{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T10:04:09Z","timestamp":1774519449841,"version":"3.50.1"},"reference-count":87,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2017,8,3]],"date-time":"2017-08-03T00:00:00Z","timestamp":1501718400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Forests"],"abstract":"<jats:p>Forests are essential resources on a global scale, not only for the ecological benefits, but also for economical and landscape purposes. However, in recent years, a large number of forest species have suffered a serious decline, with maritime pine being one of the most affected. In Portugal, the maritime pine forest has been devastated by the pine wood nematode (PWN), the causal agent of pine wilt disease. In this study, RNA-Seq data was used to characterize the maritime pine response to infection with PWN, by determining the differentially expressed genes and identifying the regulatory networks and pathways associated. The analyses showed clear differences between an early response that occurs immediately after inoculation and a late response that is observed seven days after inoculation. Moreover, differentially expressed genes related to secondary metabolism, oxidative stress and defense against pathogen infection were identified over different time points. These results provide new insights about the molecular mechanisms and metabolic pathways involved in the response of Pinus pinaster against PWN infection, which will be a useful resource in follow-up studies and for future breeding programs to select plants with lower susceptibility to this disease.<\/jats:p>","DOI":"10.3390\/f8080279","type":"journal-article","created":{"date-parts":[[2017,8,3]],"date-time":"2017-08-03T09:47:19Z","timestamp":1501753639000},"page":"279","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4948-5662","authenticated-orcid":false,"given":"Daniel","family":"Gaspar","sequence":"first","affiliation":[{"name":"Centro de Biotecnologia Agr\u00edcola e Agro-alimentar do Alentejo (CEBAL)\/Instituto Polit\u00e9cnico de Beja (IPBeja), Rua Pedro Soares, s.n.\u2014Campus IPBeja\/ESAB, Apartado 6158, 7801-908 Beja, Portugal"},{"name":"Instituto de Ci\u00eancias Agr\u00e1rias e Ambientais Mediterr\u00e2nicas (ICAAM), Universidade de \u00c9vora, N\u00facleo da Mitra, Apartado 94, 7006-554 \u00c9vora, Portugal"}]},{"given":"C\u00e2ndida","family":"Trindade","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Investiga\u00e7\u00e3o Agr\u00e1ria e Veterin\u00e1ria, I.P. (INIAV), Avenida da Rep\u00fablica, Quinta do Marqu\u00eas (edif\u00edcio sede), 2780-157 Oeiras, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3364-9434","authenticated-orcid":false,"given":"Ana","family":"Usi\u00e9","sequence":"additional","affiliation":[{"name":"Centro de Biotecnologia Agr\u00edcola e Agro-alimentar do Alentejo (CEBAL)\/Instituto Polit\u00e9cnico de Beja (IPBeja), Rua Pedro Soares, s.n.\u2014Campus IPBeja\/ESAB, Apartado 6158, 7801-908 Beja, Portugal"},{"name":"Instituto de Ci\u00eancias Agr\u00e1rias e Ambientais Mediterr\u00e2nicas (ICAAM), Universidade de \u00c9vora, N\u00facleo da Mitra, Apartado 94, 7006-554 \u00c9vora, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5976-1889","authenticated-orcid":false,"given":"Br\u00edgida","family":"Meireles","sequence":"additional","affiliation":[{"name":"Centro de Biotecnologia Agr\u00edcola e Agro-alimentar do Alentejo (CEBAL)\/Instituto Polit\u00e9cnico de Beja (IPBeja), Rua Pedro Soares, s.n.\u2014Campus IPBeja\/ESAB, Apartado 6158, 7801-908 Beja, Portugal"},{"name":"Instituto de Ci\u00eancias Agr\u00e1rias e Ambientais Mediterr\u00e2nicas (ICAAM), Universidade de \u00c9vora, N\u00facleo da Mitra, Apartado 94, 7006-554 \u00c9vora, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3892-7640","authenticated-orcid":false,"given":"Pedro","family":"Barbosa","sequence":"additional","affiliation":[{"name":"Centro de Biotecnologia Agr\u00edcola e Agro-alimentar do Alentejo (CEBAL)\/Instituto Polit\u00e9cnico de Beja (IPBeja), Rua Pedro Soares, s.n.\u2014Campus IPBeja\/ESAB, Apartado 6158, 7801-908 Beja, Portugal"},{"name":"Instituto de Ci\u00eancias Agr\u00e1rias e Ambientais Mediterr\u00e2nicas (ICAAM), Universidade de \u00c9vora, N\u00facleo da Mitra, Apartado 94, 7006-554 \u00c9vora, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7552-0164","authenticated-orcid":false,"given":"Ana","family":"Fortes","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa (FCUL), BioSystems & Integrative Sciences Institute (BIOISI), Campo Grande, 1749-016 Lisboa, Portugal"}]},{"given":"C\u00e1tia","family":"Pesquita","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa (FCUL), LaSIGE, Campo Grande, 1749-016 Lisboa, Portugal"}]},{"given":"Rita","family":"Costa","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Investiga\u00e7\u00e3o Agr\u00e1ria e Veterin\u00e1ria, I.P. (INIAV), Avenida da Rep\u00fablica, Quinta do Marqu\u00eas (edif\u00edcio sede), 2780-157 Oeiras, Portugal"}]},{"given":"Ant\u00f3nio","family":"Ramos","sequence":"additional","affiliation":[{"name":"Centro de Biotecnologia Agr\u00edcola e Agro-alimentar do Alentejo (CEBAL)\/Instituto Polit\u00e9cnico de Beja (IPBeja), Rua Pedro Soares, s.n.