Comparative analysis of RNA-Seq data reveals adventitious root development is mediated by ChIFNα in lotus japonicus

References

• Li ZY, Wang D, Bian JH, et al. Research progress on the molecular biology of Lotus corniculatus. Pratacult Sci. 2019;36(11):2871–2886.
   Google Scholar
• Pellissier V, Muratet A, Verfaillie F, et al. Pollination success of Lotus corniculatus (L.) in an urban context. Acta Oecol. 2012;39:94–100.
   Web of Science ®Google Scholar
• Long ZF, Tang CB, Meng JJ, et al. selection of pastures for water and soil conservation in mountainous karst area of Guizhou Province. Guizhou Sci. 2007;25(S1):483–493.
   Google Scholar
• Sun YX, Wang D, Bai YL, et al. Overexpression of soybean GmNHX1 in lotus root: the decrease of Na + content in body is the basis of improving salt tolerance. Chinese Sci Bull. 2006;51(11):1306–1936.
   Google Scholar
• Marcus PI, Heide LVD, Sekellick MJ. Interferon action on avian viruses. I. Oral administration of chicken interferon-alpha ameliorates Newcastle disease. J Interferon Cytokine Res. 1999;19(8):881–885.
   PubMed Web of Science ®Google Scholar
• Gabriele L, Ozato K. The role of the interferon regulatory factor (IRF) family in dendritic cell development and function. Cytokine Growth Factor Rev. 2007;18(5-6):503–510.
   PubMed Web of Science ®Google Scholar
• Wei L, Sandbulte MR, Thomas PG, et al. NFkappaB negatively regulates interferon-induced gene expression and anti-influenza activity. J Biol Chem. 2006;281(17):11678–11684.
   PubMed Web of Science ®Google Scholar
• Orchansky P, Rubinstein M, Sela I. Human interferons protect plants from virus infection. Proc Natl Acad Sci USA. 1982;79(7):2278–2280.
   PubMed Web of Science ®Google Scholar
• Devash Y, Biggs S, Sela I. Multiplication of tobacco mosaic virus in tobacco leaf disks is inhibited by (2'-5) oligoadenylate. Science. 1982;216(4553):1415–1416.
   PubMed Web of Science ®Google Scholar
• Van L. Induced resistance in plants and the role of pathogenesis-related proteins. Eur J Plant Pathol. 1997;103(9):753–765.
   Web of Science ®Google Scholar
• El-Ayouty Y, El-Manawy I, Nasih S, et al. Engineering Chlamydomonas reinhardtii for expression of functionally active human interferon-α. Mol Biotechnol. 2019;61(2):134–144.
   PubMed Web of Science ®Google Scholar
• Razmi S, Javaran MJ, Bagheri A, Biotechnology and Plant Breeding Department, Agriculture Faculty, Tarbiat Modares University, Tehran, Iran, et al. Expression of human interferon gamma in tobacco chloroplasts. Rom Biotechnol Lett. 2019;24(2):208–215.
   Web of Science ®Google Scholar
• Zhu Z, Li X, Sun Y, et al. Plant regeneration of transgenic rice and expression of exogenous human α-interferon cDNA. Sci China Ser B. 1992;2:149–155.
   Google Scholar
• Sawahel W. The production of transgenic potato plants expressing human a-interferon using lipofectin-mediated transformation. Cell Mol Biol Lett. 2002;7(1):19–29.
   PubMed Web of Science ®Google Scholar
• Ohya K, Matsumura T, Itchoda N, et al. Ability of orally administered IFN-alpha-containing transgenic potato extracts to inhibit Listeria monocytogenes infection. J Interferon Cytokine Res. 2005;25(8):459–466.
   PubMed Web of Science ®Google Scholar
• Zhu Z, Hughes KW, Huang L, et al. Expression of human α-interferon cDNA in transgenic rice plants. Plant Cell Tiss Organ Cult. 1994;36(2):197–204.
