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Article

Genome-wide identification and expression analysis of the carotenoid metabolic pathway genes in pepper (Capsicum annuum L.)

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Pages 1134-1149 | Received 31 May 2020, Accepted 12 Sep 2020, Published online: 24 Sep 2020

References

  • Yuan H, Zhang JX, Nageswaran D, et al. Carotenoid metabolism and regulation in horticultural crops. Hortic Res. 2015;2:15036.
  • Leng XP, Wang PP, Wang C, et al. Genome-wide identification and characterization of genes involved in carotenoid metabolic in three stages of grapevine fruit development. Sci Rep. 2017;7(1):4216
  • Cazzonelli CI. Carotenoids in nature: insights from plants and beyond. Funct Plant Biol. 2011;38(11):833–847.
  • Holt NE, Zigmantas D, Valkunas L, et al. Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science. 2005;307(5708):433–436.
  • Dall'Osto L, Fiore A, Cazzaniga S, et al. Different roles of alpha- and beta-branch xanthophylls in photosystem assembly and photoprotection. J Biol Chem. 2007;282(48):35056–35068.
  • Domonkos I, Kis M, Gombos Z, et al. Carotenoids, versatile components of oxygenic photosynthesis. Prog Lipid Res. 2013;52(4):539–561.
  • Howitt CA, Pogson BJ. Carotenoid accumulation and function in seeds and non-green tissues. Plant Cell Environ. 2006;29(3):435–445.
  • Franco AC, Matsubara S, Orthen B. Photoinhibition, carotenoid composition and the co-regulation of photochemical and non-photochemical quenching in neotropical savanna trees. Tree Physiol. 2007;27(5):717–725.
  • Nisar N, Li L, Lu S, et al. Carotenoid metabolism in plants. Mol Plant. 2015;8(1):68–82.
  • Milborrow BV, Lee HS. Endogenous biosynthetic precursors of (+)-abscisic acid. VI. Carotenoids and ABA are formed by the ‘non-mevalonate’ triose-pyruvate pathway in chloroplasts. Aust J Plant Physiol. 1998;25:507–512.
  • Auldridge ME, Block A, Vogel JT, et al. Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family. Plant J. 2006;45(6):982–993.
  • Havaux M. Carotenoid oxidation products as stress signals in plants. Plant J. 2014;79(4):597–606.
  • Cooper DA. Carotenoids in health and disease: recent scientific evaluations, research recommendations and the consumer. J Nutr. 2004;134(1):221S–224S.
  • Fiedor J, Burda K. Potential role of carotenoids as antioxidants in human health and disease. Nutrients. 2014;6(2):466–488.
  • Farre G, Sanahuja G, Naqvi S, et al. Travel advice on the road to carotenoids in plants. Plant Sci. 2010;179(1–2):28–48.
  • Kato M. Mechanism of carotenoid accumulation in citrus fruit. J Japan Soc Hort Sci. 2012;81(3):219–233.
  • Rodriguez-Concepcion M, Stange C. Biosynthesis of carotenoids in carrot: an underground story comes to light. Arch Biochem Biophys. 2013;539(2):110–116.
  • Ohmiya A. Qualitative and quantitative control of carotenoid accumulation in flower petals. Sci Hortic (Amsterdam). 2013;163:10–19.
  • Liu L, Shao Z, Zhang M, et al. Regulation of carotenoid metabolism in tomato. Mol Plant. 2015;8(1):28–39.
  • Vranová E, Coman D, Gruissem W. Structure and dynamics of the isoprenoid pathway network. Mol Plant. 2012;5(2):318–333.
  • Vranová E, Coman D, Gruissem W. Network analysis of the MVA and MEP pathways for isoprenoid synthesis. Annu Rev Plant Biol. 2013;64:665–700.
  • Abby JC, Christopher IC, Eleanore TW, et al. Carotenoids. In: Fabrice Rébeillé, Roland Douce, editors. Biosynthesis of vitamins in plants part A. Vitamins A, B1, B2, B3, B5. Vol. 58. Amsterdam (Netherlands): Academic Press; 2011. p. 1–36.
  • Rodriguez-Concepcion M, Boronat A. Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics. Plant Physiol. 2002;130(3):1079–1089.
  • Eisenreich W, Bacher A, Arigoni D, et al. Biosynthesis of isoprenoids via the non-mevalonate pathway. Cell Mol Life Sci. 2004;61(12):1401–1426.
  • Ruiz-Solaa MA, Rodríguez-Concepción M. Carotenoid biosynthesis in arabidopsis: a colorful pathway. The Arabidopsis Book. 2012;10:e0158.
  • Carol P, Kuntz M. A plastid terminal oxidase comes to light: Implications for carotenoid biosynthesis and chlororespiration. Trends Plant Sci. 2001;6(1):31–36.
  • Rumeau D, Peltier G, Cournac L. Chlororespiration and cyclic electron flow around PSI during photosynthesis and plant stress response. Plant Cell Environ. 2007;30(9):1041–1051.
