Comparative Transcriptome Analysis of Gene Expression Patterns in Tomato Under Dynamic Light Conditions

Agriculture Organization (FAO) of the United Nations (2014). OECD-FAO Agricultural Outlook 2013–2022, OECD Publishing.

Fu, 2017, Interaction effects of light intensity and nitrogen concentration on growth, photosynthetic characteristics and quality of lettuce (Lactuca sativa L. Var. youmaicai), Sci. Hortic., 214, 51, 10.1016/j.scienta.2016.11.020

Sago, 2016, Effects of light intensity and growth rate on tipburn development and leaf calcium concentration in butterhead lettuce, HortScience, 51, 1087, 10.21273/HORTSCI10668-16

Fan, 2013, Effects of light intensity on the growth and leaf development of young tomato plants grown under a combination of red and blue light, Sci. Hortic., 153, 50, 10.1016/j.scienta.2013.01.017

Manivannan, 2015, Blue LED light enhances growth, phytochemical contents, and antioxidant enzyme activities of Rehmannia glutinosa cultured in vitro, Hortic. Environ. Biotechnol., 56, 105, 10.1007/s13580-015-0114-1

Peng, X., Wang, T., Li, X., and Liu, S. (2017). Effects of light quality on growth, total gypenosides accuulation and photosynthesis in gynostemma pentaphyllum. Bot. Sci., 95.

Kang, 2013, Light intensity and photoperiod influence the growth and development of hydroponically grown leaf lettuce in a closed-type plant factory system, Hortic Environ. Biotechnol., 54, 501, 10.1007/s13580-013-0109-8

Zha, 2017, Effects of light quality, light intensity, and photoperiod on growth and yield of cherry radish grown under red plus blue LEDs, China Illum. Eng. J., 59, 511

Jokinen, 2017, Effects of HPS and LED lighting on cucumber leaf photosynthesis, light quality penetration and temperature in the canopy, plant morphology and yield, Agric. Food Sci., 26, 102

Zhang, 2018, Effects of environment lighting on the growth, photosynthesis, and quality of hydroponic lettuce in a plant factory, Int. J. Agric. Biol. Eng., 11, 33

Zupok, 2017, Thioredoxins play a crucial role in dynamic acclimation of photosynthesis in fluctuating light, Mol. Plant, 10, 168, 10.1016/j.molp.2016.11.012

Philipp, 2012, Acclimatory responses of Arabidopsis to fluctuating light environment: Comparison of different sunfleck regimes and accessions, Photosynth. Res., 113, 221, 10.1007/s11120-012-9757-2

Allahverdiyeva, 2015, Photoprotection of photosystems in fluctuating light intensities, J. Exp. Bot., 66, 2427, 10.1093/jxb/eru463

Huxley, 1969, The effect of fluctuating light intensity on plant growth, J. Appl. Ecol., 6, 273, 10.2307/2401541

Rascher, 2006, Dynamics of photosynthesis in fluctuating light—Commentary, Curr. Opin. Plant Biol., 9, 671, 10.1016/j.pbi.2006.09.012

Slattery, 2018, The impacts of fluctuating light on crop performance, Plant Physiol., 176, 990, 10.1104/pp.17.01234

Yin, 2000, Photosynthetic acclimation of higher plants to growth in fluctuating light environments, Photosynth. Res., 63, 97, 10.1023/A:1006303611365

Wagner, 2006, Balancing the energy flow from captured light to biomass under fluctuating light conditions, New Phytol., 169, 95, 10.1111/j.1469-8137.2005.01550.x

Renata, 2015, Exploiting heterogeneous environments: Does photosynthetic acclimation optimize carbon gain in fluctuating light?, J. Exp. Bot., 66, 2437, 10.1093/jxb/erv055

Matthews, 2017, Importance of fluctuations in light on plant photosynthetic acclimation, Plant Physiol., 173, 2163, 10.1104/pp.16.01767

Peri, 2007, Morphological, anatomical, and physiological changes of orchardgrass leaves grown under fluctuating light regimes, Agron. J., 99, 1502, 10.2134/agronj2006.0347

Jansson, 2002, Rapid regulation of light harvesting and plant fitness in the field, Science, 297, 91, 10.1126/science.1072359

Zhu, 2010, Improving photosynthetic efficiency for greater yield, Annu. Rev. Plant Biol., 61, 235, 10.1146/annurev-arplant-042809-112206

Sato, R., Kono, M., Harada, K., Ohta, H., Takaichi, S., and Masuda, S. (2017). Fluctuating-Light-Acclimation Protein1, conserved in oxygenic phototrophs, regulates H+ homeostasis and non-photochemical quenching in chloroplasts. Plant Cell Physiol.