   Web of Science ®Google Scholar
• Jiang MC, Hu CC, Lin NS, et al. Production of human IFNγ Protein in Nicotiana benthamiana plant through an enhanced expression system based on bamboo mosaic virus. Viruses. 2019;11(6):509.
   PubMed Web of Science ®Google Scholar
• Sekellick MJ, Ferrandino AF, Hopkins DA, et al. Chicken interferon gene: cloning, expression, and analysis. J Interferon Res. 1994;14(2):71–79.
   PubMedGoogle Scholar
• Sela I. Interferon-like factor from virus-infected plants. Presp Virol. 1981;11:129–139.
   Google Scholar
• Song L, Zhao D, Tian X, et al. Expression of ChIFN-α in transgenic tobacco causes resistance to tobacco mosaic virus. J Agric Sci Tech Iran. 2010;12(1):118–122.
   Google Scholar
• Pandi-Perumal SR, Trakht I, Srinivasan V, et al. Physiological effects of melatonin: role of melatonin receptors and signal transduction pathways. Prog Neurobiol. 2008;85(3):335–353.
   PubMed Web of Science ®Google Scholar
• Chen H, Feng Y, Zhou J, et al. Research advance of plant root biology. World For Res. 2013;26(5):25–29.
   Google Scholar
• Lakehal A, Bellini C. Control of adventitious root formation: insights into synergistic and antagonistic hormonal interactions. Physiol Plant. 2019;165(1):90–100.
   PubMed Web of Science ®Google Scholar
• Bollmark M, Kubát B, Eliasson L. Variation in endogenous cytokinin content during adventitious root formation in pea cuttings. J Plant Physiol. 1988;132(3):262–265.
   Web of Science ®Google Scholar
• Li S-W, Shi R-F, Leng Y. De novo characterization of the mung bean transcriptome and transcriptomic analysis of adventitious rooting in seedlings using RNA-Seq. PLoS One. 2015;10(7):e0132969.
   PubMed Web of Science ®Google Scholar
• Villacorta-Martín C, Sánchez-García AB, Villanova J, et al. Gene expression profiling during adventitious root formation in carnation stem cuttings. BMC Genomics. 2015;16(1):789
   PubMedGoogle Scholar
• Libao C, Minrong Z, Zhubing H, et al. Comparative transcriptome analysis revealed the cooperative regulation of sucrose and IAA on adventitious root formation in lotus (Nelumbo nucifera Gaertn). BMC Genomics. 2020;21(1):653.
   PubMed Web of Science ®Google Scholar
• Tian Z, Hong H, Kang X, et al. Transcriptome analysis of the effect of cutting age on adventitious root formation of populus. Bot Res. 2019;08(03):293–306.
   Google Scholar
• Wang J, Xia J, Xiao HL, et al. Study on the ecological and mechanical properties of root system of slope protecting plants. J Hubei Univ Technol. 2019;34(4):77–80.
   Web of Science ®Google Scholar
• Subramaniyam S, Mathiyalagan R, Natarajan S, et al. Transcript expression profiling for adventitious roots of Panax ginseng Meyer. Gene. 2014;546(1):89–96.
   PubMed Web of Science ®Google Scholar
• Chen K, Guo B, Yu C, et al. Comparative transcriptome analysis provides new insights into the molecular regulatory mechanism of adventitious root formation in Ramie (Boehmeria nivea L.). 2020. DOI. 10.21203/rs.3.rs-23123/v1.
   Google Scholar
• Du W, Ban Y, Nie H, et al. A comparative transcriptome analysis leads to new insights into the molecular events governing root formation in mulberry softwood cuttings. Plant Mol Biol Rep. 2016;34(2):365–373.
   Web of Science ®Google Scholar
• Fukuda Y, Hirao T, Mishima K, et al. Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don. BMC Plant Biol. 2018;18(1):201–214.
   PubMedGoogle Scholar
• Song L, Zhao DG. Optimization of culture conditions for Lotus japonicus regeneration in vitro. Mol Plant Breed. 2015;13(04):910–914.
   Google Scholar
• Song L, Zhao DG, Wu YJ. Transient expression of chicken alpha interferon gene in lettuce. J Zhe Jiang Univ Sci B. 2008;9(5):351–355.