\u2014Campus IPBeja\/ESAB, Apartado 6158, 7801-908 Beja, Portugal"},{"name":"Instituto de Ci\u00eancias Agr\u00e1rias e Ambientais Mediterr\u00e2nicas (ICAAM), Universidade de \u00c9vora, N\u00facleo da Mitra, Apartado 94, 7006-554 \u00c9vora, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2017,8,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1104\/pp.123.3.959","article-title":"Compression wood-responsive proteins in developing xylem of maritime pine (Pinus pinaster Ait.)","volume":"123","author":"Plomion","year":"2000","journal-title":"Plant Physiol."},{"key":"ref_2","first-page":"1","article-title":"IFN6\u2014\u00c1reas dos usos do solo e das esp\u00e9cies florestais de Portugal continental","volume":"1","author":"Uva","year":"2013","journal-title":"Inst. Conserv. Nat. Florestas I.P."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Mota, M.M., Futai, K., and Vieira, P. (2009). Pine Wilt Disease And The Pinewood Nematode, Bursaphelenchus Xylophilus. Integrated Management of Fruit Crops Nematodes, Springer.","DOI":"10.1007\/978-1-4020-9858-1_11"},{"key":"ref_4","unstructured":"Futai, K., Sutherland, J.R., and Takeuchi, Y. (2008). Pine Wilt Disease, Springer."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1163\/156854199508757","article-title":"First report of Bursaphelenchus xylophilus in Portugal and in Europe","volume":"1","author":"Mota","year":"1999","journal-title":"Nematology"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Farjon, A. (2010). A Handbook of the World\u2019s Conifers, Brill.","DOI":"10.1163\/9789047430629"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1163\/156854101300106937","article-title":"Bursaphelenchus xylophilus (Nematoda: Aphelenchoididae) associated with Monochamus galloprovincialis (Coleoptera: Cerambycidae) in Portugal","volume":"3","author":"Sousa","year":"2001","journal-title":"Nematology"},{"key":"ref_8","first-page":"193","article-title":"Transmission of the pine wood nematode Bursaphelenchus xylophilus through oviposition activity of Monochamus galloprovincialis (Coleoptera: Cerambycidae)","volume":"18","author":"Naves","year":"2007","journal-title":"Entomol. Fenn."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/forestry\/69.1.35","article-title":"The pine wood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle (= B. lignicolus Mamiya and Kiyohara): An assessment of the current position","volume":"69","author":"Fielding","year":"1996","journal-title":"Forestry"},{"key":"ref_10","first-page":"133","article-title":"Transmission of Bursaphelenchus xylophilus through Oviposition Wounds of Monochamm carolinensis (Coleoptera: Cerambycidae)","volume":"24","author":"Edwards","year":"1992","journal-title":"J. Nematol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/j.1439-0418.2006.01111.x","article-title":"Transmission of the pine wood nematode Bursaphelenchus xylophilus through feeding activity of Monochamus galloprovincialis (Col., Cerambycidae)","volume":"131","author":"Naves","year":"2007","journal-title":"J. Appl. Entomol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/BF02348216","article-title":"Physiological process of the symptom development and resistance mechanism in pine wilt disease","volume":"2","author":"Fukuda","year":"1997","journal-title":"J. For. Res."},{"key":"ref_13","first-page":"2","article-title":"A brief account of forest tree improvment in China","volume":"14","author":"Jusheng","year":"1985","journal-title":"Genet. Resour. Inf."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Parchman, T.L., Geist, K.S., Grahnen, J.A., Benkman, C.W., and Buerkle, C.A. (2010). Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. BMC Genom., 11.","DOI":"10.1186\/1471-2164-11-180"},{"key":"ref_16","first-page":"429","article-title":"Comparative Studies between Portuguese and Japanese Isolates of the Pinewood Nematode, Bursaphelenchus xylophilus","volume":"38","author":"Mota","year":"2006","journal-title":"J. Nematol."},{"key":"ref_17","first-page":"133","article-title":"Biology of Monochamus galloprovincialis (Coleoptera, Cerambycidae) in the Pine Wilt Disease Affected Zone, Southern Portugal","volume":"16","author":"Naves","year":"2008","journal-title":"Silva Lusit."