Kromdijk, 2016, Improving photosynthesis and crop productivity by accelerating recovery from photoprotection, Science, 354, 857, 10.1126/science.aai8878

Li, 2009, Sensing and Responding to Excess Light, Annu. Rev. Plant Boil., 60, 239, 10.1146/annurev.arplant.58.032806.103844

Nikkanen, 2014, Thioredoxin-dependent regulatory networks in chloroplasts under fluctuating light conditions, Philos. Trans. R. Soc. B Biol. Sci., 369, 20130224, 10.1098/rstb.2013.0224

Morales, 2018, Dynamic modelling of limitations on improving leaf CO2 assimilation under fluctuating irradiance, Plant Cell Environ., 41, 589, 10.1111/pce.13119

Schneider, 2019, Fluctuating light interacts with time of day and leaf development stage to reprogram gene expression, Plant Physiol., 179, 1632, 10.1104/pp.18.01443

Lichtenthaler, 1983, Determinations of total carotenoids and chlorophylls a and b of leaf extracts in different solvents, Analysis, 11, 591

Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923

Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S.L. (2013). TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14.

Trapnell, 2014, Erratum: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat. Protoc., 9, 2513, 10.1038/nprot1014-2513a

Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.

Van der Auwera, G.A., Carneiro, M.O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., and Thibault, J. (2013). From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinform., 43.

Wang, 2010, ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res., 38, e164, 10.1093/nar/gkq603

Kanehisa, 2007, KEGG for linking genomes to life and the environment, Nucleic Acids Res., 36, D480, 10.1093/nar/gkm882

Robinson, 2010, edgeR: A Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616

McCarthy, 2012, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res., 40, 4288, 10.1093/nar/gks042

Bos, 2000, Morphological analysis of leaf growth of maize: Responses to temperature and light intensity, NJAS-Wagening. J. Life Sci., 48, 181, 10.1016/S1573-5214(00)80013-5

Deng, 2012, Integrated effects of light intensity and fertilization on growth and flavonoid accumulation in Cyclocarya paliurus, J. Agric. Food Chem., 60, 6286, 10.1021/jf301525s

Hogewoning, 2010, Blue light dose-responses of leaf photosynthesis, morphology, and chemical composition of Cucumis sativus grown under different combinations of red and blue light, J. Exp. Bot., 61, 3107, 10.1093/jxb/erq132

Li, 2019, Effect of supplemental blue light intensity on the growth and quality of Chinese kale, Hortic Environ. Biotechnol., 60, 49, 10.1007/s13580-018-0104-1

Sanchez, 2011, Abiotic stress and the plant circadian clock, Plant Signal. Behav., 6, 223, 10.4161/psb.6.2.14893

Zervoudakis, 2012, Influence of light intensity on growth and physiological characteristics of Common Sage (Salvia officinalis L.), Braz. Arch. Biol. Technol., 55, 89, 10.1590/S1516-89132012000100011

Kaiser, 2018, Fluctuating light takes crop photosynthesis on a rollercoaster ride, Plant Physiol., 176, 977, 10.1104/pp.17.01250

Michelet, L., Zaffagnini, M., Morisse, S., Sparla, F., Perez-Perez, M.E., Francia, F., Danon, A., Marchand, C.H., Fermani, S., and Trost, P. (2013). Redox regulation of the Calvin—Benson cycle: Something old, something new. Front Plant Sci., 4.

