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Transcriptome Analysis of Persian Oak (Quercus brantii L.) Decline Using RNA-seq Technology

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Abstract

Since the late 1980s, the oak decline has affected the Zagros oak forests in western Iran. Persian oak (Quercus brantii L.) the most important tree species of these forests has been damaged more than any other plant species. In the present study, the RNA sequencing technique was used for the first time to identify key genes and molecular mechanisms involved in Persian oak decline. The RNA was extracted from the leaves of healthy and declined oak trees, and sequenced using the Illumina HiSeq 2500 platform (2 × 150 bp paired-end reads). De novo transcriptome assembly of Persian oak revealed 56,743 unigenes and 6049 differentially expressed genes (DEGs) between declined and control samples. The results of gene ontology analysis showed that most of the DEGs involved in oak decline belong to the group of stress-responsive genes. In general, oak decline samples showed significant reductions in gene expression associated with “photosynthesis and storage of sugar” and “protein synthesis and related processes.” Additionally, DEGs related to the starch degradation pathway were up-regulated, whereas DEGs associated with acetate-mevalonate (MVA), biosynthesis of lignin, and lignases pathways were down-regulated. The present study's findings can be an effective step in identifying the genes involved in oak decline and deciphering the relationship between this phenomenon and biotic and abiotic stresses.

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Data Availability

The raw sequencing reads produced in this study have been deposited at NCBI in the Short Read Archive (SRA) database under the bio project number PRJNA786780. Data are available here: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA786780/ and will be made publicly accessible after the publication of the manuscript.

Abbreviations

ATM:

Atmospheric pressure

C:

Leaf stomatal conductance

CO2_out:

Co2 at the leaf chamber outlet

CO2_in:

Co2 at the inlet of the analyzer

E:

Transpiration rate

IntCO2 :

Internal CO2

internal_T:

Temp of analyzer environment

KAAS:

KEGG automatic annotation server

MS:

Mass spectrometry

NGS:

Next-generation sequencing

NR:

Non-redundant database

par:

Photosynthesis active radiation

PDB:

Protein data bank

pn:

Net photosynthesis rate

RefSeq:

Reference sequence database

RHin, RHout:

Inlet/outlet relative humidity

T (air):

Temp of ambient air in the leaf chamber

T (leaf):

Temp of leaf

VpD:

Vapor pressure deficit

References

  • Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aghajani H, Mohadjer MRM, Bari E, Ohno KM, Shirvany A, Asef MR (2018) Assessing the biodiversity of wood decay fungi in northern forests of Iran. Proc Natl Acad Sci India Sect Biol Sci 88:1463–1469

    Article  CAS  Google Scholar 

  • Ahmadi S, Ghaderi F, Safaee D (2020) Oak charcoal rot disease in Iran. Plant Pathol 9:1

    CAS  Google Scholar 

  • Altschul SF, Koonin EV (1998) Iterated profile searches with PSI-BLAST—a tool for discovery in protein databases. Trends Biochem Sci 23:444–447

    Article  CAS  PubMed  Google Scholar 

  • Amir Ahmadi B, Zolfaghari R, Mirzaei MR (2015) Relation between Dieback of Quercus brantii Lindl. trees with ecological and sylvicultural factors, (study area: Dena protected area). Ecology of Iranian Forest 3:19–27

    Google Scholar 

  • Andrews S, Krueger F, Segonds-Pichon A, Biggins L, Krueger C, Wingett S (2020) FastQC: a quality control tool for high throughput sequence data [Online]. 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 16 Jan 2022

  • Ashrafi J, Hosseini A, Hosseinzadeh J, Mirabolfathi M (2018) Investigation on oak charcoal disease in dieback affected forests of Ilam province. Iran J Forest Range Prot Res 16:1–12

    Google Scholar 

  • Bellincampi D, Cervone F, Lionetti V (2014) Plant cell wall dynamics and wall-related susceptibility in plant–pathogen interactions. Front Plant Sci 5:228

