Acosta, K., Appenroth, K.J., Borisjuk, L., Edelman, M., Heinig, U., Jansen, M.A.K., Oyama, T., Pasaribu, B., Schubert, I., Sorrels, S., et al. (2021). Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era. Plant Cell 33, 3207–3234. https://doi.org/10. 1093/plcell/koab189.
Alonso-Blanco, C., Aarts, M.G.M., Bentsink, L., Keurentjes, J.J.B., Reymond, M., Vreugdenhil, D., and Koornneef, M. (2009). What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21, 1877– 1896. https://doi.org/10.1105/tpc.109.068114.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. https://doi. org/10.1016/s0022-2836(05)80360-2.
Aschoff, J., and Pohl, H. (1978). Phase relations between a circadian rhythm and its zeitgeber within the range of entrainment. Naturwissenschaften 65, 80–84. https://doi.org/ 10.1007/bf00440545.
Barrett, R.D.H., and Schluter, D. (2008). Adaptation from standing genetic variation. Trends Ecol. Evol. 23, 38–44. https://doi.org/10. 1016/j.tree.2007.09.008.
Beppu, T., and Takimoto, A. (1981). Geographical distribution and cytological variation ofLemna paucicostata Hegelm. in Japan. Bot. Mag. Tokyo 94, 11–20. https://doi.org/10.1007/bf02490199.
Bo¨ hlenius, H., Huang, T., Charbonnel-Campaa, L., Brunner, A.M., Jansson, S., Strauss, S.H., and Nilsson, O. (2006). CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312, 1040–1043. https://doi.org/10.1126/science.1126038.
Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170.
Boyle, E.A., Li, Y.I., and Pritchard, J.K. (2017). An expanded view of complex traits: from polygenic to omnigenic. Cell 169, 1177–1186. https://doi. org/10.1016/j.cell.2017.05.038.
Brown, S.A., Kunz, D., Dumas, A., Westermark, P.O., Vanselow, K., Tilmann-Wahnschaffe, A., Herzel, H., and Kramer, A. (2008). Molecular insights into human daily behavior. Proc. Natl. Acad. Sci. USA 105, 1602–1607. https://doi.org/ 10.1073/pnas.0707772105.
Dixon, L.E., Hodge, S.K., van Ooijen, G., Troein, C., Akman, O.E., and Millar, A.J. (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytol. 203, 568–577. https://doi.org/10.1111/ nph.12853.
Dominoni, D.M., Helm, B., Lehmann, M., Dowse, H.B., and Partecke, J. (2013). Clocks for the city: circadian differences between forest and city songbirds. Proc. Biol. Sci. 280, 20130593. https:// doi.org/10.1098/rspb.2013.0593.
Feiner, N., Brun-Usan, M., and Uller, T. (2021). Evolvability and evolutionary rescue. Evol. Dev. 23, 308–319. https://doi.org/10.1111/ede.12374.
Fujita, G., Naoe, S., and Miyashita, T. (2015). Modernization of drainage systems decreases gray-faced buzzard occurrence by reducing frog densities in paddy-dominated landscapes. Landsc. Ecol. Eng. 11, 189–198. https://doi.org/ 10.1007/s11355-014-0263-x.
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011). Full- length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652. https://doi.org/10.1038/ nbt.1883.
Graf, A., Schlereth, A., Stitt, M., and Smith, A.M. (2010). Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc. Natl. Acad. Sci. USA 107, 9458–9463. https://doi.org/10.1073/pnas.0914299107.
Granada, A.E., Bordyugov, G., Kramer, A., and Herzel, H. (2013). Human chronotypes from a theoretical perspective. PLoS One 8, e59464. https://doi.org/10.1371/journal.pone.0059464.
Greenham, K., Lou, P., Puzey, J.R., Kumar, G., Arnevik, C., Farid, H., Willis, J.H., and McClung, C.R. (2017). Geographic variation of plant circadian clock function in natural and agricultural settings. J. Biol. Rhythms 32, 26–34. https://doi. org/10.1177/0748730416679307.
Greenham, K., and McClung, C.R. (2015). Integrating circadian dynamics with physiological processes in plants. Nat. Rev. Genet. 16, 598–610. https://doi.org/10.1038/nrg3976.
