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Research Article

Genome-wide identification and expression analysis of lipoxygenase genes in Tartary buckwheat

ORCID Icon, , , &
Pages 273-286 | Received 19 Oct 2019, Accepted 02 Mar 2020, Published online: 12 Mar 2020

References

  • Liu S, Lu X, Zhou J, et al. Research advance on the structure, molecular modification, and fermentation of lipoxygenases. Biotechnology Bulletin 2015;31(12):31–41.
  • Regdel D, Schewe T, Kühn H. Comparative characteristics of lipoxygenase isoenzymes from green pea seeds. Biochemistry 1995;60(6):715–721.
  • Chen Z, Chen X, Yan H, et al. The lipoxygenase gene family in poplar: identification, classification, and expression in response to MeJA treatment. PLoS One. 2015;10(4):e0125526.
  • Bailly C, Bogatek-Leszczynska R, Côme D, et al. Changes in activities of antioxidant enzymes and lipoxygenase during growth of sunflower seedlings from seeds of different vigour. Seed Sci Res. 2002;12(1):47–55.
  • Zhang B, Yin XR, Li X, et al. Lipoxygenase gene expression in ripening kiwifruit in relation to ethylene and aroma production. J Agric Food Chem. 2009;57(7):2875–2881.
  • Springer A, Kang C, Rustgi S, et al. Programmed chloroplast destruction during leaf senescence involves 13-lipoxygenase (13-LOX). Proc Natl Acad Sci USA. 2016;113(12):3383–3388.
  • Ogunola OF, Hawkins LK, Mylroie E, et al. Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance. PLoS One. 2017;12(7):e0181265.
  • Nuñez A, Savary BJ, Foglia TA, et al. Purification of lipoxygenase from Chlorella: production of 9- and 13-hydroperoxide derivatives of linoleic acid. Lipids 2002;37(11):1027–1032.
  • Kacperska A, Kubacka-Zgbalska M. Is lipoxygenase involved in the formation of ethylene from ACC? Physiol Plant. 1985;64(3):333–338.
  • Zhou Z, Chang X, You F, et al. Analysis of molecular evolution and codon bias of lipoxygenase(LOX) gene family in tea tree. J Agric Sci Technol 2017;19(12):43–51.
  • Liu H, He R, Zhang H, et al. Analysis of synonymous codon usage Bias in Maize. Mol Biol Rep. 2010;37(2):677–684.
  • Zhang L, Li X, Ma B, et al. The tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance. Mol Plant. 2017;10(9):1224–1237.
  • Jiang P, Burczynski F, Campbell C, et al. Rutin and flavonoid contents in three buckwheat species Fagopyrum esculentum, F. tataricum, and F. homotropicum and their protective effects against lipid peroxidation. Food Res Int. 2007;40(3):356–364.
  • Aghdam MS, Asghari M, Khorsandi O, et al. Alleviation of postharvest chilling injury of tomato fruit by salicylic acid treatment. J Food Sci Technol. 2014;51(10):2815–2820.
  • Padilla MN, Hernandez ML, Sanz C, et al. Stress-dependent regulation of 13-lipoxygenases and 13-hydroperoxide lyase in olive fruit mesocarp. Phytochemistry 2014;102:80–88.
  • Zhao Y, Zhou J, Xing D. Phytochrome B-mediated activation of lipoxygenase modulates an excess red light-induced defence response in Arabidopsis. J Exp Bot. 2014;65(17):4907–4918.
  • Zhang R, Wang Z. Effects of light on lipoxygenase activity and membrane lipid peroxidation in young leaves of wheat. Acta Bot Boreal-Occid Sin. 1994;14(3):198–202.
  • Anstis PJP, Friend J. The effect of light on lipoxygenase activity in dwarf pea seedlings. Phytochemistry 1974;13(12):2709–2712.
  • Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic acids Res. 2011;39(suppl):W29–W37.
  • Li M, Li L, Dunwell JM, et al. Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae. BMC Genomics. 2014;15(1):1–12.
  • Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23(21):2947–2948.
  • Ding S, Xin F, Du H, et al. Genome-wide analysis of maize OSCA family members and their involvement in drought stress. PeerJ. 2019;7:e6765.
  • 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.
  • Gu Z, Cavalcanti A, Chen FC, et al. Extent of gene duplication in the genomes of drosophila, nematode, and yeast. Mol Biol Evol. 2002;19(3):256–262.
  • Lozano R, Hamblin M, Prochnik S, et al. Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC Genomics 2015;16(1):360.
  • Wang Y, Tang H, Debarry JD, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49–e49.
  • Krzywinski M, Schein J, Birol I, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–1645.
  • Bailey TL, Johnson J, Grant CE, et al. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39–W49.
  • Chou KC, Shen HB. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One. 2010;5(6):e11335.
  • Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
  • Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31(2):166–169.
  • Zhang T, Song C, Li S, et al. RNA sequencing and coexpression analysis reveal key genes involved in α-linolenic acid biosynthesis in perillafrutescens seed. Int J Mol Sci. 2017;18(11):2433.
  • Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
  • Umate P. Genome-wide analysis of lipoxygenase gene family in Arabidopsis and rice. Plant Signal Behav. 2011;6(3):335–338.
  • Liu SQ, Liu XH, Jiang LW. Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber. Genet Mol Res. 2011;10(4):2613.