   PubMed Web of Science ®Google Scholar
• Wang Y, Song F, Zhu J, et al. GSA: Genome Sequence Archive. Genom Proteom Bioinf. 2017;15(1):14–18.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Zhao W, Xiao J, et al. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res. 2020;48(D1):D24-D33.
   Web of Science ®Google Scholar
• Hartley SW, Mullikin JC. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. BMC Bioinform. 2015;16(1):1–7.
   PubMedGoogle Scholar
• Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
   PubMed Web of Science ®Google Scholar
• Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–169.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, et al. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. OMICS: A Journal of Integrative Biology. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Zhang T, Song C, Song L, et al. RNA sequencing and coexpression analysis reveal key genes involved in α-linolenic acid biosynthesis in Perilla frutescens seed. IJMS. 2017;18(11):2433.
   Google Scholar
• Zheng Y, Jiao C, Sun H, et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol Plant. 2016;9(12):1667–1670.
   PubMed Web of Science ®Google Scholar
• Smoot ME, Ono K, Ruscheinski J, et al. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011; 27(3):431–432.
   PubMed Web of Science ®Google Scholar
• Untergasser A, Cutcutache I, Koressaar T, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta c(T)) method. Methods. 2001;25(4):402–408.
   PubMed Web of Science ®Google Scholar
• Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–1202.
   PubMed Web of Science ®Google Scholar
• Guang Q, Song L, Zhao DG. Effect of low temperature stress on physiological responses of transgenic ChIFN-α lotus plant (Lotus corniculatus L.) to cold. Mol Plant Breed. 2015;13(12):2849–2853.
   Google Scholar
• Wu YJ, Zhao DG, Zhan SN, et al. A study on the insect-resistant mechanism of ChIFN-γ transgenic tobacco. J Yunnan Univ. 2010;32(4):473–479.
   Google Scholar
• Pop TI, Pamfil D, Bellini C. Auxin control in the formation of adventitious roots. Not Bot Hort Agrobot Cluj. 2011;39(1):307–316.
   Web of Science ®Google Scholar
• Chanclud E, Lacombe B. Plant hormones: key players in gut microbiota and human diseases? Trends Plant Sci. 2017;22(9):754–758.
   PubMed Web of Science ®Google Scholar
• Shang C, Yang H, Ma S, et al. Physiological and transcriptomic changes during the early phases of adventitious root formation in mulberry stem hardwood cuttings. IJMS. 2019;20(15):3707.
   Google Scholar
• Ellenberg J, Swedlow JR, Barlow M, et al. A call for public archives for biological image data. Nat Methods. 2018;15(11):849–854.
   PubMed Web of Science ®Google Scholar
• Varaud E, Brioudes F, Szécsi J, et al. Auxin response factor8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp. Plant Cell. 2011;23(3):973–983.
   PubMed Web of Science ®Google Scholar
• Yin X, Yi K, Zhao Y, et al. Revealing the full-length transcriptome of Caucasian clover rhizome development. BMC Plant Biol. 2020;20(1):429.
   PubMed Web of Science ®Google Scholar
• Mu J, Tan H, Hong S, et al. Arabidopsis transcription factor genes NF-YA1, 5, 6, and 9 play redundant roles in male gametogenesis, embryogenesis, and seed development. Mol Plant. 2013;6(1):188–201.
   PubMed Web of Science ®Google Scholar
• Zanetti ME, Rípodas C, Niebel A. Plant NF-Y transcription factors: key players in plant–microbe interactions, root development and adaptation to stress. Biochim Biophys Acta Gene Regul Mech. 2017;1860(5):645–654.
   PubMed Web of Science ®Google Scholar
• Swain S, Myers ZA, Siriwardana CL, et al. The multifaceted roles of NUCLEAR FACTOR-Y in Arabidopsis thaliana development and stress responses. Biochim Biophys Acta Gene Regul Mech. 2017;1860(5):636–644.