  • Forster B, Pogson BJ, Osmond CB. Lutein from deepoxidation of lutein epoxide replaces zeaxanthin to sustain an enhanced capacity for nonphotochemical chlorophyll fluorescence quenching in avocado shade leaves in the dark. Plant Physiol. 2011;156(1):393–403.
  • Guzman I, Hamby S, Romero J, et al. Variability of carotenoid biosynthesis in orange colored Capsicum spp. Plant Sci. 2010;179(1–2):49–59.
  • Jeknic Z, Morre JT, Jeknic S, et al. Cloning and functional characterization of a gene for capsanthin-capsorubin synthase from tiger lily (lilium lancifolium thunb.‘splendens’). Plant Cell Physiol. 2012;53:1899–1912.
  • Tan BC, Joseph LM, Deng WT, et al. Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family. Plant J. 2003;35(1):44–56.
  • Walter MH, Strack D. Carotenoids and their cleavage products: biosynthesis and functions. Nat Prod Rep. 2011;28(4):663–692.
  • Auldridge ME, McCarty DR, Klee HJ. Plant carotenoid cleavage oxygenases and their apocarotenoid products. Curr Opin Plant Biol. 2006b;9(3):315–321.
  • Zhang XH, Liu HQ, Guo QW, et al. Genome-wide identification, phylogenetic relationships, and expression analysis of the carotenoid cleavage oxygenase gene family in pepper. Genet Mol Res. 2016;15(4):15048695.
  • Han YJ, Wang XH, Chen WC, et al. Differential expression of carotenoid-related genes determines diversified carotenoid coloration in flower petal of Osmanthus fragrans. Tree Genet. Genomes. 2014;10(2):329–338.
  • Han Y, Wu M, Cao L, et al. Characterization of OfWRKY3, a transcription factor that positively regulates the carotenoid cleavage dioxygenase gene OfCCD4 in Osmanthus fragrans. Plant Mol Biol. 2016;91(4–5):485–496.
  • Lu T, Zhang G, Sun L, et al. Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. Peer J. 2017;5:e3653.
  • Chen MY, Li K, Li HP, et al. The glutathione peroxidase gene family in Gossypium hirsutum: genome-wide identification, classification, gene expression and functional analysis. Sci Rep. 2017;7:44743.
  • Sun Q, Wang GH, Zhang X, et al. Genome-wide identification of the TIFY gene family in three cultivated Gossypium species and the expression of JAZ genes. Sci Rep. 2017;7:42418.
  • Guo YW, Guo HL, Li X, et al. Two type III polyketide synthases from Polygonum cuspidatum: gene structure evolutionary route and metabolites. Plant Biotechnol Rep. 2013;7(3):371–381.
  • Gao W, Xu FC, Guo DD, et al. Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress. BMC Plant Biol. 2018;18(1):15.
  • Zhang G, Lu T, Miao W, et al. Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium. Peer J. 2017;5:e4126.
  • Oliveira C, Silva-Ferreira AC, Mendes-Pinto MM, et al. Carotenoid compounds in grapes and their relationship to plant water status. J Agric Food Chem. 2003;51(20):5967–5971.
  • Mendes-Pinto MM, Silva-Ferreira AC, Caris-Veyrat C, et al. Carotenoid, chlorophyll, and chlorophyll-derived compounds in grapes and port wines. J Agric Food Chem. 2005;53(26):10034–10041.
  • Zhang R, Murat F, Pont C, et al. Paleo-evolutionary plasticity of plant disease resistance genes. BMC Genomics. 2014;15:187.
  • Meyers BC, Dickerman AW, Michelmore RW, et.al. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 1999;20(3):317–332.
  • Paterson AH, Bowers JE, Bruggmann R, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457:551–556.
  • Huang S, Gao Y, Liu J, et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics. 2012;287(6):495–513.
  • Kumar S, Stecher G, Li M, et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–1549.
  • Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696–704.
  • Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005;21(9):2104–2105.
  • Myung-Shin K, Seungill K, Jongbum J, et al. Global gene expression profiling for fruit organs and pathogen infections in the pepper, Capsicum annuum L. Sci Data. 2018;5:180103.
  • Kang W, Sim YM, Koo N, et al. Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L. Sci Data. 2020;7(1):17. [
  • 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.
  • Neetu C, Aashima N, Jitendra P, et al. Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression prowling and phylogenetic analysis. Mol Genet Genomics. 2010;283:13–33.
  • Chothia C, Gough J, Vogel C, et al. Evolution of the protein repertoire. Science. 2003;300(5626):1701–1703.
  • Liang JY, Xia JY, Liu LL, et al. Global patterns of the responses of leaf-level photosynthesis and respiration in terrestrial plants to experimental warming. J. Plant Ecol. 2013;6(6):437–447.
  • Zhao Q, Chen W, Bian J, et al. Proteomics and phosphoproteomics of heat stress-responsive mechanisms in spinach. Front Plant Sci. 2018;9:800.