  • Hilbers M, Rossi A, Finazzi Agrò A, et al. The primary structure of a lipoxygenase from the shoots of etiolated lentil seedlings derived from its cDNA. Biochim Biophys Acta. 1994;1211(2):239–242.
  • Stamm S, Benari S, Rafalska I, et al. Function of alternative splicing. Gene 2013;514(1):1–30.
  • Li J, Song Y, Wang Z. Cloning and expression pattern of Salvia miltiorrhiza lipoxygenase gene (SmLOX). Shaanxi J Agric Sci. 2013;59(4):19–23.
  • Huang J, Cai M, Long Q, et al. OsLOX2, a rice type I lipoxygenase, confers opposite effects on seed germination and longevity. Transgenic Res. 2014;23(4):643–655.
  • Magadum S, Banerjee U, Murugan P, et al. Gene duplication as a major force in evolution. J Genet. 2013;92(1):155–161.
  • Wright F. The effective number of codons used in a gene. Gene 1990;87(1):23–29.
  • Zhang B, Chen K, Bowen J, et al. Differential expression within the LOX gene family in ripening kiwifruit. J Exp Bot. 2006;57(14):3825–3836.
  • Andreou A, Feussner I, Hause B, et al. Lipoxygenases - structure and reaction mechanism. Phytochemistry 2009;69(13):1504–1510.
  • Song Y, Love MH, Murphy P. Subcellular localization of lipoxygenase‐1 and‐2 in germinating soybean seeds and seedlings. J Am Oil Chem Soc. 1990;67(12):961–965.
  • Farmaki T, Sanmartin M, Jimenez P, et al. Differential distribution of the lipoxygenase pathway enzymes within potato chloroplasts. J Exp Bot. 2007;58(3):555–568.
  • Mazur R, Trzcinska-Danielewicz J, Kozlowski P, et al. Dark-chilling and subsequent photo-activation modulate expression and induce reversible association of chloroplast lipoxygenase with thylakoid membrane in runner bean (Phaseolus coccineus L.). Plant Physiol Biochem. 2018;122:102.
  • Bell E, Creelman RA, Mullet JE. A chloroplast lipoxygenase is required for wound-induced jasmonic acid accumulation in Arabidopsis. Proc Natl Acad Sci USA. 1995;92(19):8675–8679.
  • Zheng SJ, van Dijk JP, Bruinsma M, et al. Sensitivity and speed of induced defense of cabbage (Brassica oleracea L.): dynamics of BoLOX expression patterns during insect and pathogen attack. Mol Plant Microbe Interact. 2007;20(11):1332–1345.
  • Rangel M, Machado OL, Da CM, et al. Accumulation of chloroplast-targeted lipoxygenase in passion fruit leaves in response to methyl jasmonate. Phytochemistry. 2002;60(6):619–625.
  • Wang YX, Lin ZF, Guo JY, et al. The lipoxygenase activity of pea chloroplasts in relation to leaf senescence and membrane lipid peroxidation. Acta Phytophysiol Sin 1990;16(1):57–62.
  • Mur LAJ, Kenton P, Atzorn R, et al. The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiol. 2006;140(1):249–262.
  • Bell E, Mullet JE. Characterization of an Arabidopsis lipoxygenase gene responsive to methyl jasmonate and wounding. Plant Physiol. 1993;103(4):1133–1137.
  • Bhardwaj PK, Kaur J, Sobti RC, et al. Lipoxygenase in Caragana jubata responds to low temperature, abscisic acid, methyl jasmonate and salicylic acid. Gene 2011;483(1-2):49–53.
  • Losvik A, Beste L, Glinwood R, et al. Overexpression and down-regulation of barley lipoxygenase LOX2.2 affects jasmonate-regulated genes and aphid fecundity. Int J Mol Sci. 2017;18(12):2765.
  • Dossa K, Wei X, Li D, et al. Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. Bmc Plant Biol. 2016;16(1):171.
  • Caldelari D, Wang G, Farmer EE, et al. Arabidopsis lox3 lox4 double mutants are male sterile and defective in global proliferative arrest. Plant Mol Biol. 2011;75(1-2):25–33.
  • He Y, Fukushige H, Hildebrand DF, et al. Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence. Plant Physiol. 2002;128(3):876–884.
  • Vellosillo T, Martínez M, López MA, et al. Oxylipins produced by the 9-lipoxygenase pathway in Arabidopsis regulate lateral root development and defense responses through a specific signaling cascade. Plant Cell. 2007;19(3):831–846.
  • Kaye Peterman T, Rattigan E, Enriquez A, et al. Immunological characterization of Arabidopsis thaliana lipoxygenase: expression of the LOX1 gene product in Escherichia coli and polyclonal antibody production. Plant Physiol Biochem. 1994;32(3):443–450.
  • Melan MA, Dong X, Endara ME, et al. An Arabidopsis thaliana lipoxygenase gene can be induced by pathogens, abscisic acid, and methyl jasmonate. Plant Physiol. 1993;101(2):441–450.
  • Zhang D, Jiang C, Huang C, et al. The light‐induced transcription factor FtMYB116 promotes accumulation of rutin in Fagopyrum tataricum. Plant Cell Environ. 2019;42(4):1340–1351.
  • Anstis PJP, Friend J, Gardner DCJ. The role of xanthoxin in the inhibition of pea seedling growth by red light. Phytochemistry 1975;14(1):31–35.
  • Melan MA, Enriquez A, Peterman TK. The LOX1 gene of arabidopsis is temporally and spatially regulated in germinating seedlings. Plant Physiol. 1994;105(1):385–393.
  • Fontaine V, Hartwell J, Jenkins G, et al. Arabidopsis thaliana contains two phosphoenolpyruvate carboxylase kinase genes with different expression patterns. Plant Cell Environ. 2002;25(1):115–122.