592,648 | 5,594,162 | 504 | 5.02 | 57,401.84 | Nucleus |
Gorai.003G140600 | EIN3 | Chr503 | 40,374,524 | 40,377,941 | 615 | 5.54 | 70,282.28 | Nucleus |
Gorai.004G227800 | EIN3 | Chr504 | 56,214,497 | 56,218,239 | 614 | 5.66 | 70,437.6 | Nucleus |
Gorai.007G241000 | EIL3 | Chr507 | 34,165,596 | 34,167,386 | 482 | 5.33 | 56,260.32 | Nucleus |
Gorai.009G071400 | EIL3 | Chr509 | 5,075,017 | 5,078,672 | 601 | 5.74 | 68,489.99 | Nucleus |
Gorai.009G105400 | EIN3 | Chr509 | 7,642,067 | 7,645,836 | 612 | 5.56 | 70,090.19 | Nucleus |
Gorai.010G128700 | EIL3 | Chr510 | 27,860,507 | 27,863,910 | 686 | 6.02 | 78,137.1 | Nucleus |
Gorai.013G250300 | EIL3 | Chr513 | 56,813,952 | 56,816,039 | 363 | 9.35 | 41,574.39 | Nucleus |
Gorai.013G266300 | EIN3 | Chr513 | 57,906,440 | 57,909,956 | 594 | 5.17 | 67,508.2 | Nucleus |
Ga01G2390 | EIN3 | Chr201 | 106,813,982 | 106,815,826 | 614 | 5.58 | 69,535.33 | Nucleus |
Ga02G0423 | EIL3 | Chr202 | 6,411,513 | 6,413,030 | 505 | 5.06 | 57,317.58 | Nucleus |
Ga05G0722 | EIL3 | Chr205 | 6,269,696 | 6,272,122 | 601 | 5.66 | 67,740.02 | Nucleus |
Ga05G1071 | EIN3 | Chr205 | 9,262,923 | 9,264,764 | 613 | 5.44 | 69,477.4 | Nucleus |
Ga06G1279 | EIL3 | Chr206 | 53,063,302 | 53,065,786 | 631 | 5.83 | 71,738.04 | Nucleus |
Ga08G2308 | EIN3 | Chr208 | 122,216,099 | 122,217,940 | 613 | 5.47 | 69,513.56 | Nucleus |
Ga13G2636 | EIL3 | Chr213 | 122,248,180 | 122,249,780 | 363 | 8.61 | 40,688.25 | Nucleus |
Ga13G2790 | EIN3 | Chr213 | 123,477,839 | 123,479,629 | 596 | 5.2 | 67,105.58 | Nucleus |
Ga14G2078 | EIL3 | tig00017874 | 3742 | 6220 | 663 | 5.88 | 75,328.17 | Nucleus |
miRNAs | Li1-0DPA | WT-0DPA | log2.Fold | q value | Li1-8DPA | WT-8DPA | log2.Fold | q value |
---|---|---|---|---|---|---|---|---|
ghr-miR156a | 296.01 | 153.324 | 0.94906 | 5.26 × 10−18 | 254.3824 | 350.725 | −0.4633 | 0.00071 |
ghr-miR156c | 49.3349 | 51.108 | −0.0509 | 0.057793 | 13.38854 | 58.4542 | −2.1263 | 3.65 × 10−8 |
ghr-miR169a | 0.77709 | 0.2271 | −0.1263 | 0.089546 | 26.77709 | 29.2271 | −0.1263 | 0.08955 |
ghr-miR394b | 17267.2 | 22589.7 | −0.3876 | 1.09 × 10−27 | 13910.7 | 18150 | −0.3838 | 1.49 × 10−52 |
ghr-miR7491 | 296.01 | 1226.59 | −2.0509 | 9.25 × 10−107 | 200.8282 | 233.817 | −0.2194 | 0.05341 |
ghr-miR7495a | 641.354 | 153.324 | 2.0645 | 3.97 × 10−89 | 240.9938 | 555.315 | −1.2043 | 4.48 × 10−24 |
ghr-miR7497 | 49.3349 | 51.108 | −0.0509 | 0.057793 | 13.38854 | 0 | 4.7429 | 1.49 × 10−5 |
ghr-miR7502 | 172.672 | 204.432 | −0.2436 | 0.099541 | 66.94272 | 146.135 | −1.1263 | 2.12 × 10−7 |
ghr-miR7504b | 493.349 | 766.62 | −0.6359 | 1.28 × 10−7 | 388.2678 | 409.179 | −0.0757 | 0.05005 |
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Salih, H.; He, S.; Li, H.; Peng, Z.; Du, X. Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. Plants 2020, 9, 128. https://doi.org/10.3390/plants9010128
Salih H, He S, Li H, Peng Z, Du X. Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. Plants. 2020; 9(1):128. https://doi.org/10.3390/plants9010128
Chicago/Turabian StyleSalih, Haron, Shoupu He, Hongge Li, Zhen Peng, and Xiongming Du. 2020. "Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development" Plants 9, no. 1: 128. https://doi.org/10.3390/plants9010128
APA StyleSalih, H., He, S., Li, H., Peng, Z., & Du, X. (2020). Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. Plants, 9(1), 128. https://doi.org/10.3390/plants9010128