Aihara, K., Naramoto, S., Hara, M., and Mizoguchi, T. (2014). Increase in vascular pattern complexity caused by mutations in LHY and CCA1 in Arabi- dopsis thaliana under continuous light. Plant Biotechnol. 31, 43–47. https:// doi.org/10.5511/plantbiotechnology.13.1015a.
Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11, R106. https://doi.org/10.1186/gb-2010-11-10- r106.
Bhadra, U., Thakkar, N., Das, P., and Pal Bhadra, M. (2017). Evolution of circa- dian rhythms: from bacteria to human. Sleep Med. 35, 49–61. https://doi.org/ 10.1016/j.sleep.2017.04.008.
Brown, S.A. (2014). Circadian clock-mediated control of stem cell division and differentiation: beyond night and day. Development 141, 3105–3111. https:// doi.org/10.1242/dev.104851.
Campbell, L., and Turner, S. (2017). Regulation of vascular cell division. J. Exp. Bot. 68, 27–43. https://doi.org/10.1093/jxb/erw448.
Collins, C., Maruthi, N.M., and Jahn, C.E. (2015). CYCD3 D-type cyclins regu- late cambial cell proliferation and secondary growth in Arabidopsis. J. Exp. Bot. 66, 4595–4606. https://doi.org/10.1093/jxb/erv218.
de Jager, S.M., Scofield, S., Huntley, R.P., Robinson, A.S., den Boer, B.G.W., and Murray, J.A.H. (2009). Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc. Plant Mol. Biol. 71, 345–365. https://doi.org/10.1007/s11103-009-9527-5.
De Veylder, L., Beeckman, T., and Inze´ , D. (2007). The ins and outs of the plant cell cycle. Nat. Rev. Mol. Cell Biol. 8, 655–665. https://doi.org/10.1038/ nrm2227.
Desvoyes, B., de Mendoza, A., Ruiz-Trillo, I., and Gutierrez, C. (2014). Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. J. Exp. Bot. 65, 2657–2666. https://doi.org/10. 1093/jxb/ert411.
Dewitte, W., Scofield, S., Alcasabas, A.A., Maughan, S.C., Menges, M., Braun, N., Collins, C., Nieuwland, J., Prinsen, E., Sundaresan, V., and Murray, J.A.H. (2007). Arabidopsis CYCD3 D-type cyclins link cell proliferation and endo- cycles and are rate-limiting for cytokinin responses. Proc. Natl. Acad. Sci. USA 104, 14537–14542. https://doi.org/10.1073/pnas.0704166104.
Dierickx, P., Van Laake, L.W., and Geijsen, N. (2018). Circadian clocks: from stem cells to tissue homeostasis and regeneration. EMBO Rep. 19, 18–28. https://doi.org/10.15252/embr.201745130.
Endo, M., Shimizu, H., Nohales, M.A., Araki, T., and Kay, S.A. (2014). Tissue- specific clocks in Arabidopsis show asymmetric coupling. Nature 515, 419–422. https://doi.org/10.1038/nature13919.
Ezer, D., Jung, J.H., Lan, H., Biswas, S., Gregoire, L., Box, M.S., Charoensa- wan, V., Cortijo, S., Lai, X., Sto¨ ckle, D., et al. (2017). The evening complex co- ordinates environmental and endogenous signals in Arabidopsis. Nat. Plants 3, 17087. https://doi.org/10.1038/nplants.2017.87.
Fukuda, H., Ukai, K., and Oyama, T. (2012). Self-arrangement of cellular circa- dian rhythms through phase-resetting in plant roots. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 86, 041917. https://doi.org/10.1103/PhysRevE.86.041917.
Fung-Uceda, J., Lee, K., Seo, P.J., Polyn, S., De Veylder, L., and Mas, P. (2018). The circadian clock sets the time of DNA replication licensing to regu- late growth in Arabidopsis. Dev. Cell 45, 101–113.e4. https://doi.org/10.1016/j. devcel.2018.02.022.
Golden, S.S., Ishiura, M., Johnson, C.H., and Kondo, T. (1997). Cyanobacterial circadian rhythms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 327–354. https://doi.org/10.1146/annurev.arplant.48.1.327.
Harashima, H., and Schnittger, A. (2010). The integration of cell division, growth and differentiation. Curr. Opin. Plant Biol. 13, 66–74. https://doi.org/ 10.1016/j.pbi.2009.11.001.