   PubMed Web of Science ®Google Scholar
• Li A, Lakshmanan P, He W, et al. Transcriptome profiling provides molecular insights into auxin-induced adventitious root formation in sugarcane (Saccharum spp. interspecific hybrids) Microshoots. Plants. 2020;9(8):931.
   Google Scholar
• Lee SI, Muthusamy M, Nawaz MA, et al. Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa. Mol Genet Genomics. 2019;294(6):1403–1420.
   PubMed Web of Science ®Google Scholar
• Tong J, Chen J, Zhu J, et al. Effects of rice C2C2 zinc finger protein gene OsLSD2 on the growth and nitrogen utilization of nipponbare. Chinese J Rice Sc. 2014;28(4):435–441.
   Google Scholar
• Chen K, Li H, Chen Y, et al. TaSCL14, a novel wheat (Triticum aestivum L.) GRAS gene, regulates plant growth, photosynthesis, tolerance to photooxidative stress, and senescence. J Genet Genomics. 2015;42(1):21–32.
   PubMed Web of Science ®Google Scholar
• Kong X, Tian H, Yu Q, et al. PHB3 maintains root stem cell niche identity through ROS-responsive AP2/ERF transcription factors in Arabidopsis. Cell Rep. 2018;22(5):1350–1363.
   PubMed Web of Science ®Google Scholar
• Upadhyay S, Jeena GS, Kumar S, et al. Asparagus racemosus bZIP transcription factor-regulated squalene epoxidase (ArSQE) promotes germination and abiotic stress tolerance in transgenic tobacco. Plant Sci. 2020;290:110291.
   PubMed Web of Science ®Google Scholar
• Wang L, Xu Y, Zhang C, et al. OsLIC, a novel CCCH-type zinc finger protein with transcription activation, mediates rice architecture via brassinosteroids signaling. PloS One. 2008;3(10):e3521
   PubMed Web of Science ®Google Scholar
• Chai G, Kong Y, Zhu M, et al. Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development. J Exp Bot. 2015;66(9):2595–2609.
   PubMed Web of Science ®Google Scholar
• Sun Q, Huang J, Guo Y, et al. A cotton NAC domain transcription factor, GhFSN5, negatively regulates secondary cell wall biosynthesis and anther development in transgenic Arabidopsis. Plant Physiol Biochem. 2020;146:303–314.
   PubMed Web of Science ®Google Scholar
• Li T, Yang S, Kang X, et al. The bHLH transcription factor gene AtUPB1 regulates growth by mediating cell cycle progression in Arabidopsis. Biochem Biophys Res Commun. 2019;518(3):565–572.
   PubMed Web of Science ®Google Scholar
• Safi A, Medici A, Szponarski W, et al. The world according to GARP transcription factors. Curr Opin Plant Biol. 2017;39:159–167.
   PubMed Web of Science ®Google Scholar
• Shen X, Hu Z, Xiang X, et al. Overexpression of a stamen-specific R2R3-MYB gene BcMF28 causes aberrant stamen development in transgenic Arabidopsis. Biochem Biophys Res Commun. 2019;518(4):726–731.
   PubMed Web of Science ®Google Scholar
• Yu LH, Miao ZQ, Qi GF, et al. MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals. Mol Plant. 2014;7(11):1653–1669.
   PubMed Web of Science ®Google Scholar
• De Folter S, Shchennikova AV, Franken J, et al. A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis. Plant J. 2006;47(6):934–946.
   PubMed Web of Science ®Google Scholar
• Ripoll JJ, Roeder AH, Ditta GS, et al. A novel role for the floral homeotic gene APETALA2 during Arabidopsis fruit development. Development. 2011;138(23):5167–5176.
   PubMed Web of Science ®Google Scholar
• Laity JH, Lee BM, Wright PE. Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol. 2001;11(1):39–46.
   PubMed Web of Science ®Google Scholar
• Segal DJ, Stege JT, Barbas IIC. Zinc fingers and a green thumb: manipulating gene expression in plants. Curr Opin Struct Biol. 2003;6(2):163–168.
   Google Scholar