Haberlandt G. Kulturversuche mit isolierten Pflanzenzellen. Sitzungsber Math-Naturwiss Kl Akad Wiss Wien. 1902;111:69–92.
Google Scholar
Steward FC, Mapes MO, Mears K. Growth and organized development of cultured cells. II. Organization in cultures grown from freely suspended cell. Am J Bot. 1958;45(10):705–8.
Article
Google Scholar
George EF. Plant tissue culture procedure - background. In: George EF, Hall MA, De Klerk GJ, editors. Plant propagation by tissue culture, vol. 1. 3rd ed. Dordrecht: Springer; 2008. p. 1–28.
Google Scholar
Espinosa-Leal CA, Puente-Garza CA, García-Lara S. In vitro plant tissue culture: means for production of biological active compounds. Planta. 2018;248(1):1–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Skoog F, Miller CO. Chemical regulation of growth and organ formation in plant tissues cultured in vitro. Symp Soc Exp Biol. 1957;11:118–30.
CAS
PubMed
Google Scholar
Raspor M, Motyka V, Kaleri AR, Ninković S, Tubić L, Cingel A, Ćosić T. Integrating the roles for cytokinin and auxin in de novo shoot organogenesis: from hormone uptake to signaling outputs. Int J Mol Sci. 2021;22(16):8554.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ikeuchi M, Favero DS, Sakamoto Y, Iwase A, Coleman D, Rymen B, et al. Molecular mechanisms of plant regeneration. Annu Rev Plant Biol. 2019;70(1):377–406.
Article
CAS
PubMed
Google Scholar
Fan M, Xu C, Xu K, Hu Y. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Res. 2012;22(7):1169–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daimon Y, Takabe K, Tasaka M. The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli. Plant Cell Physiol. 2003;44(2):113–21.
Article
CAS
PubMed
Google Scholar
Kareem A, Durgaprasad K, Sugimoto K, Du Y, Pulianmackal Ajai J, Trivedi Zankhana B, et al. PLETHORA genes control regeneration by a two-step mechanism. Curr Biol. 2015;25(8):1017–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meng WJ, Cheng ZJ, Sang YL, Zhang MM, Rong XF, Wang ZW, et al. Type-B ARABIDOPSIS RESPONSE REGULATORs specify the shoot stem cell niche by dual regulation of WUSCHEL. Plant Cell. 2017;29(6):1357–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang J, Tian C, Zhang C, Shi B, Cao X, Zhang T-Q, et al. Cytokinin signaling activates WUSCHEL expression during axillary meristem initiation. Plant Cell. 2017;29(6):1373–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang T-Q, Lian H, Zhou C-M, Xu L, Jiao Y, Wang J-W. A two-step model for de novo activation of WUSCHEL during plant shoot regeneration. Plant Cell. 2017;29(5):1073–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zubo YO, Blakley IC, Yamburenko MV, Worthen JM, Street IH, Franco-Zorrilla JM, et al. Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis. Proc Natl Acad Sci U S A. 2017;114(29):E5995–6004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shi B, Zhang C, Tian C, Wang J, Wang Q, Xu T, et al. Two-step regulation of a meristematic cell population acting in shoot branching in Arabidopsis. PLoS Genet. 2016;12(7):e1006168.
Article
PubMed
PubMed Central
CAS
Google Scholar
Che P, Lall S, Nettleton D, Howell SH. Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture. Plant Physiol. 2006;141(2):620–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang S, Poretska O, Sieberer T. ALTERED MERISTEM PROGRAM1 restricts shoot meristem proliferation and regeneration by limiting HD-ZIP III-mediated expression of RAP2.6L. Plant Physiol. 2018;177(4):1580–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ikeuchi M, Iwase A, Rymen B, Lambolez A, Kojima M, Takebayashi Y, et al. Wounding triggers callus formation via dynamic hormonal and transcriptional changes. Plant Physiol. 2017;175(3):1158–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iwase A, Mitsuda N, Koyama T, Hiratsu K, Kojima M, Arai T, et al. The AP2/ERF transcription factor WIND1 controls cell dedifferentiation in Arabidopsis. Curr Biol. 2011;21(6):508–14.
Article
CAS
PubMed
Google Scholar
Iwase A, Harashima H, Ikeuchi M, Rymen B, Ohnuma M, Komaki S, et al. WIND1 promotes shoot regeneration through transcriptional activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis. Plant Cell. 2017;29(1):54–69.
Article
CAS
PubMed
Google Scholar
Watad AA, Ahroni A, Zuker A, Shejtman H, Nissim A, Vainstein A. Adventitious shoot formation from carnation stem segments: a comparison of different culture procedures. Scientia Hortic. 1996;65(4):313–20.