Hamann, E., Pauli, C.S., Joly-Lopez, Z., Groen, S.C., Rest, J.S., Kane, N.C., Purugganan, M.D., and Franks, S.J. (2021). Rapid evolutionary changes in gene expression in response to climate fluctuations. Mol. Ecol. 30, 193–206. https://doi.org/10.1111/mec.15583.
Hayama, R., Yokoi, S., Tamaki, S., Yano, M., and Shimamoto, K. (2003). Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422, 719–722. https://doi.org/10.1038/nature01549.
Helm, B., Visser, M.E., Schwartz, W., Kronfeld- Schor, N., Gerkema, M., Piersma, T., and Bloch, G. (2017). Two sides of a coin: ecological and chronobiological perspectives of timing in the wild. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160246. https://doi.org/10.1098/rstb.2016. 0246.
Hut, R.A., Paolucci, S., Dor, R., Kyriacou, C.P., and Daan, S. (2013). Latitudinal clines: an evolutionary view on biological rhythms. Proc. Biol. Sci. 280, 20130433. https://doi.org/10.1098/rspb.2013. 0433.
Ihaka, R., and Gentleman, R. (1996). R: a language for data analysis and graphics. J. Comput. Graph Stat. 5, 299–314. https://doi.org/10.1080/ 10618600.1996.10474713.
Imamura, S.-I., Muramatsu, M., Kitajo, S.I., and Takimoto, A. (1966). Varietal difference in photoperiodic behavior of pharbitis nil. Mag. Tokyo 79, 714–721. https://doi.org/10.15281/ jplantres1887.79.714.
Isoda, M., Ito, S., and Oyama, T. (2022). Interspecific divergence of circadian properties in duckweed plants. Plant Cell Environ. 45, 1942– 1953. https://doi.org/10.1111/pce.14297.
Hirschie Johnson, C., Elliott, J.A., and Foster, R. (2003). Entrainment of circadian programs. Chronobiol. Int. 20, 741–774. https://doi.org/10. 1081/cbi-120024211.
Karimi, M., Inze´ , D., and Depicker, A. (2002). GATEWAY™ vectors for Agrobacterium-medi- ated plant transformation. Trends Plant Sci. 7, 193–195. https://doi.org/10.1016/s1360-1385(02) 02251-3.
Katayama, N., Baba, Y.G., Kusumoto, Y., and Tanaka, K. (2015). A review of post-war changes in rice farming and biodiversity in Japan. Agric. Syst. 132, 73–84. https://doi.org/10.1016/j.agsy.2014. 09.001.
Katayama, T. (1977). Studies on the photoperiodism in the genus oryza. Jpn. Agric. Res. Q. 11, 12–17.
Landolt, E. (1986). Biosystematic investigation in the family of duckweeds (‘‘Lemnaceae’’). Vol. 2: the family of ‘‘Lemnaceae’’ - a monographic study. Volume 1. Vero¨ ffentlichungen des Geobotanischen Institutes der ETH, Stiftung Rubel, Zu¨ rich 78, 142–146.
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359. https://doi.org/10.1038/ nmeth.1923.
Lankinen, P. (1993). North–south differences in circadian eclosion rhythm in European populations of Drosophila subobscura. Heredity 71, 210–218. https://doi.org/10.1038/hdy.1993. 126.
Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323. https://doi.org/10.1186/ 1471-2105-12-323. Matuszewski, S., Hermisson, J., and Kopp, M. (2015). Catch me if you can: adaptation from standing genetic variation to a moving phenotypic optimum. Genetics 200, 1255–1274. https://doi.org/10.1534/genetics.115.178574.
Meng, X., Muszynski, M.G., and Danilevskaya, O.N. (2011). The FT-like ZCN8 gene functions as a floral activator and is involved in photoperiod sensitivity in maize. Plant Cell 23, 942–960. https://doi.org/10.1105/tpc.110.081406.
Michael, T.P., Park, S., Kim, T.-S., Booth, J., Byer, A., Sun, Q., Chory, J., and Lee, K. (2007). Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock. PLoS One 2, e795. https://doi. org/10.1371/journal.pone.0000795.