    Article  PubMed  PubMed Central  Google Scholar 

  • Bernacchi CJ, Portis AR, Nakano H, Von Caemmerer S, Long SP (2002) Temperature response of mesophyll conductance. Implications for the determination of Rubisco enzyme kinetics and for limitations to photosynthesis in vivo. Plant Physiol 130:1992–1998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berry J, Bjorkman O (1980) Photosynthetic response and adaptation to temperature in higher plants. Annu Rev Plant Physiol 31:491–543

    Article  Google Scholar 

  • Bhuiyan EA, Hossain MZ, Muyeen S, Fahim SR, Sarker SK, Das SK (2021) Towards next-generation virtual power plant: technology review and frameworks. J Renew Sustain Energy Rev 150:111358

    Article  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boutigny A-L, Barreau C, Atanasova-Penichon V, Verdal-Bonnin M-N, Pinson-Gadais L, Richard-Forget F (2009) Ferulic acid, an efficient inhibitor of type B trichothecene biosynthesis and Tri gene expression in Fusarium liquid cultures. Mycol Res 113:746–753

    Article  CAS  PubMed  Google Scholar 

  • Casaretto JA, El-Kereamy A, Zeng B, Stiegelmeyer SM, Chen X, Bi Y-M, Rothstein SJ (2016) Expression of OsMYB55 in maize activates stress-responsive genes and enhances heat and drought tolerance. BMC Genomics 17:1–15

    Article  Google Scholar 

  • Ceschin DG, Pires NS, Mardirosian MN, Lascano CI, Venturino A (2020) The Rhinella arenarum transcriptome: de novo assembly, annotation, and gene prediction. Sci Rep 10:1–8

    Article  Google Scholar 

  • Coelho AC, Lima M, Neves D, Cravador A (2006) Genetic diversity of two evergreen oaks [Quercus suber (L.) and Quercus ilex subsp. rotundifolia (Lam.)] in Portugal using AFLP markers. Silvae Genet 55:105–118

    Article  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Djami-Tchatchou A, Straker C (2012) The isolation of high-quality RNA from the fruit of avocado (Persea Americana Mill.). S Afr J Bot 78:44–46

    Article  CAS  Google Scholar 

  • Dong X, Huang L, Chen Q, Lv Y, Sun H, Liang Z (2020) Physiological and anatomical differences and differentially expressed genes reveal yellow leaf coloration in Shumard oak. Plants 9:169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99:175–185

    Article  CAS  PubMed  Google Scholar 

  • Galván JV, Valledor L, Cerrillo RMN, Pelegrín EG, Jorrín-Novo JV (2011) Studies of variability in Holm oak (Quercus ilex subsp. Ballota [Desf.] Samp.) through acorn protein profile analysis. J Proteomics 74:1244–1255

    Article  Google Scholar 

  • Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    Article  CAS  PubMed  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guarín A, Taylor AH (2005) Drought triggered tree mortality in mixed conifer forests in Yosemite National Park, California, USA. For Ecol Manag 218:229–244

    Article  Google Scholar 

  • Guerrero-Sánchez VM (2020) Integration of Bioinformatics to molecular research in forest species: the case of Holm oak (Quercus ilex). PhD Thesis, Helvia Repositorio Institucional de la Universidad de Córdoba, Spain

  • Guerrero-Sanchez VM, Maldonado-Alconada AM, Amil-Ruiz F, Jorrin-Novo JV (2017) Holm oak (Quercus ilex) transcriptome. De novo sequencing and assembly analysis. Front Mol Biosci 4:70

    Article  PubMed  PubMed Central  Google Scholar 

  • Guerrero-Sanchez VM, Maldonado-Alconada AM, Amil-Ruiz F, Verardi A, Jorrín-Novo JV, Rey M-D (2019) Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome. PLoS ONE 14:e0210356

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guhr A, Horn MA, Weig AR (2017) Vitamin B2 (riboflavin) increases drought tolerance of Agaricus bisporus. Mycologia 109:860–873