Article
Google Scholar
Ajithkumar D, Seeni S. Rapid clonal multiplication through in vitro axillary shoot proliferation of Aegle marmelos (L.) Corr., a medicinal tree. Plant Cell Rep. 1998;17(5):422–6.
Article
CAS
PubMed
Google Scholar
Tiwari V, Tiwari KN, Singh BD. Comparative studies of cytokinins on in vitro propagation of Bacopa monniera. Plant Cell Tissue Organ Cult. 2001;66(1):9–16.
Article
CAS
Google Scholar
Rao MS, Purohit SD. In vitro shoot bud differentiation and plantlet regeneration in Celastrus paniculatus Willd. Biol Plant. 2006;50(4):501–6.
Article
CAS
Google Scholar
Sanikhani M, Frello S, Serek M. TDZ induces shoot regeneration in various Kalanchoë blossfeldiana Poelln. Cultivars in the absence of auxin. Plant Cell Tissue Organ Cult. 2006;85(1):75–82.
Article
CAS
Google Scholar
Yoshimatsu K, Shimomura K. Efficient shoot formation on internodal segments and alkaloid formation in the regenerates of Cephaelis ipecacuanha A. Richard. Plant Cell Rep. 1991;9(10):567–70.
Article
CAS
PubMed
Google Scholar
Chatterjee SK, Nandi RP, Ghosh NC. Cultivation and utilization of ipecac in west Bengal. In: Atal CK, Kapur BM, editors. Cultivation and utilization of medicinal plants. Jammu-Tawi: Regional Research Laboratory, Council of Scientific and Industrial Research; 1982. p. 295–301.
Google Scholar
Trease GE, Evans WC. Phamacognosy. 13th ed. London: Bailliere Tindall; 1989.
Google Scholar
Koike I, Taniguchi K, Shimomura K, Umehara M. Dynamics of endogenous indole-3-acetic acid and cytokinins during adventitious shoot formation in ipecac. J Plant Growth Regul. 2017;36(4):805–13.
Article
CAS
Google Scholar
Koike I, Watanabe S, Okazaki K, Hayashi KI, Kasahara H, Shimomura K, et al. Endogenous auxin determines the pattern of adventitious shoot formation on internodal segments of ipecac. Planta. 2020;251(3):73.
Article
CAS
PubMed
Google Scholar
Kakimoto T. Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 2001;42(7):677–85.
Article
CAS
PubMed
Google Scholar
Takei K, Sakakibara H, Sugiyama T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J Biol Chem. 2001;276(28):26405–10.
Article
CAS
PubMed
Google Scholar
Takei K, Yamaya T, Sakakibara H. Arabidopsis CYP735A1 and CYP735A2 encode cytokinin hydroxylases that catalyze the biosynthesis of trans-Zeatin. J Biol Chem. 2004;279(40):41866–72.
Article
CAS
PubMed
Google Scholar
Kuroha T, Tokunaga H, Kojima M, Ueda N, Ishida T, Nagawa S, et al. Functional analyses of LONELY GUY cytokinin-activating enzymes reveal the importance of the direct activation pathway in Arabidopsis. Plant Cell. 2009;21(10):3152–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, et al. Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature. 2007;445(7128):652–5.
Article
CAS
PubMed
Google Scholar
Yoneyama K, Mori N, Sato T, Yoda A, Xie X, Okamoto M, et al. Conversion of carlactone to carlactonoic acid is a conserved function of MAX1 homologs in strigolactone biosynthesis. New Phytol. 2018;218(4):1522–33.
Article
CAS
PubMed
Google Scholar
Duan J, Yu H, Yuan K, Liao Z, Meng X, Jing Y, et al. Strigolactone promotes cytokinin degradation through transcriptional activation of CYTOKININ OXIDASE/DEHYDROGENASE 9 in rice. Proc Natl Acad Sci U S A. 2019;116(28):14319–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Okazaki K, Watanabe S, Koike I, Kawada K, Ito S, Nakamura H, et al. Strigolactone signaling inhibition increases adventitious shoot formation on internodal segments of ipecac. Planta. 2021;253(6):123.
Article
CAS
PubMed
Google Scholar
Ito S, Umehara M, Hanada A, Kitahata N, Hayase H, Yamaguchi S, et al. Effects of triazole derivatives on strigolactone levels and growth retardation in rice. PLoS One. 2011;6(7):e21723.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kawada K, Takahashi I, Arai M, Sasaki Y, Asami T, Yajima S, et al. Synthesis and biological evaluation of novel triazole derivatives as strigolactone biosynthesis inhibitors. J Agric Food Chem. 2019;67(22):6143–9.