Helfer, A., Nusinow, D.A., Chow, B.Y., Gehrke, A.R., Bulyk, M.L., and Kay, S.A. (2011). LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr. Biol. 21, 126–133. https:// doi.org/10.1016/j.cub.2010.12.021.
Hut, R.A., and Beersma, D.G.M. (2011). Evolution of time-keeping mecha- nisms: early emergence and adaptation to photoperiod. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2141–2154. https://doi.org/10.1098/rstb.2010. 0409.
Inoue, K., Araki, T., and Endo, M. (2018). Oscillator networks with tissue-spe- cific circadian clocks in plants. Semin. Cell Dev. Biol. 83, 78–85. https://doi. org/10.1016/j.semcdb.2017.09.002.
Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lo¨ nner- berg, P., and Linnarsson, S. (2014). Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11, 163–166. https://doi.org/10. 1038/nmeth.2772.
Kang, C.Y., Lian, H.L., Wang, F.F., Huang, J.R., and Yang, H.Q. (2009). Cryp- tochromes, phytochromes, and COP1 regulate light-controlled stomatal development in Arabidopsis. Plant Cell 21, 2624–2641. https://doi.org/10. 1105/tpc.109.069765.
Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360. https://doi.org/10. 1038/nmeth.3317.
Kondo, Y., Ito, T., Nakagami, H., Hirakawa, Y., Saito, M., Tamaki, T., Shirasu, K., and Fukuda, H. (2014). Plant GSK3 proteins regulate xylem cell differenti- ation downstream of TDIF-TDR signalling. Nat. Commun. 5, 3504. https:// doi.org/10.1038/ncomms4504.
Kondo, Y., Nurani, A.M., Saito, C., Ichihashi, Y., Saito, M., Yamazaki, K., Mit- suda, N., Ohme-Takagi, M., and Fukuda, H. (2016). Vascular cell induction cul- ture system using Arabidopsis leaves (VISUAL) reveals the sequential differen- tiation of sieve element-like cells. Plant Cell 28, 1250–1262. https://doi.org/10. 1105/tpc.16.00027.
Kowalska, E., Moriggi, E., Bauer, C., Dibner, C., and Brown, S.A. (2010). The circadian clock starts ticking at a developmentally early stage. J. Biol. Rhythms 25, 442–449. https://doi.org/10.1177/0748730410385281.
Kubo, M., Nishiyama, T., Tamada, Y., Sano, R., Ishikawa, M., Murata, T., Imai, A., Lang, D., Demura, T., Reski, R., and Hasebe, M. (2019). Single-cell tran- scriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation. Nucleic Acids Res. 47, 4539–4553. https://doi. org/10.1093/nar/gkz181.
Kuwabara, A., and Gruissem, W. (2014). Arabidopsis RETINOBLASTOMA- RELATED and Polycomb group proteins: cooperation during plant cell differ- entiation and development. J. Exp. Bot. 65, 2667–2676. https://doi.org/10. 1093/jxb/eru069.
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. https://doi.org/10.1186/gb-2009-10-3-r25.
Li, L., Yu, X., Thompson, A., Guo, M., Yoshida, S., Asami, T., Chory, J., and Yin, Y. (2009). Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J. 58, 275–286. https://doi.org/10.1111/j.1365-313X.2008.03778.x.
Li, G., Siddiqui, H., Teng, Y., Lin, R., Wan, X.y., Li, J., Lau, O.S., Ouyang, X., Dai, M., Wan, J., et al. (2011). Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat. Cell Biol. 13, 616–622. https://doi.org/ 10.1038/ncb2219.
Li, Q.F., Lu, J., Yu, J.W., Zhang, C.Q., He, J.X., and Liu, Q.Q. (2018). The bras-sinosteroid-regulated transcription factors BZR1/BES1 function as a coordi- nator in multisignal-regulated plant growth. Biochim. Biophys. Acta Gene Regul. Mech. 1861, 561–571. https://doi.org/10.1016/j.bbagrm.2018.04.003.
Malucelli, F., Ottmann, T., and Pretolani, D. (1993). Efficient labelling algo- rithms for the maximum noncrossing matching problem. Discrete Appl. Math. 47, 175–179. https://doi.org/10.1007/978-3-642-77489-8_30.