    Article  CAS  PubMed  Google Scholar 

  • Gururani MA, Venkatesh J, Tran LSP (2015) Regulation of photosynthesis during abiotic stress-induced photoinhibition. Mol Plant 8:1304–1320

    Article  CAS  PubMed  Google Scholar 

  • Hosseini SZ, Ismaili A, Nazarian-Firouzabadi F, Fallahi H, Rezaei Nejad A, Sohrabi SS (2021) Dissecting the molecular responses of lentil to individual and combined drought and heat stresses by comparative transcriptomic analysis. Genomics 113:693–705

    Article  CAS  PubMed  Google Scholar 

  • Houssaini DE, Khriji S, Besbes K, Kanoun O (2018) Wireless sensor networks in agricultural applications. In: Kanoun O (ed) Energy harvesting for wireless sensor networks: technology, components, and system design. De Gruyter, Oldenbourg, pp 323–342

    Chapter  Google Scholar 

  • Jacob P, Hirt H, Bendahmane A (2017) The heat-shock protein/chaperone network and multiple stress resistance. Plant Biotechnol J 15:405–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jorge I, Navarro RM, Lenz C, Ariza D, Jorrín J (2006) Variation in the holm oak leaf proteome at different plant developmental stages, between provenances and in response to drought stress. Proteomics 6:S207–S214

    Article  PubMed  Google Scholar 

  • Kabera JN, Semana E, Mussa AR, He X (2014) Plant secondary metabolites: biosynthesis, classification, function and pharmacological properties. J Pharm Pharmacol 2:377–392

    Google Scholar 

  • Kabrick JM, Dey DC, Jensen RG, Wallendorf M (2008) The role of environmental factors in the oak decline and mortality in the Ozark Highlands. For Ecol Manage 255:1409–1417

    Article  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karami K (2016) Occurrence of Charcoal disease (Biscogniauxia Mediterranea) in oak forests. J Conserv Util Nat Resour 5:53–72

    Google Scholar 

  • Karami J, Kavoosi M, Babanezhad M (2015) Description of the symptoms and the evaluation of the co-occurrence of different severity of charcoal disease in Quercus castaneifolia. Nat Ecosyst IRAN 6:1–14

    Google Scholar 

  • Karami M, Badehian Z, Ahmadi A, Rajabi M (2019) Investigating the signs of decline and its impact on the total phenolic compounds, flavonoids, and protein of the leaves Quercus brantii (Case Study: Lorestan province). J Plant Ecosyst Conserv 6:155–176

    Google Scholar 

  • Kavosi MR, Yavarian R, Mohamadzadeh A, Karami J (2018) The effect of biological compounds and fungicides to combat Biscogniauxia mediterranea causal agent of “charcoal disease” in vitro. For Res Dev 3:343–360

    Google Scholar 

  • Kim HN, Jin HY, Kwak MJ, Khaine I, You HN, Lee TY, Ahn TH, Woo SY (2017) Why does Quercus suber species decline in Mediterranean areas? J Asia-Pacific Biodivers 10:337–341

    Article  Google Scholar 

  • Kooh Soltani S, Alesheikh AA, Ghermezcheshmeh B, Mehri S (2018) An evaluation of potential Oak decline Forest of the Zagros using GIS, RS, FAHP methods. Iran J Ecohydrol 5:713–725

    Google Scholar 

  • Kroymann J, Donnerhacke S, Schnabelrauch D, Mitchell-Olds T (2003) Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc Natl Acad Sci USA 100:14587–14592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lawlor DW, Cornic G (2002) Photosynthetic carbon assimilation and associated metabolism in relation to water deficits in higher plants. Plant Cell Environ 25:275–294

    Article  CAS  PubMed  Google Scholar 

  • Leininger T (1996) Oak physiology under temperature and drought stress as it relates to the oak decline syndrome. Annu Abstr Phytopathol 86:387

    Google Scholar 

  • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:1–16

    Article  Google Scholar 

  • Linares JC, Camarero JJ, Carreira JA (2010) Competition modulates the adaptation capacity of forests to climatic stress: insights from recent growth decline and death in relict stands of the Mediterranean fir Abies pinsapo. J Ecol 98:592–603