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1163\/156854112X632673","article-title":"The pine wood nematode, Bursaphelenchus xylophilus, in Portugal: Possible introductions and spread routes of a serious biological invasion revealed by molecular methods","volume":"14","author":"Valadas","year":"2012","journal-title":"Nematology"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Vicente, C.S.L., Nascimento, F., Espada, M., Barbosa, P., Mota, M., Glick, B.R., and Oliveira, S. (2012). Characterization of Bacteria Associated with Pinewood Nematode Bursaphelenchus xylophilus. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0046661"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Santos, C.S., Pinheiro, M., Silva, A.I., Egas, C., and Vasconcelos, M.W. (2012). Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-599"},{"key":"ref_21","first-page":"131","article-title":"Ein einfache Methode zur Auffindung von Anklyostomum (Nematoden) Larven in Erdproben","volume":"57","author":"Baermann","year":"1917","journal-title":"Ned. Tijdschr. Geneeskd."},{"key":"ref_22","first-page":"23","article-title":"The variety of resistances among pine species to pine wood nematode, Bursaphelenchus lignicolus","volume":"51","author":"Futai","year":"1979","journal-title":"Bull. Kyoto Univ. For."},{"key":"ref_23","first-page":"291","article-title":"A micromethod for high throughput RNA extraction in forest trees","volume":"40","author":"Herrera","year":"2007","journal-title":"Biol. Res."},{"key":"ref_24","unstructured":"(2016, September 20). FastQC\u2014A Quality Control Tool for High Throughput Sequence Data. Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_25","unstructured":"(2016, September 20). Sickle: A Windowed Adaptive Trimming Tool for FASTQ Files Using Quality. Available online: https:\/\/github.com\/najoshi\/sickle."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1101\/gr.9.9.868","article-title":"CAP3: A DNA sequence assembly program","volume":"9","author":"Huang","year":"1999","journal-title":"Genome Res."},{"key":"ref_28","unstructured":"Haas, B. (2016, May 16). TransDecoder (Find Coding Regions Within Transcripts). Available online: http:\/\/transdecoder.github.io."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: Towards a more sustainable future","volume":"44","author":"Finn","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_32","first-page":"114","article-title":"Multiple alignment using hidden Markov models","volume":"3","author":"Eddy","year":"1995","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"i192","DOI":"10.1093\/bioinformatics\/btw277","article-title":"RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes","volume":"32","author":"Srivastava","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"Robinson","year":"2010","journal-title":"Genome Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Sebastiana, M., Vieira, B., Lino-Neto, T., Monteiro, F., Figueiredo, A., Sousa, L., Pais, M.S., Tavares, R., and Paulo, O.S. (2014). Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0098376"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Yoav","year":"1995","journal-title":"J. R. Stat. Soc."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"W71","DOI":"10.1093\/nar\/gkm306","article-title":"Primer3Plus, an enhanced web interface to Primer3","volume":"35","author":"Untergasser","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"W116","DOI":"10.1093\/nar\/gki442","article-title":"InterProScan: Protein domains identifier","volume":"33","author":"Quevillon","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_45","first-page":"108","article-title":"CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories","volume":"9","author":"Jie","year":"2008","journal-title":"Online J. Bioinform."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","article-title":"BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks","volume":"21","author":"Maere","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G.D. (2010). Enrichment map: A network-based method for gene-set enrichment visualization and interpretation. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0013984"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/mp\/ssp106","article-title":"Phenylpropanoid Biosynthesis","volume":"3","author":"Vogt","year":"2010","journal-title":"Mol. Plant"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/aob\/mch107","article-title":"Phenylpropanoids, phenylalanine ammonia lyase and peroxidases in elicitor-challenged cassava (Manihot esculenta) suspension cells and leaves","volume":"94","author":"Day","year":"2004","journal-title":"Ann. Bot."