Naranjo, 2016, Type-f thioredoxins have a role in the short-term activation of carbon metabolism and their loss affects growth under short-day conditions in Arabidopsis thaliana, J. Exp. Bot., 67, 1951, 10.1093/jxb/erw017

Bailey, 2001, Acclimation of Arabidopsis thaliana to the light environment: The existence of separate low light and high light responses, Planta, 213, 794, 10.1007/s004250100556

Ballottari, 2007, Contrasting behavior of higher plant photosystem I and II antenna systems during acclimation, J. Biol. Chem., 282, 8947, 10.1074/jbc.M606417200

Ljudmila, 2007, The roles of specific xanthophylls in light utilization, Planta, 225, 423

Kurepin, 2007, Uncoupling light quality from light irradiance effects in Helianthus annuus shoots: Putative roles for plant hormones in leaf and internode growth, J. Exp. Bot., 58, 2145, 10.1093/jxb/erm068

Franklin, 2005, Phytochromes and shade-avoidance responses in plants, Ann. Bot., 96, 169, 10.1093/aob/mci165

Monica, 2007, Post-translational modifications regulate the ticking of the circadian clock, Nat. Rev. Mol. Cell Biol., 8, 139, 10.1038/nrm2106

Nakamichi, 2016, Improvement of Arabidopsis biomass and cold-, drought-, and salinity-stress tolerance by modified circadian clock-associated PSEUDO-RESPONSE REGULATORs, Plant Cell Physiol., 57, 1085, 10.1093/pcp/pcw057

Millar, 2005, The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development, Plant Cell, 17, 705, 10.1105/tpc.104.027920

Brownfield, L., Hafidh, S., Borg, M., Sidorova, A., Mori, T., Twell, D., and Copenhaver, G.P. (2009). A plant germline-specific integrator of sperm specification and cell cycle progression. PLoS Genet., 5.

Urao, 1993, An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence, Plant Cell, 5, 1529

Chapple, 2001, AtMYB4: A transcription factor general in the battle against UV, Trends Plant Sci., 6, 135, 10.1016/S1360-1385(01)01915-X

Nagaoka, 2003, Salt tolerance-related protein STO binds to a MYB transcription factor homologue and confers salt tolerance in Arabidopsis, J. Exp. Bot., 54, 2231, 10.1093/jxb/erg241

Agarwal, 2006, A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance, J. Biol. Chem., 281, 37636, 10.1074/jbc.M605895200

Shen, 2017, PacMYBA, a sweet cherry R2R3-MYB transcription factor, is a positive regulator of salt stress tolerance and pathogen resistance, Plant Physiol Biochem., 112, 302, 10.1016/j.plaphy.2017.01.015

Alam, 2015, Cucumber necrosis virus recruits cellular heat shock protein 70 homologs at several stages of infection, J. Virol., 90, 3302, 10.1128/JVI.02833-15

Frydman, 2001, Folding of newly translated proteins In Vivo: The role of molecular chaperones, Annu. Rev. Biochem., 70, 603, 10.1146/annurev.biochem.70.1.603

Taipale, 2010, HSP90 at the hub of protein homeostasis: Emerging mechanistic insights, Nat. Rev. Mol. Cell Biol., 11, 515, 10.1038/nrm2918

Young, 2004, Pathways of chaperone-mediated protein folding in the cytosol, Nat. Rev. Mol. Cell Biol., 5, 781, 10.1038/nrm1492

Xie, 2014, The role of R2R3MYB transcription factors in plant stress tolerance, J. Anim. Plant Sci., 24, 1821

Kissoudis, C., Seifi, A., Yan, Z., Islam, A.T., van der Schoot, H., van de Wiel, C.C., Visser, R.G., van der Linden, C.G., and Bai, Y. (2016). Ethylene and abscisic acid signaling pathways differentially influence tomato resistance to combined powdery mildew and salt stress. Front. Plant Sci., 7.