    Article  Google Scholar 

  • Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B (2014) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ 37:1250–1258

    Article  CAS  PubMed  Google Scholar 

  • López-Hidalgo C, Guerrero-Sánchez VM, Gómez-Gálvez I, Sánchez-Lucas R, Castillejo-Sánchez MA, Maldonado-Alconada AM, Valledor L, Jorrín-Novo JV (2018) A multi-omics analysis pipeline for the metabolic pathway reconstruction in the orphan species Quercus ilex. Front Plant Sci 9:935

    Article  PubMed  PubMed Central  Google Scholar 

  • Mahdavi A, Saidi S, Iranmanesh Y, Naderi M (2020) Biomass and carbon stocks in three types of Persian oak (Quercus brantii var. persica) of Zagros forests in a semi-arid area. Iran J Arid Land 12:1–9

    Google Scholar 

  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J 17:10–12

    Article  Google Scholar 

  • McLaughlin S, Downing D, Blasing T, Cook E, Adams H (1987) An analysis of climate and competition as contributors to decline of red spruce in high elevation Appalachian forests of the eastern United States. Oecologia 72:487–501

    Article  CAS  PubMed  Google Scholar 

  • Mead A, Peñaloza Ramirez J, Bartlett MK, Wright JW, Sack L, Sork VL (2019) Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations. Mol Ecol 28:5248–5264

    Article  CAS  PubMed  Google Scholar 

  • Meireles B, Usié A, Barbosa P, Fortes AM, Folgado A, Chaves I, Carrasquinho I, Costa RL, Gonçalves S, Teixeira RT (2018) Characterization of the cork formation and production transcriptome in Quercus cerris × suber hybrids. Physiol Mol Biol Plants 24:535–549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mevy J-P, Loriod B, Liu X, Corre E, Torres M, Büttner M, Haguenauer A, Reiter IM, Fernandez C, Gauquelin T (2020) Response of Downy Oak (Quercus pubescens Willd.) to climate change: transcriptome assembly, differential gene analysis and targeted metabolomics. Plants 9:1149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mir Abolfathi M (2013) Outbreak of charcoal disease on Quercus spp and Zelkova carpinifolia trees in forests of Zagros and Alborz mountains in Iran. Iranian J Plant Pathol 49:257–263

    Google Scholar 

  • Moradi A, Abkenar KT, Mohammadian MA, Shabanian N (2017) Effects of dust on forest tree health in Zagros oak forests. Environ Monit Assess 189:549

    Article  CAS  PubMed  Google Scholar 

  • Moradi N, Sadravi M (2017) Four important oak diseases in Iran. Plant Pathol Sci 6:14–23

    Article  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185

    Article  PubMed  PubMed Central  Google Scholar 

  • Mukherjee A (2020) Role of DnaK-DnaJ proteins in PSII repair. Plant Physiol 182:1804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nafisi M, Fimognari L, Sakuragi Y (2015) Interplays between the cell wall and phytohormones in interaction between plants and necrotrophic pathogens. Phytochemistry 112:63–71

    Article  CAS  PubMed  Google Scholar 

  • Nagashima Y, von Schaewen A, Koiwa H (2018) Function of N-glycosylation in plants. Plant Sci 274:70–79

    Article  CAS  PubMed  Google Scholar 

  • Ohama N, Sato H, Shinozaki K, Yamaguchi-Shinozaki K (2017) Transcriptional regulatory network of plant heat stress response. Trends Plant Sci 22:53–65

    Article  CAS  PubMed  Google Scholar 

  • Ostakh E, Soosani J, Abdolkhani A, Naghavi H (2019) Impact of decline on the concentration of chemical elements in the wood of declined and healthy Brant`s oak (Quercus brantii Lindl.). Iran J for Poplar Res 27:413–424

