Expressional profiling study of lavandula angustifolia l. in response to drought stress by using transcriptome analysis.

Document Type : Research Paper

Authors

1 Nuclear Agriculture P.H.D. Student, Department of Plant Breeding and Biothechnology,Faculty of Plant Production,Gorgan University of Agricultural Sciences and Natural Resources,Gorgan,Iran

2 Associate Professor, Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.

3 Assistant Professor in Biotechnology/ faculty of Agriculture and Plant Improvement, Shiraz University.

Abstract

Objective
Drought stress is a major problem that plagues world's arable lands and poses major limitations to plant growth and productivity. Lavandula angustifolia L. is a medicinal and aromatic plant that has great value for its essential oil. Due to the relatively resistant nature of this plant to water deficit, it can be a good substitute for plants with high water demand. To identification of some of genes involved in response to drought stress, we carried out transcriptome analysis under normal and drought condition using RNA-Seq.
 
Materials and methods
Illumina HiSeq. 2000 was applied for sequencing of flower and leaf mRNAs under control and stress conditions. Also the activity of some antioxidant enzymes  and level of Malondialdehyde and Dityrosine were measured.
 
Results
Among a total of 264126 transcripts, 1083 DEGs in flower and 150 DEGs in leaf were identified in response to the drought stress. Gene Ontology Enrichment of drought responsive DEGs including catalytic activity, response to stimulus and binding were identified. KEGG analysis showed different pathways associated with stress such as biosynthesis of secondary metabolites, glutathione and proline metabolism and plant hormone signal transduction. Also some unigenes related to antioxidant enzymes were highlighted in response to drought.
 
Conclusion
 The transcriptome data generated here is the first report of RNA-Seq for Lavandula angustifolia L. under drought stress. Biochemical analysis results in this study were consistent with the RNA-seq results. Our findings offer insights into the molecular networks of Lavandula angustifolia L.  in response to drought stress.