Mermigka, G., Amprazi, M., Mentzelopoulou, A., Amartolou, A., and Sarris,P.F. (2020). Plant and animal innate immunity complexes: fighting different en- emies with similar weapons. Trends Plant Sci. 25, 80–91. https://doi.org/10. 1016/j.tplants.2019.09.008.
Michael, T.P., Mockler, T.C., Breton, G., McEntee, C., Byer, A., Trout, J.D., Ha- zen, S.P., Shen, R., Priest, H.D., Sullivan, C.M., et al. (2008). Network discovery pipeline elucidates conserved time-of-day–specific cis-regulatory modules. PLoS Genet. 4, e14. https://doi.org/10.1371/journal.pgen.0040014.
Nakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., Toyooka, K., Matsuoka, K., Jinbo, T., and Kimura, T. (2007). Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng. 104, 34–41. https://doi.org/10.1263/jbb.104.34.
Nelms, B., and Walbot, V. (2019). Defining the developmental program leading to meiosis in maize. Science 364, 52–56. https://doi.org/10.1126/science. aav6428.
Nishimura, T., Yokota, E., Wada, T., Shimmen, T., and Okada, K. (2003). An Arabidopsis ACT2 dominant-negative mutation, which disturbs F-actin poly- merization, reveals its distinctive function in root development. Plant Cell Physiol. 44, 1131–1140. https://doi.org/10.1093/pcp/pcg158.
Niwa, Y., Ito, S., Nakamichi, N., Mizoguchi, T., Niinuma, K., Yamashino, T., and Mizuno, T. (2007). Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabi- dopsis thaliana. Plant Cell Physiol. 48, 925–937. https://doi.org/10.1093/pcp/ pcm067.
Nusinow, D.A., Helfer, A., Hamilton, E.E., King, J.J., Imaizumi, T., Schultz, T.F., Farre´ , E.M., and Kay, S.A. (2011). The ELF4-ELF3-LUX complex links the circa- dian clock to diurnal control of hypocotyl growth. Nature 475, 398–402. https:// doi.org/10.1038/nature10182.
Paulose, J.K., Rucker, E.B., and Cassone, V.M. (2012). Toward the beginning of time: circadian rhythms in metabolism precede rhythms in clock gene expression in mouse embryonic stem cells. PLoS One 7, e49555. https:// doi.org/10.1371/journal.pone.0049555.
Quint, M., Drost, H.G., Gabel, A., Ullrich, K.K., Bo¨ nn, M., and Grosse, I. (2012). A transcriptomic hourglass in plant embryogenesis. Nature 490, 98–101. https://doi.org/10.1038/nature11394.
Ryu, K.H., Huang, L., Kang, H.M., and Schiefelbein, J. (2019). Single-cell RNA sequencing resolves molecular relationships among individual plant cells. Plant Physiol. 179, 1444–1456. https://doi.org/10.1104/pp.18.01482pp.18.01482.
Saito, M., Kondo, Y., and Fukuda, H. (2018). BES1 and BZR1 redundantly pro- mote phloem and xylem differentiation. Plant Cell Physiol. 59, 590–600. https://doi.org/10.1093/pcp/pcy012.
Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., and Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502. https://doi.org/10.1038/nbt.3192.
Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A., and Coupland, G. (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93, 1219–1229. https://doi.org/10.1016/S0092-8674(00)81465-8.
Setty, M., Tadmor, M.D., Reich-Zeliger, S., Angel, O., Salame, T.M., Kathail, P., Choi, K., Bendall, S., Friedman, N., and Pe’er, D. (2016). Wishbone iden- tifies bifurcating developmental trajectories from single-cell data. Nat. Bio- technol. 34, 637–645. https://doi.org/10.1038/nbt.3569.
Sharma, M., Pandey, A., and Pandey, G.K. (2014). b-catenin in plants and an- imals: common players but different pathways^I2-catenin in plants and animals: common players but different pathways. Front. Plant Sci. 5, 143. https://doi. org/10.3389/fpls.2014.00143.
Shimada, T.L., Shimada, T., and Hara-Nishimura, I. (2010). A rapid and non- destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana. Plant J. 61, 519–528. https://doi.org/10.1111/j.1365- 313X.2009.04060.x.