  • Hao F, Zhao S, Dong H, et al. Nia1 and Nia2 are involved in exogenous salicylic acid-induced nitric oxide generation and stomatal closure in Arabidopsis. J Integr Plant Biol. 2010;52(3):298–307.
  • Pang Y, Li J, Qi B, et al. Aquaporin AtTIP5;1 as an essential target of gibberellins promotes hypocotyl cell elongation in Arabidopsis thaliana under excess boron stress. Funct Plant Biol. 2018;45(3):305–314.
  • Lü D, Wang W, Miao C. ATHK1 acts downstream of hydrogen peroxide to mediate ABA signaling through regulation of calcium channel activity in Arabidopsis guard cells. Chin Sci Bull. 2013;58(3):336–343.
  • Ma XN, Zhang XR, Yang L, et al. Hydrogen peroxide plays an important role in PERK4-mediated abscisic acid-regulated root growth in Arabidopsis. Functional Plant Biol. 2019;46(2):165–174.
  • Wang K, He JN, Zhao Y, et al. EAR1 negatively regulates ABA signaling by enhancing 2C protein phosphatase activity. Plant Cell. 2018;30(4):815–834.
  • Li W, de Ollas C, Dodd IC. Long-distance ABA transport can mediate distal tissue responses by affecting local ABA concentrations. J Integr Plant Biol. 2018;60(1):16–33.
  • Sun L, Ma L, He S, et al. AtrbohD functions downstream of ROP2 and positively regulates waterlogging response in Arabidopsis. Plant Signal Behav. 2018;13(9):1–5.
  • Li L, Hou M, Cao L, et al. Glutathione S-transferases modulate Cu tolerance in Oryza sativa. Environ Exp Bot. 2018;155:313–320.
  • Guo S, Dai S, Singh PK. et al. A membrane-bound NAC-like transcription factor OsNTL5 represses the flowering in Oryza sativa. Front Plant Sci. 2018;9:555.
  • Zhao X, Wang YL, Qiao XR, et al. Phototropins function in high-intensity blue light-induced hypocotyl phototropism in Arabidopsis by altering cytosolic calcium. Plant Physiol. 2013;162(3):1539–1551.
  • Zhao X, Li YY, Xiao HL, et al. Nitric oxide blocks blue light-induced K + influx by elevating the cytosolic Ca2+ concentration in Vicia faba L. guard cells. J Integr Plant Biol. 2013;55(6):527–536.
  • Lv S, Yu D, Sun Q, et al. Activation of gibberellin 20-oxidase 2 undermines auxin-dependent root and root hair growth in NaCl-stressed Arabidopsis seedlings. Plant Growth Regul. 2018;84(2):225–236.
  • Zhao X, Wang YJ, Wang YL, et al. Extracellular Ca2+ alleviates NaCl-induced stomatal opening through a pathway involving H2O2-blocked Na+ influx in Vicia guard cells. J Plant Physiol. 2011;168(9):903–910.
  • Ma L, Zhang H, Sun L, et al. NADPH oxidase AtrbohD and AtrbohF function in ROS-dependent regulation of Na+/K+ homeostasis in Arabidopsis under salt stress . J Exp Bot. 2012;63(1):305–317.
  • Qi J, Song CP, Wang B, et al. Reactive oxygen species signaling and stomatal movement in plant responses to drought stress and pathogen attack. J Integr Plant Biol. 2018;60(9):805–826.
  • Wang PT, Liu H, Hua HJ, et al. A vacuole localized beta-glucosidase contributes to drought tolerance in Arabidopsis. Chin Sci Bull. 2011;56(33):3538–3546.
  • Xu LH, Wang WY, Guo JJ, et al. Zinc improves salt tolerance by increasing reactive oxygen species scavenging and reducing Na+ accumulation in wheat seedlings. Biologia Plant. 2014;58(4):751–757.
  • Li W, Zhao F, Fang W, et al. Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique. Front Plant Sci. 2015;116:732.
  • Zhang J, Wang F, Zhang C, et al. A novel VIGS method by agroinoculation of cotton seeds and application for elucidating functions of GhBI-1 in salt-stress response. Plant Cell Rep. 2018;37(8):1091–1100.
  • Xu F, Liu H, Xu Y, et al. Heterogeneous expression of the cotton R2R3-MYB transcription factor GbMYB60 increases salt sensitivity in transgenic Arabidopsis. Plant Cell Tiss Organ Cult. 2018;133(1):15–25.
  • Li K, Yang FB, Miao YC, et al. Abscisic acid signaling is involved in regulating the mitogen-activated protein kinase cascade module AIK1-MKK5-MPK6. BMC Plant Biol. 2017;12(5):e1321188.
  • Liu LY, Li N, Yao CP, et al. Functional analysis of the ABA-responsive protein family in ABA and stress signal transduction in Arabidopsis. Chin Sci Bull. 2013;58(31):3721–3730.
  • Song Y, Xiang F, Zhang G, et al. Abscisic acid as an internal integrator of multiple physiological processes modulates leaf senescence onset in Arabidopsis thaliana. Front Plant Sci. 2016;197:181.