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"70","DOI":"10.3389\/fpls.2013.00070","article-title":"Modifying lignin to improve bioenergy feedstocks: Strengthening the barrier against pathogens?","volume":"4","author":"Sattler","year":"2013","journal-title":"Front. Plant Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1016\/S0022-2275(20)39958-2","article-title":"Regulation of HMG-CoA reductase activity in plants","volume":"35","author":"Stermer","year":"1994","journal-title":"J. Lipid Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/978-1-4939-0606-2_2","article-title":"Measuring the activity of 1-deoxy-d-xylulose 5-phosphate synthase, the first enzyme in the MEP pathway, in plant extracts","volume":"1153","author":"Wright","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/s11101-011-9211-7","article-title":"Chalcone synthase and its functions in plant resistance","volume":"10","author":"Dao","year":"2011","journal-title":"Phytochem. Rev."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1110\/ps.03395404","article-title":"Chalcone isomerase family and fold: No longer unique to plants","volume":"13","author":"Gensheimer","year":"2004","journal-title":"Protein Sci."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Liu, F., Guo, J., Bai, P., Duan, Y., Wang, X., Cheng, Y., Feng, H., Huang, L., and Kang, Z. (2012). Wheat TaRab7 GTPase Is Part of the Signaling Pathway in Responses to Stripe Rust and Abiotic Stimuli. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0037146"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1104\/pp.106.089458","article-title":"Plant Glutathione Peroxidases Are Functional Peroxiredoxins Distributed in Several Subcellular Compartments and Regulated during Biotic and Abiotic Stresses","volume":"142","author":"Navrot","year":"2006","journal-title":"Plant Physiol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.4161\/psb.6.10.17088","article-title":"Plant dehydrins and stress tolerance: Versatile proteins for complex mechanisms","volume":"6","author":"Hanin","year":"2011","journal-title":"Plant Signal. Behav."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Wegrzyn, J.L., Lee, J.M., Tearse, B.R., and Neale, D.B. (2008). TreeGenes: A forest tree genome database. Int. J. Plant Genom., 412875.","DOI":"10.1155\/2008\/412875"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1114\/1.1313771","article-title":"Strategies for the Physiome Project","volume":"28","author":"Bassingthwaighte","year":"2000","journal-title":"Ann. Biomed. Eng."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"e0018","DOI":"10.1199\/tab.0018","article-title":"Purine and pyrimidine nucleotide synthesis and metabolism","volume":"1","author":"Moffatt","year":"2002","journal-title":"Arabidopsis Book"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"763","DOI":"10.3923\/pjbs.2008.763.767","article-title":"Sequence analysis of GDSL lipase gene family in Arabidopsis thaliana","volume":"11","author":"Ling","year":"2008","journal-title":"Pak. J. Biol. Sci."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1105\/tpc.105.034819","article-title":"Secretome Analysis Reveals an Arabidopsis Lipase Involved in Defense against Alternaria brassicicola","volume":"17","author":"Oh","year":"2005","journal-title":"Plant Cell"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/S1357-2725(03)00213-9","article-title":"The translationally controlled tumour protein (TCTP)","volume":"36","author":"Bommer","year":"2004","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"5471","DOI":"10.1093\/jxb\/err226","article-title":"A jacalin-related lectin-like gene in wheat is a component of the plant defence system","volume":"62","author":"Xiang","year":"2011","journal-title":"J. Exp. Bot."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"11356","DOI":"10.3390\/ijms140611356","article-title":"Characterization of the Pinus massoniana transcriptional response to Bursaphelenchus xylophilus infection using suppression subtractive hybridization","volume":"14","author":"Xu","year":"2013","journal-title":"Int. J. Mol. Sci."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/s10725-015-0134-y","article-title":"Expansion and evolution of thaumatin-like protein (TLP) gene family in six plants","volume":"79","author":"Cao","year":"2016","journal-title":"Plant Growth Regul."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1007\/s00299-010-0826-8","article-title":"The superfamily of thaumatin-like proteins: Its origin, evolution, and expression towards biological function","volume":"29","author":"Liu","year":"2010","journal-title":"Plant Cell Rep."