Keywords

References

توحیدی نژاد فاطمه، محمدآبادی محمدرضا، اسمعیلی زاده کشکوئیه علی، نجمی نوری عذرا (1393) مقایسه سطوح مختلف بیان ژنRheb  در بافت­های مختلف بز کرکی راینی. مجله بیوتکنولوژی کشاورزی 6(4)، 50-35. 
توکلی‌نکو حسین، حاجی‌میر‌رحیمی سید‌داوود، مرادی محمدرضا (1395) بسته‌ی کارآفرینی کشت و پرورش اسطوخودوس. چاپ اول، انتشارات اسرار علم، 18-17.
جعفری دره­در امیر حسین، محمدآبادی محمدرضا، اسمعیلی زاده کشکوئیه علی، ریاحی مدوار علی (1395) بررسی بیان ژنCIB4  در بافت­های مختلف گوسفند کرمانی با استفاده از Real Time qPCR. مجله پژوهش در نشخوارکنندگان 4(4)، 132-119.
شهابی امین، طهمورث­پور مجتبی، کاظمی­پور علی (1398) بازسازی، آنالیز و مقایسه توپولوژی شبکه‌ ژنی مبتنی برداده‌های RNA-Seq دخیل در صفات چند فاکتوره تولید مثلی و باروری. مجله بیوتکنولوژی کشاورزی 11(2)، 78-57.
صادقی داریوش، مرتضویان سید محمدمهدی، بختیاری زاده محمدرضا (1397) ارزیابی توالی رونوشت گیاه دارویی زیره سبز (Cuminum cyminum) با استفاده از RNA-Seq. مجله بیوتکنولوژی کشاورزی 9(4)، 116-101.
علی­سلطانی ارغوان، شیران بهروز، ابراهیمی اسماعیل و همکاران (1394) الگوی بیان ژن­های مرتبط با فرایند متابولیک ماکرومولکول­ها تحت تنش سرما در بادام (Prunus dulcis Mill) از طریق تجزیهRNA-seq . ژنتیک نوین 10(1)، 32-21.
References
Adal AM, Sarker LS, Malli RPN et al. (2019) RNA-Seq in the discovery of a sparsely expressed scent-determining monoterpene synthase in lavender (Lavandula). Planta 249(1), 271-290. 
Aebi H (1984) Catalase in vitro. Methods Enzymol 105, 121-126.
Ali M, Hussain RM, Rehman NU et al. (2018) De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.). Dna Res 25(6), 597-617.
AliSoltani A, Shiran B, Ebrahimi E et al. (2015) Expression of genes related to macromolecule metabolic process under cold stress in almond (Prunus dulcis Mill) using RNA-seq analysis. Mod Genet J 10, 21-32 (In Persian).
Amado R, Aeschbach R, Neukom H (1984) Dityrosine: in vitro production and characterization.  Methods Enzymol 107, 377-388.
Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress and signal transduction. Annu Rev Plant Biol 55, 373-399.
Arora A, Sairam RK, Srivastava GC (2002) Oxidative stress and antioxidant system in plants. Plant Physiol 82, 1227-1237.
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinform 30, 2114-2120.
Brady JD, Fry SC (1997) Formation of Di-lsodityrosine and Loss of lsodityrosine in the cell walls of tomato cell-suspension cultures treated with Funga1 Elicitors. Plant Physiol 115, 87-92.
Chaves MM, Maroco JP, Pereira JS (2003) Understanding plant response to drought-from genes to the whole plant. Funct Plant Biol 30, 239-264.
Dugas DV, Monaco MK, Olsen A et al. (2011) Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. Bmc Genomics 12, 514.
Feller U, Vaseva II (2014) Extreme climatic events: Impacts of drought and high temperature on physiological processes in agronomically important plants. Front Environ Sci 2, 39.
Fujii H, Zhu JK (2009) Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress. Proc Natl Acad Sci 106, 8380-8385. 
Gigon A, Matos AR, Laffray D et al. (2004) Effect of drought stress on lipid metabolism in the leaves of Arabidopsis thaliana(ecotype Columbia). Ann Bot 94, 345-351. 
Gilbert D (2016) Accurate & complete gene construction with EvidentialGene. Galaxy Community Conference Bloomington. https://doi.org/10.7490/f1000research.1112467.1
Gong H, Zhu X, Chen K et al. (2005) Silicon alleviates oxidative damage of wheat plants in pots under drought. Plant Sci 169, 313-321.
Gorantla M, Babu PR, Lachagari VBR et al. (2006) Identification of stress responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J Exp Bot 58, 253-265.
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61, 1041-1052.
Jafari Darehdor AH, Mohammadabadi MR, Esmailizadeh AK, Riahi Madvar A (2016) Investigating expression of CIB4 gene in different tissues of Kermani Sheep using Real Time qPCR. J Rumin Res 4, 119-132 (In Persian).
Javot H, Maurel C (2002) The role of aquaporins in root water uptake. Ann Bot 90, 301-313.
Jin J, Panicker D, Wang Q et al. (2014) Next generation sequencing unravels thebiosynthetic ability of Spearmint (Menthaspicata) peltate glandular trichomes through comparative transcriptomics. Bmc Plant Biol 14, 2-30.
Kandpal Rajendra P, Vaidyanathan CS, Kumar Udaya M (1981) Alterations in the activities of the enzymes of proline metabolism in Ragi (Eleusine coracana) leaves during water stress. J Biosci 3(4), 361-370.
Klute A. (1986) Water retention: Laboratory methods. Methods of Soil Analysis, Part 1, Physical and Mineralogical Methods, ASA and SSSA, Madison, 635-662.
Kumar S, Trivedi PK (2018) Glutathione S-Transferases: Role in Combating Abiotic Stresses Including Arsenic Detoxification in Plants. Front Plant Sci 9, 751. 
Li B, Dewey C (2011) RSEM: accurate transcript quantification from RNASeq data with or without a reference genome. Bmc bioinform 12, 323. 
Li H, Li J, Dong Y et al. (2019) Time-series transcriptome provides insights into the gene regulation network involved in the volatile terpenoid metabolism during the flower development of lavender, Bmc Plant Biol 19, 313. 
Lis-Balchin M (2002) Lavender: The Genus Lavandula (1st edn), Taylor and Francis Inc., CRC Press, New York, pp. 1-2.