Michael, T.P., Salome´ , P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., McPeek, M.A., Alonso, J.M., Ecker, J.R., and McClung, C.R. (2003). Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302, 1049–1053. https://doi.org/10.1126/science.1082971.
Miwa, K., Serikawa, M., Suzuki, S., Kondo, T., and Oyama, T. (2006). Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses. Plant Cell Physiol. 47, 601–612. https://doi.org/10.1093/ pcp/pcj027.
Mu¨ ller, N.A., Wijnen, C.L., Srinivasan, A., Ryngajllo, M., Ofner, I., Lin, T., Ranjan, A., West, D., Maloof, J.N., Sinha, N.R., et al. (2016). Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat. Genet. 48, 89–93. https://doi.org/10.1038/ng.3447.
Muranaka, T., Okada, M., Yomo, J., Kubota, S., and Oyama, T. (2015). Characterisation of circadian rhythms of various duckweeds. Plant Biol. 17, 66–74.
Muranaka, T., and Oyama, T. (2016). Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles. Sci. Adv. 2, e1600500. https://doi.org/10.1126/ sciadv.1600500.
Nagel, D.H., and Kay, S.A. (2012). Complexity in the wiring and regulation of plant circadian networks. Curr. Biol. 22, R648–R657. https://doi. org/10.1016/j.cub.2012.07.025.
Nakamichi, N., Ito, S., Oyama, T., Yamashino, T., Kondo, T., and Mizuno, T. (2004). Characterization of plant circadian rhythms by employing Arabidopsis cultured cells with bioluminescence reporters. Plant Cell Physiol. 45, 57–67. https:// doi.org/10.1093/pcp/pch003.
Natuhara, Y. (2013). Ecosystem services by paddy fields as substitutes of natural wetlands in Japan. Ecol. Eng. 56, 97–106. https://doi.org/10.1016/j. ecoleng.2012.04.026.
Pittendrigh, C.S. (1960). Circadian rhythms and the circadian organization of living systems. Cold Spring Harb. Symp. Quant. Biol. 25, 159–184. https://doi.org/10.1101/sqb.1960.025.01.015.
Pivarciova, L., Vaneckova, H., Provaznik, J., Wu, B.C.-H., Pivarci, M., Peckova, O., Bazalova, O., Cada, S., Kment, P., Kotwica-Rolinska, J., and Dolezel, D. (2016). Unexpected geographic variability of the free running period in the linden bug Pyrrhocoris apterus. J. Biol. Rhythms 31, 568–576. https://doi.org/10.1177/ 0748730416671213.
Qin, Z., Bai, Y., Muhammad, S., Wu, X., Deng, P., Wu, J., An, H., and Wu, L. (2019). Divergent roles of FT-like 9 in flowering transition under different day lengths in Brachypodium distachyon. Nat. Commun. 10, 812. https://doi.org/10.1038/ s41467-019-08785-y.
Ray, P.M., and Alexander, W.E. (1966). Photoperiodic adaptation to latitude in Xanthium strumarium. Am. J. Bot. 53, 806–816. https://doi. org/10.1002/j.1537-2197.1966.tb06837.x.
Rees, H., Joynson, R., Brown, J.K.M., and Hall, A. (2021). Naturally occurring circadian rhythm variation associated with clock gene loci in Swedish Arabidopsis accessions. Plant Cell Environ. 44, 807–820. https://doi.org/10.1111/ pce.13941.
Re´ mi, J., Merrow, M., and Roenneberg, T. (2010). A circadian surface of entrainment: varying T, t, and photoperiod in Neurospora crassa. J. Biol. Rhythms 25, 318–328. https://doi.org/10.1177/ 0748730410379081.
Rieseberg, L.H., Widmer, A., Arntz, A.M., Burke, B., Carr, D.E., Abbott, R.J., and Meagher, T.R. (2003). The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358, 1141–1147. https://doi.org/10.1098/rstb.2003.1283.
Saini, R., Jaskolski, M., and Davis, S.J. (2019). Circadian oscillator proteins across the kingdoms of life: structural aspects. BMC Biol. 17, 13. https://doi.org/10.1186/s12915-018-0623-3.