Article
CAS
PubMed
Google Scholar
Matsuo N, Makino M, Banno H. Arabidopsis ENHANCER OF SHOOT REGENERATION (ESR)1 and ESR2 regulate in vitro shoot regeneration and their expressions are differentially regulated. Plant Sci. 2011;181(1):39–46.
Article
CAS
PubMed
Google Scholar
Skirycz A, Radziejwoski A, Busch W, Hannah MA, Czeszejko J, Kwaśniewski M, et al. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J. 2008;56(5):779–92.
Article
CAS
PubMed
Google Scholar
Moghaddas Sani H, Hamzeh-Mivehroud M, Silva AP, Walshe JL, Mohammadi SA, Rahbar-Shahrouziasl M, et al. Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana. Bioimpacts. 2018;8(3):167–76.
Article
PubMed
PubMed Central
CAS
Google Scholar
Riou-Khamlichi C, Huntley R, Jacqmard A, Murray JAH. Cytokinin activation of Arabidopsis cell division through a D-type cyclin. Science. 1999;283(5407):1541–4.
Article
CAS
PubMed
Google Scholar
Menges M, Samland AK. Planchais Sv, Murray JAH: the D-type cyclin CYCD3;1 is limiting for the G1-to-S-phase transition in Arabidopsis. Plant Cell. 2006;18(4):893–906.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dewitte W, Scofield S, Alcasabas AA, Maughan SC, Menges M, Braun N, et al. Arabidopsis CYCD3 D-type cyclins link cell proliferation and endocycles and are rate-limiting for cytokinin responses. Proc Natl Acad Sci U S A. 2007;104(36):14537–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, et al. The main auxin biosynthesis pathway in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108(45):18512–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, et al. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108(45):18518–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shuai B, Reynaga-Peña CG, Springer PS. The lateral organ Boundaries gene defines a novel, plant-specific gene family. Plant Physiol. 2002;129(2):747–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aida M, Beis D, Heidstra R, Willemsen V, Blilou I, Galinha C, et al. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell. 2004;119(1):109–20.
Article
CAS
PubMed
Google Scholar
Lee HW, Kim NY, Lee DJ, Kim J. LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis. Plant Physiol. 2009;151(3):1377–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ckurshumova W, Smirnova T, Marcos D, Zayed Y, Berleth T. Irrepressible MONOPTEROS/ARF5 promotes de novo shoot formation. New Phytol. 2014;204(3):556–66.
Article
CAS
PubMed
Google Scholar
Anastasiou E, Kenz S, Gerstung M, MacLean D, Timmer J, Fleck C, et al. Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling. Dev Cell. 2007;13(6):843–56.
Article
CAS
PubMed
Google Scholar
Wang J-W, Schwab R, Czech B, Mica E, Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell. 2008;20(5):1231–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aida M, Tsubakimoto Y, Shimizu S, Ogisu H, Kamiya M, Iwamoto R, et al. Establishment of the embryonic shoot meristem involves activation of two classes of genes with opposing functions for meristem activities. Int J Mol Sci. 2020;21(16):5864.
Article
CAS
PubMed Central
Google Scholar
Banno H, Ikeda Y, Niu Q-W, Chua N-H. Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell. 2001;13(12):2609–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Staswick PE, Serban B, Rowe M, Tiryaki I. Maldonado MnT, Maldonado MC, Suza W: characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell. 2005;17(2):616–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang W, Schuster C, Beahan CT, Charoensawan V, Peaucelle A, Bacic A, et al. Regulation of meristem morphogenesis by cell wall synthases in Arabidopsis. Curr Biol. 2016;26(11):1404–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iwase A, Mita K, Favero DS, Mitsuda N, Sasaki R, Kobayshi M, et al. WIND1 induces dynamic metabolomic reprogramming during regeneration in Brassica napus. Dev Biol. 2018;442(1):40–52.
Article
CAS
PubMed
Google Scholar
Larriba E, Sánchez-García AB, Justamante MS, Martínez-Andújar C, Albacete A, Pérez-Pérez JM. Dynamic hormone gradients regulate wound-induced de novo organ formation in tomato hypocotyl explants. Int J Mol Sci. 2021;22(21):11843.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maeda Y, Konishi M, Kiba T, Sakuraba Y, Sawaki N, Kurai T, et al. A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis. Nat Commun. 2018;9(1):1376.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gamborg OL, Miller RA, Ojima K. Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res. 1968;50(1):151–8.
Article
CAS
PubMed
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1):10–2.
Article
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512.
Article
CAS
PubMed
Google Scholar
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2.
Article
PubMed
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 2013;10(1):71–3.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26(1):139–40.
Article
PubMed
PubMed Central
CAS
Google Scholar
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11(3):R25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–6.
Article
CAS
PubMed
Google Scholar
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523.
Article
PubMed
PubMed Central
CAS
Google Scholar