Liu S, Lv Z, Liu Y et al. (2018) Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana. Genet Mol Biol 41(3), 624-637. 
Malli RPN, Adal AM, Sarker LS et al. (2018) De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production. Planta 249, 251-256.
Maurel C, Chrispeels MJ (2001) Aquaporins: a molecular entry into plant water relations, Plant Physiol 125, 135-138.
Mehta RH, Ponnuchamy M, Kumar J et al. (2017) Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomic 17, 1-25.
Min H, Chen C, Wei S (2016) Identification of drought tolerant mechanisms in maize seedlings based on transcriptome analysis of recombination inbred lines. Front Plant Sci 7, 1080.
Minami M, Yoshikawa H (1979) A simplified assay method of superoxide dismutase activity for clinical use. Clin Chim Acta 92, 337-342.
Mohammadabadi MR, Jafari Darehdor AH, Bordbar F (2017) Molecular analysis of CIB4 gene and protein in Kermani sheep. Brazil J Med Biol Res 50, e6177.
Mohammadabadi MR, Tohidinejad F (2017) Charachteristics determination of Rheb gene and protein in Raini Cashmere goat. Iran. J. Appl. Anim. Sci 7 (2), 289-295.
Mortazavi A, Williams BA, McCue K (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628.
Munne-Bosch S, Penuelas J (2003) Photo and antioxidative protection and a role for salicylic acid during drought and recovery field grown Phillyrea angustifolia. Planta 217, 758-766.
Nakasugi K, Crowhurst R, Bally J, Waterhouse P (2014) Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. Plos One 9(3): e91776. 
Noctor G, Mhamdi A, Chaouch S et al. (2012) Glutathione in plants: an integrated overview. Plant Cell Env 35(2), 454-484.
Nongpiur R, Soni P, Karan R et al. (2012) Histidine kinases in plants: cross talk between hormone and stress responses. Plant Signal Behav 7(10), 1230-1237. 
Nunes DS, Linck VM, Silva AL et al. (2015) Psychopharmacology of Essential Oils. In Handbook of Essential Oils: Science, Technology and Applications. Eds. CRC Press, London, UK, pp. 297-314.
Ohkawa H, Ohishi N, Yagi Y (1979) Assay of lipid peroxides in tissues by thiobarbituric acid reaction. Ann Biochem 95, 351-358.
Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12, 87-98. 
Pan L, Zhang X, Wang J et al (2016) Transcriptional Profiles of Drought-Related Genes in Metabolic Processes and Antioxidant Defenses in Lolium multiflorum. Front Plant Sci 7, 519.
Pan Y, Wu LJ, Yu ZL (2006) Effect of salt and drought on antioxidant enzymes activities and SOD isoenzymes of liquorice (Glycyrrhiza uralensis Fisch). Plant Growth Regul 49, 157-165.
Peleg Z, Blumwald E (2011) Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol 14, 290-295.
Sadeghi D, Mortazavian SMM, Bakhtyari Zadeh MR (2017) Transcriptome analysis of cumin (Cuminum cyminum L.) using RNA-Seq. Agric Biotechnol J 9, 101-116 (In Persian).
Schnable PS, Ware D, Fulton RS et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115. 
Shahabi A, Tahmoorespur M, Kazemi-Pour A (2019) Reconstruction, analysis and comparison of gene networks topology based on RNA-Seq data involved in reproductive and fertility complex traits. Agric Biotechnol J 11, 57-78 (In Persian).
Sharma P, Jha AB, Dubey RS, Pessarakli M (2012) Reactive oxygen species, oxidative damage and antioxidative defense mechanism in plants under stressful conditions. J of Botany, 1-26.
Shelden MC, Roessner U (2013) Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals. Front Plant Sci 4, 123. 
Shigeoka S (2002) Regulation and function of ascorbate peroxidase isoenzymes. J Exp Bot 53, 1305-1319.
Simao FA, Waterhouse RM, Ioannidis P et al. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinform 31, 3210-3212. 
Tavackoli nekoo H, Hajimir Rahimi SD, Moradi M (2017) Lavander growing Entrepreneurship package. Asrare Elm Press. Iran, pp 17-18 (In Persian).
Tohidinejad F, Mohammadabadi MR, Esmailizadeh AK, Najmi Noori A (2015) Comparison of different levels of Rheb gene expression in different tissues of Raini Cashmir goat. Agric Biotechnol J 6, 35-50 (in Persian).
Tunnacliffe A, Wise MJ (2007) The continuing conundrum of the LEA proteins. Naturwissenschaften 94, 791-812.
Verbruggen N, Hermans C (2008) Proline accumulation in plants. J. Amino Acids 35, 753-759.
Vining KJ, Johnson SR, Ahkami A et al. (2017) Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. Mol Plant 10, 323-339.
Wang SY, Jiao H, Faust M (1991) Changes in ascorbate, glutathione and related enzyme activities during thiodiazuron-induced bud break of apple. Plant Physiol 82, 231-236.
Wu S, Ning F, Zhang Q et al. (2017) Enhancing omics research of crop responses to drought under field conditions. Front Plant Sci 8, 174.
Ye G, Ma Y, Feng Z, Zhang X (2018) Transcriptomic analysis of drought stress
responses of sea buckthorn (Hippophae rhamnoides subsp. sinensis) by RNA-Seq. PLoS
ONE 13, e0202213. 
Zhang X, Allan AC, Li C (2015) De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens. Int J Mol Sci 16, 11550-11573. 
Zhou SM, Chen LM, Liu SQ et al. (2015) De Novo Assembly and Annotation of the      
Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform. Plos One 10, e0133312.
Agricultural Biotechnology Journal
Volume 12, Issue 1
April 2020
Pages 101-124

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