Wu, 2017, Shade inhibits leaf size by controlling cell proliferation and enlargement in soybean, Sci. Rep., 7, 9259, 10.1038/s41598-017-10026-5

Sandalio, 2016, Leaf epinasty and auxin: A biochemical and molecular overview, Plant Sci., 253, 187, 10.1016/j.plantsci.2016.10.002

Osterlund, 2000, Targeted destabilization of HY5 during light-regulated development of Arabidopsis, Nature, 405, 462, 10.1038/35013076

Nakazawa, 2010, DFL1, an auxin-responsive GH3 gene homologue, negatively regulates shoot cell elongation and lateral root formation, and positively regulates the light response of hypocotyl length, Plant J., 25, 213

Vandenbussche, 2005, Reaching out of the shade, Curr. Opin. Plant Biol., 8, 462, 10.1016/j.pbi.2005.07.007

Tanaka, 2010, Overexpression of chlorophyllide a oxygenase (CAO) enlarges the antenna size of photosystem II in Arabidopsis thaliana, Plant J., 26, 365, 10.1046/j.1365-313X.2001.2641034.x

Spangfort, 1995, Chlorophyll a/b-binding proteins, pigment conversions, and early light- induced proteins in a chlorophyll b-less barley mutant, Plant Physiol., 107, 873, 10.1104/pp.107.3.873

Espineda, 1999, The AtCAO gene, encoding chlorophyll a oxygenase, is required for chlorophyll b synthesis in Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA, 96, 10507, 10.1073/pnas.96.18.10507

Sobotka, 2013, Inhibition of chlorophyll biosynthesis at the protochlorophyllide reduction step results in the parallel depletion of Photosystem I and Photosystem II in the cyanobacterium Synechocystis PCC, Planta, 237, 497, 10.1007/s00425-012-1761-4

Izui, 2004, Phosphoenolpyruvate carboxylase: A new era of structural biology, Annu. Rev. Plant Biol., 55, 69, 10.1146/annurev.arplant.55.031903.141619

Park, 2011, The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): Recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs, Biochem. J., 436, 15, 10.1042/BJ20110078

2000, Physiological implications of the kinetics of maize leaf phosphoenolpyruvate carboxylase, Plant Physiol., 123, 149, 10.1104/pp.123.1.149

Westhoff, 2000, Evolution of C4 phosphoenolpyruvate carboxylase in flaveria, a conserved serine residue in the carboxyl-terminal part of the enzyme is a major determinant for C4-specific characteristics, J. Biol. Chem., 275, 27917, 10.1074/jbc.M909832199

Peroza, 2015, A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics, Anal. Biochem., 474, 1, 10.1016/j.ab.2014.12.019

Schluepmann, 2012, Metabolism control over growth: A case for trehalose-6-phosphate in plants, J. Exp. Bot., 63, 3379, 10.1093/jxb/err311

Wahl, 2013, Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana, Science, 339, 704, 10.1126/science.1230406

Lunn, 2006, Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADP glucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana, Biochem. J., 397, 139, 10.1042/BJ20060083

Schluepmann, 2004, Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering, Plant Physiol., 135, 969, 10.1104/pp.104.039743

Cabib, 1958, The biosynthesis of trehalose-6-phosphate, J. Biol. Chem., 231, 259, 10.1016/S0021-9258(19)77303-7

Jang, 2003, Expression of a Bifunctional Fusion of the Escherichia coli Genes for Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase in Transgenic Rice Plants Increases Trehalose Accumulation and Abiotic Stress Tolerance without Stunting Growth1, Plant Physiol., 131, 516, 10.1104/pp.007237

Elbein, D.A. (2003). New insights on trehalose: A multifunctional molecule. Glycobiology, 13.

Garg, 2002, Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses, Proc. Natl. Acad. Sci. USA, 99, 15898, 10.1073/pnas.252637799

Goddijn, 2015, Trehalose metabolism in plants, Plant J. Cell Mol. Biol., 79, 544

Caputto, 1950, Isolation of the coenzyme of the galactose phosphate-glucose phosphate transformation, J. Biol. Chem., 184, 333, 10.1016/S0021-9258(19)51153-X

Yang, 2001, Activation of a mitogen-activated protein kinase pathway is involved in disease resistance in tobacco, Proc. Natl. Acad. Sci. USA, 98, 741, 10.1073/pnas.98.2.741

Mizoguchi, 2010, Characterization of two cDNAs that encode MAP kinase homologues in Arabidopsis thaliana and analysis of the possible role of auxin in activating such kinase activities in cultured cells, Plant J., 5, 111, 10.1046/j.1365-313X.1994.5010111.x