    Google Scholar 

  • Panahi P, Jamzad Z, Pourmajidian M, Fallah A, Pourhashemi M, Sohrabi H (2012) Taxonomic revision of the Quercus brantii complex (Fagaceae) in Iran with emphasis on leaf and pollen micromorphology. Acta Bot Hungar 54:355–375

    Article  Google Scholar 

  • Plomion C, Aury J-M, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G (2018) Oak genome reveals facets of long lifespan. Nat Plants 4:440–452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pogorelko G, Lionetti V, Bellincampi D, Zabotina O (2013) Cell wall integrity: targeted post-synthetic modifications to reveal its role in plant growth and defense against pathogens. Plant Signal Behav 8:e25435

    Article  PubMed  PubMed Central  Google Scholar 

  • Pourhashemi M, Jahanbazi Goujani H, Hoseinzadeh J, Sk B, Iranmanesh Y, Khodakarami Y (2017) The history of oak decline in Zagros forests. Iran Nat 2:37–30

    Google Scholar 

  • Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C (2018) The draft genome sequence of cork oak. Sci Data 5:180069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rivals E, Bruyere C, Toffano-Nioche C, Lecharny A (2006) Formation of the Arabidopsis pentatricopeptide repeat family. Plant Physiol 141:825–839

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    Article  CAS  PubMed  Google Scholar 

  • Rostamian M (2017) The relationship between oak charcoal disease (Biscogniauxia mediterranea) and borer beetles in the Zagros forests, Khorram Abad. J Wood for Sci Technol 24:110–142

    Google Scholar 

  • Roushani Nia F, Naji H, Bazgir M, Naderi M (2018) Effect of simulated dust storm on some bio-chemical features of Persian oak (Quercus brantii Lindl.). Environ Eros Res J 8:59–73

    Google Scholar 

  • Shiran B, Mashayekhi S, Jahanbazi H, Soltani A, Bruschi P (2011) Morphological and molecular diversity among populations of Quercus brantii Lindl. in western forest of Iran. Plant Biosyst 145:452–460

    Article  Google Scholar 

  • Sisakht Nejad M, Zolfaghari R (2015) The effect of water stress on gas exchange in two Iranian oak species (Quercus brantii) and Vyvl (Quercus libani). Zagros for Res 1:15–31

    Google Scholar 

  • Sohrabi SS, Ismaili A, Nazarian-Firouzabadi F, Fallahi H, Hosseini SZ (2022) Identification of key genes and molecular mechanisms associated with temperature stress in lentil. Gene 807:145952

    Article  CAS  PubMed  Google Scholar 

  • Soltani N, Best T, Grace D, Nelms C, Shumaker K, Romero-Severson J, Moses D, Schuster S, Staton M, Carlson J (2020) Transcriptome profiles of Quercus rubra responding to increased O 3 stress. BMC Genomics 21:1–18

    Article  Google Scholar 

  • Song L, Florea L (2015) Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. GigaScience 4:48

    Article  PubMed  PubMed Central  Google Scholar 

  • Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL (2016) First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae). G3 Genes Genomes Genet 6:3485–3495

    CAS  Google Scholar 

  • Spieß N, Oufir M, Matušíková I, Stierschneider M, Kopecky D, Homolka A, Burg K, Fluch S, Hausman J-F, Wilhelm E (2012) Ecophysiological and transcriptomic responses of oak (Quercus robur) to long-term drought exposure and rewatering. Environ Exp Bot 77:117–126

    Article  Google Scholar 

  • Starkey DA, Oak SW, Ryan GW, Tainter FH, Redmond C, Brown H (1989) Evaluation of oak decline areas in the south. USDA Forest Service—Southern Region–Regional Office, Atlanta, p 36

  • Takahashi S, Murata N (2008) How do environmental stresses accelerate photoinhibition? Trends Plant Sci 13:178–182

    Article  CAS  PubMed  Google Scholar 

  • Thalmann M, Santelia D (2017) Starch as a determinant of plant fitness under abiotic stress. New Phytol 214:943–951