Shulse, C.N., Cole, B.J., Ciobanu, D., Lin, J., Yoshinaga, Y., Gouran, M., Turco, G.M., Zhu, Y., O’Malley, R.C., Brady, S.M., and Dickel, D.E. (2019). High- throughput single-cell transcriptome profiling of plant cell types. Cell Rep. 27, 2241–2247.e4. https://doi.org/10.1016/j.celrep.2019.04.054.
Sun, N., Yu, X., Li, F., Liu, D., Suo, S., Chen, W., Chen, S., Song, L., Green, C.D., McDermott, J., et al. (2017). Inference of differentiation time for single cell transcriptomes using cell population reference data. Nat. Commun. 8, 1856. https://doi.org/10.1038/s41467-017-01860-2.
Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T.W., Gaudinier, A., Young, N.F., Trabucco, G.M., Veling, M.T., Lamothe, R., et al. (2015). An Ara- bidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575. https://doi.org/10.1038/nature14099.
Tsuchiya, Y., Umemura, Y., and Yagita, K. (2020). Circadian clock and cancer: from a viewpoint of cellular differentiation. Int. J. Urol. 27, 518–524. https://doi. org/10.1111/iju.14231.
Voß, U., Wilson, M.H., Kenobi, K., Gould, P.D., Robertson, F.C., Peer, W.A., Lucas, M., Swarup, K., Casimiro, I., Holman, T.J., et al. (2015). The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nat. Commun. 6, 7641. https://doi.org/10.1038/ncomms8641.
Weger, M., Diotel, N., Dorsemans, A.C., Dickmeis, T., and Weger, B.D. (2017). Stem cells and the circadian clock. Dev. Biol. 431, 111–123. https://doi.org/10. 1016/j.ydbio.2017.09.012.
Yagita, K., Horie, K., Koinuma, S., Nakamura, W., Yamanaka, I., Urasaki, A., Shigeyoshi, Y., Kawakami, K., Shimada, S., Takeda, J., and Uchiyama, Y. (2010). Development of the circadian oscillator during differentiation of mouse embryonic stem cells in vitro. Proc. Natl. Acad. Sci. USA 107, 3846–3851. https://doi.org/10.1073/pnas.0913256107.
Yamaguchi, M., Mitsuda, N., Ohtani, M., Ohme-Takagi, M., Kato, K., and De- mura, T. (2011). VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J. 66, 579–590. https://doi.org/10.1111/j.1365-313X.2011.04514.x.
Yamaguchi, N., Winter, C.M., Wu, M.F., Kwon, C.S., William, D.A., and Wag- ner, D. (2014). PROTOCOLS: chromatin immunoprecipitation from Arabidop- sis tissues. Arabidopsis Book 12, e0170. https://doi.org/10.1199/tab.0170.
Yamazaki, K., Kondo, Y., Kojima, M., Takebayashi, Y., Sakakibara, H., and Fu- kuda, H. (2018). Suppression of DELLA signaling induces procambial cell for- mation in culture. Plant J. 94, 48–59. https://doi.org/10.1111/tpj.13840.
Yin, Y., Wang, Z.Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T., and Chory, J. (2002). BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109, 181–191. https://doi.org/10.1016/s0092-8674(02)00721-3.
Youn, J.H., and Kim, T.W. (2015). Functional insights of plant GSK3-like ki- nases: multi-taskers in diverse cellular signal transduction pathways. Mol. Plant 8, 552–565. https://doi.org/10.1016/j.molp.2014.12.006.
Yu, X., Li, L., Zola, J., Aluru, M., Ye, H., Foudree, A., Guo, H., Anderson, S., Aluru, S., Liu, P., et al. (2011). A brassinosteroid transcriptional network re- vealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J. 65, 634–646. https://doi.org/10.1111/j.1365-313X.2010. 04449.x.
Yu, X., Rollins, D., Ruhn, K.A., Stubblefield, J.J., Green, C.B., Kashiwada, M., Rothman, P.B., Takahashi, J.S., and Hooper, L.V. (2013). TH17 cell differenti- ation is regulated by the circadian clock. Science 342, 727–730. https://doi. org/10.1126/science.1243884.
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., and Liu, X.S. (2008). Model- based analysis of ChIP-seq (MACS). Genome Biol. 9, R137. https://doi.org/ 10.1186/gb-2008-9-9-r137.