Salmela, M.J., and Weinig, C. (2019). The fitness benefits of genetic variation in circadian clock regulation. Curr. Opin. Plant Biol. 49, 86–93. https://doi.org/10.1016/j.pbi.2019.06.003.
Sawa, M., Nusinow, D.A., Kay, S.A., and Imaizumi, T. (2007). FKF1 and GIGANTEA complex forma- tion is required for day-length measurement in Arabidopsis. Science 318, 261–265. https://doi. org/10.1126/science.1146994.
Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675. https://doi. org/10.1038/nmeth.2089.
Sella, G., and Barton, N.H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annu. Rev. Genomics Hum. Genet. 20, 461–493. https://doi. org/10.1146/annurev-genom-083115-022316.
Selmecki, A.M., Maruvka, Y.E., Richmond, P.A., Guillet, M., Shoresh, N., Sorenson, A.L., De, S., Kishony, R., Michor, F., Dowell, R., and Pellman, D. (2015). Polyploidy can drive rapid adaptation in yeast. Nature 519, 349–352. https://doi.org/10. 1038/nature14187.
Se´ mon, M., and Wolfe, K.H. (2007). Consequences of genome duplication. Curr. Opin. Genet. Dev. 17, 505–512. https://doi.org/ 10.1016/j.gde.2007.09.007.
Steed, G., Ramirez, D.C., Hannah, M.A., and Webb, A.A.R. (2021). Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 372, eabc9141. https://doi. org/10.1126/science.abc9141.
Sua´ rez-Lo´ pez, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., and Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410, 1116–1120. https://doi. org/10.1038/35074138.
Sun, L., Dong, A., Griffin, C., and Wu, R. (2021). Statistical mechanics of clock gene networks underlying circadian rhythms. Appl. Phys. Rev. 8, 021313. https://doi.org/10.1063/5.0029993.
Townsley, B.T., Covington, M.F., Ichihashi, Y., Zumstein, K., and Sinha, N.R. (2015). BrAD-seq: breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front. Plant Sci. 6, 366. https://doi.org/10.3389/fpls.2015.00366. Urbanova´ , V., Bazalova´ , O., Vaneˇˇckova´ , H., and Dolezel, D. (2016). Photoperiod regulates growth of male accessory glands through juvenile hormone signaling in the linden bug, Pyrrhocoris apterus. Insect. Biochem. Mol. Biol. 70, 184–190. https://doi.org/10.1016/j.ibmb. 2016.01.003.
Wang, W., Kerstetter, R.A., and Michael, T.P. (2011). Evolution of genome size in duckweeds (lemnaceae). J. Bot. 2011, 1–9. https://doi.org/10. 1155/2011/570319.
Yanovsky, M.J., and Kay, S.A. (2002). Molecular basis of seasonal time measurement in Arabidopsis. Nature 419, 308–312. https://doi. org/10.1038/nature00996.
Yoshida, A., Taoka, K.-I., Hosaka, A., Tanaka, K., Kobayashi, H., Muranaka, T., Toyooka, K., Oyama, T., and Tsuji, H. (2021). Characterization of frond and flower development and identification of FT and FD genes from duckweed Lemna aequinoctialis Nd. Front. Plant Sci. 12, 697206. https://doi.org/10.3389/fpls.2021.697206.
Yukawa, I., and Takimoto, A. (1976). Flowering response of Lemna paucicostata in Japan. Bot. Mag. Tokyo 89, 241–250. https://doi.org/10. 1007/bf02488346.
Zhang, X., Henriques, R., Lin, S.-S., Niu, Q.-W., and Chua, N.-H. (2006). Agrobacterium- mediated transformation of Arabidopsis thaliana using the floral dip method. Nat. Protoc. 1, 641–646. https://doi.org/10.1038/nprot.2006.97.
Zielinski, T., Moore, A.M., Troup, E., Halliday, K.J., and Millar, A.J. (2014). Strengths and limitations of period estimation methods for circadian data. PLoS One 9, e96462. https://doi.org/10.1371/ journal.pone.0096462.
論文の公開元へ