    Article  CAS  PubMed  Google Scholar 

  • Tongo A, Jalilvand H, Hosseininasr M, Naji H (2020) Variation in anatomical properties and hydraulic conductivity of Persian oak (Quercus brantii Lindl.) trees affected by Dieback. Ecopersia 8:117–124

    Google Scholar 

  • Torre S, Tattini M, Brunetti C, Fineschi S, Fini A, Ferrini F, Sebastiani F (2014) RNA-seq analysis of Quercus pubescens leaves: de novo transcriptome assembly, annotation and functional markers development. PLoS One 9:e112487

    Article  PubMed  PubMed Central  Google Scholar 

  • Underwood W (2012) The plant cell wall: a dynamic barrier against pathogen invasion. Front Plant Sci 3:85

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Usié A, Simões F, Barbosa P, Meireles B, Chaves I, Gonçalves S, Folgado A, Almeida MH, Matos J, Ramos AM (2017) Comprehensive analysis of the cork oak (Quercus suber) transcriptome involved in the regulation of bud sprouting. Forests 8:486

    Article  Google Scholar 

  • Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11:1–14

    Article  Google Scholar 

  • Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:1–13

    Article  Google Scholar 

  • Wise R, Olson A, Schrader S, Sharkey T (2004) Electron transport is the functional limitation of photosynthesis in field-grown Pima cotton plants at high temperature. Plant Cell Environ 27:717–724

    Article  CAS  Google Scholar 

  • Xu W, Zhang N, Jiao Y, Li R, Xiao D, Wang Z (2014) The grapevine basic helix-loop-helix (bHLH) transcription factor positively modulates CBF-pathway and confers tolerance to cold-stress in Arabidopsis. Mol Biol Rep 41:5329–5342

    Article  CAS  PubMed  Google Scholar 

  • Zarafshar M, Negahdarsaber M, Jahanbazi Gojani H, Pourhashemi M, Bordbar SK, Matinizedeh M, Abbasi A (2020) Dieback in pure stands of Brant’s oak (Quercus brantii Lindl.) in southern Zagros forests, Kohmareh Sorkhi region of Fars province. Iran J for 12:291–303

    Google Scholar 

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Authors and Affiliations

  1. Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, 68149-84896, Iran

    Masoume Safari, Ahmad Ismaili, Seyed Sajad Sohrabi & Farhad Nazarian-Firouzabadi

  2. Department of Water Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, 68149-84896, Iran

    Hasan Torabi Podeh

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  1. Masoume Safari
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Contributions

MS conducted the experiments and drafted the manuscript. AI conceived the project and supervised and coordinated the research. SSS analyzed transcriptome data and supported some experiments in the laboratory. FNF and HTP revised and edited the manuscript.

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Correspondence to Ahmad Ismaili.

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10528_2022_10283_MOESM5_ESM.xlsx

Supplementary Table S5 BLASTx results for all unigenes in transcriptome assembly against (a) NR; (b) RefSeq; (c) UniProtKB/Swiss-Prot and (d) PDB databases (XLSX 5873 kb)

Fig. S1 BUSCO results for Persian oak transcriptome assembly (JPG 427 kb)

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Fig. S2 Histogram of Gene Ontology (GO) classifications of Persian oak transcriptome assembly. The results are summarized in three main categories: biological process (BP), molecular function (MF), and cellular component (CC) (JPG 502 kb)

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Fig. S3 Top 10 KEGG metabolic pathways enriched by the differentially expressed genes involved in Persian oak decline (JPG 366 kb)

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Fig. S4 Heat map of TF-DE involved in Persian oak decline. The average FPKM of all transcripts related to each TF gene was used (JPG 639 kb)

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Safari, M., Ismaili, A., Sohrabi, S. et al. Transcriptome Analysis of Persian Oak (Quercus brantii L.) Decline Using RNA-seq Technology. Biochem Genet 61, 879–900 (2023). https://doi.org/10.1007/s10528-022-10283-8

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  • DOI: https://doi.org/10.1007/s10528-022-10283-8

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