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.biotechadv.2011.12.003","article-title":"Genetic engineering of cytokinin metabolism: Prospective way to improve agricultural traits of crop plants","volume":"31","author":"Galuszka","year":"2013","journal-title":"Biotechnol. Adv."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.cj.2016.01.010","article-title":"Phytohormones and their metabolic engineering for abiotic stress tolerance in crop plants","volume":"4","author":"Wani","year":"2016","journal-title":"Crop J."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1093\/treephys\/tpn034","article-title":"Identification of genes upregulated by pinewood nematode inoculation in Japanese red pine","volume":"29","author":"Shin","year":"2009","journal-title":"Tree Physiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1146\/annurev.arplant.56.032604.144224","article-title":"Plant-specific calmodulin-binding proteins","volume":"56","author":"Yellin","year":"2005","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1093\/treephys\/28.7.1099","article-title":"Carbohydrate-related genes and cell wall biosynthesis in vascular tissues of loblolly pine (Pinus taeda)","volume":"28","author":"Nairn","year":"2008","journal-title":"Tree Physiol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s00425-015-2394-1","article-title":"Heat stress affects the cytoskeleton and the delivery of sucrose synthase in tobacco pollen tubes","volume":"243","author":"Parrotta","year":"2016","journal-title":"Planta"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.pbi.2004.05.009","article-title":"Plant disease resistance protein signaling: NBS\u2013LRR proteins and their partners","volume":"7","author":"Belkhadir","year":"2004","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nrmicro925","article-title":"Cellulosomes: Plant-cell-wall-degrading enzyme complexes","volume":"2","author":"Doi","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"12","DOI":"10.3389\/fenrg.2014.00012","article-title":"Lignin Biodegradation with Laccase-Mediator Systems","volume":"2","author":"Christopher","year":"2014","journal-title":"Front. Energy Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1093\/jexbot\/52.358.1143","article-title":"Drought differentially affects expression of a PR-10 protein, in needles of maritime pine (Pinus pinaster Ait.) seedlings","volume":"52","author":"Dubos","year":"2001","journal-title":"J. Exp. Bot."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/gb-2006-7-4-212","article-title":"Plant NBS-LRR proteins: Adaptable guards","volume":"7","author":"McHale","year":"2006","journal-title":"Genome Biol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.2478\/s11756-014-0431-3","article-title":"Auxins in defense strategies","volume":"69","author":"Carna","year":"2014","journal-title":"Biologia (Bratisl)"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"13","DOI":"10.4161\/psb.6.1.14037","article-title":"Phospholipases in action during plant defense signaling","volume":"6","author":"Canonne","year":"2011","journal-title":"Plant Signal. Behav."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"24540","DOI":"10.1074\/jbc.M309882200","article-title":"Differential roles of tau class glutathione S-transferases in oxidative stress","volume":"279","author":"Kilili","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1023\/A:1006163030646","article-title":"Characterization of a pine multigene family containing elicitor-responsive stilbene synthase genes","volume":"39","author":"Schwekendiek","year":"1999","journal-title":"Plant Mol. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"3335","DOI":"10.1073\/pnas.042698899","article-title":"A stilbene synthase from Japanese red pine (Pinus densiflora): Implications for phytoalexin accumulation and down-regulation of flavonoid biosynthesis","volume":"99","author":"Kodan","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.pmpp.2005.05.004","article-title":"Identification of a superoxide dismutase gene from the conifer pathogen Heterobasidion annosum","volume":"66","author":"Karlsson","year":"2005","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"}],"container-title":["Forests"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4907\/8\/8\/279\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:45:06Z","timestamp":1760208306000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4907\/8\/8\/279"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,3]]},"references-count":87,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2017,8]]}},"alternative-id":["f8080279"],"URL":"https:\/\/doi.org\/10.3390\/f8080279","relation":{},"ISSN":["1999-4907"],"issn-type":[{"value":"1999-4907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,3]]}}}