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dc.contributor.author | Hernandez-Escribano, Laura![]() |
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dc.contributor.author | Visser, Erik A.![]() |
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dc.contributor.author | Iturritxa, Eugenia![]() |
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dc.contributor.author | Raposo, Rosa![]() |
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dc.contributor.author | Naidoo, Sanushka![]() |
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dc.date.accessioned | 2020-04-09T14:32:24Z | |
dc.date.available | 2020-04-09T14:32:24Z | |
dc.date.issued | 2020-01-08 | |
dc.description | Additional file 1 Symptoms at the shoot tip of inoculated (left side) and mock-inoculated (right side) Pinus pinaster seedlings by the end of the experiment (33 dpi). | en_ZA |
dc.description | Additional file 2. Statistics for each TransABySS and Trinity assembly. N seq: number of transcripts; N bases: number of bases; Mean length: mean length of the transcripts; N50: N50 value; Ns: number of unknown bases; % GC: guanine and cytosine content; trinity-N: in silico normalized trinity assembly; trinity-nN: non-normalized trinity assemblies. * Best quality preliminary assemblies selected to generate the final assembly. | en_ZA |
dc.description | Additional file 3. Comparative statistics between normalized (Norm) and non-normalized (N-norm) Trinity preliminary assemblies. Kmer value; % of mapped fragments; % of good mapping; AS: assembly score; OP: optimal score; OC: optimal cutoff; Number of good contigs; % good contigs. | en_ZA |
dc.description | Additional file 4. BUSCO analysis against the embryophyta lineage database comparing the last Pinus de novo transcriptomes published. P. patula v1.0 [110]; P. patula v2.0 and P. tecunumanii [108]. | en_ZA |
dc.description | Additional file 5. Pinus pinaster de novo transcriptome annotation. | en_ZA |
dc.description | Additional file 6. Pinus pinaster de novo transcriptome annotation by Mercator tool. | en_ZA |
dc.description | Additional file 7. mapped reads for each species. Number of differential expressed (DE) genes for Pinus pinaster and DE genes for Fusarium circinatum at each time point in inoculated samples (FDR < 0.05; |log2(Fold Change)| > 0.5). Ppin: P. pinaster; Fcir: F. circinatum;HC: high confident. | en_ZA |
dc.description | Additional file 8. Principal component analyses (PCA) for Pinus pinaster (above) and Fusarium circinatum (below) rlog data of the differential expression gene analysis (DESeq2). In red: mock-inoculated samples; in blue: inoculated samples at 3 dpi; in green: inoculated samples at 5 dpi; in yellow: inoculated samples at 10 dpi. | en_ZA |
dc.description | Additional file 9. Clustering of Pinus pinaster and Fusarium circinatum differential expressed (DE) genes. For each cluster with gene ontology (GO) enriched terms, number of genes and percentage for genes are indicated. | en_ZA |
dc.description | Additional file 10. Significantly enriched GO terms identified from Pinus pinaster genes in each cluster. | en_ZA |
dc.description | Additional file 11: Phytohormone related differentially expressed (DE) genes in Pinus pinaster. | en_ZA |
dc.description | Additional file 12: Pathogenesis related (PR) genes differentially expressed (DE) in Pinus pinaster. | en_ZA |
dc.description | Additional file 13: Significantly enriched GO terms identified from high confidence expressed Fusarium circinatum genes. | en_ZA |
dc.description | Additional file 14: Hormone related differential expressed (DE) genes in Fusarium circinatum. | en_ZA |
dc.description | Additional file 15: Fusarium circinatum DE genes related to hormone production with hits in the Pathogen Host Interaction (PHI) database. | en_ZA |
dc.description | Additional file 16:. RNA-seq data statistics for each sample at each time point, before and after filtering and trimming. Dpi: days post-inoculation; BR: biological replicate, RIN: RNA Integrity Number; Q 30: Phred quality score 30. | en_ZA |
dc.description.abstract | BACKGROUND : Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circinatum, the molecular mechanisms of defense in this host are still unknown. Phytohormones produced by the plant and by the pathogen are known to play a crucial role in determining the outcome of plant-pathogen interactions. Therefore, the aim of this study was to determine the role of phytohormones in F. circinatum virulence, that compromise host resistance. RESULTS : A high quality P. pinaster de novo transcriptome assembly was generated, represented by 24,375 sequences from which 17,593 were full length genes, and utilized to determine the expression profiles of both organisms during the infection process at 3, 5 and 10 days post-inoculation using a dual RNA-sequencing approach. The moderate resistance shown by Pinus pinaster at the early time points may be explained by the expression profiles pertaining to early recognition of the pathogen, the induction of pathogenesis-related proteins and the activation of complex phytohormone signaling pathways that involves crosstalk between salicylic acid, jasmonic acid, ethylene and possibly auxins. Moreover, the expression of F. circinatum genes related to hormone biosynthesis suggests manipulation of the host phytohormone balance to its own benefit. CONCLUSIONS : We hypothesize three key steps of host manipulation: perturbing ethylene homeostasis by fungal expression of genes related to ethylene biosynthesis, blocking jasmonic acid signaling by coronatine insensitive 1 (COI1) suppression, and preventing salicylic acid biosynthesis from the chorismate pathway by the synthesis of isochorismatase family hydrolase (ICSH) genes. These results warrant further testing in F. circinatum mutants to confirm the mechanism behind perturbing host phytohormone homeostasis. | en_ZA |
dc.description.department | Biochemistry | en_ZA |
dc.description.department | Forestry and Agricultural Biotechnology Institute (FABI) | en_ZA |
dc.description.department | Genetics | en_ZA |
dc.description.department | Microbiology and Plant Pathology | en_ZA |
dc.description.librarian | am2020 | en_ZA |
dc.description.sponsorship | Laura Hernández was supported by a fellowship from INIA (FPI-INIA) and additional funding for a Short-Term Scientific Mission in the Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa, was provided by Pinestrength Cost Action (FP1406). Financial support for this research was provided by project RTA 2017–00063-C04–01 (Programa Estatal I + D + i, INIA, Spain). EAV was supported through the Technology Innovation Agency (TIA) South Africa, Forest Molecular Genetics Cluster Program. SN was supported by the National Research Foundation (NRF) of South Africa, Y-rated grant program. | en_ZA |
dc.description.uri | https://bmcgenomics.biomedcentral.com | en_ZA |
dc.identifier.citation | Hernandez-Escribano, L., Visser, E.A., Iturritxa, E. et al. 2020, 'The transcriptome of Pinus pinaster under Fusarium circinatum challenge', BMC Genomics, vol. 21, art. 28, pp. 1-18. | en_ZA |
dc.identifier.issn | 1471-2164 (online) | |
dc.identifier.other | 10.1186/s12864-019-6444-0 | |
dc.identifier.uri | http://hdl.handle.net/2263/74112 | |
dc.language.iso | en | en_ZA |
dc.publisher | BioMed Central | en_ZA |
dc.rights | © The Author(s). 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License. | en_ZA |
dc.subject | Pinus pinaster | en_ZA |
dc.subject | Salicylic acid | en_ZA |
dc.subject | Jasmonic acid | en_ZA |
dc.subject | Fusarium circinatum | en_ZA |
dc.subject | Fungal hormone production | en_ZA |
dc.subject | Defense response | en_ZA |
dc.subject | De novo transcriptome assembly | en_ZA |
dc.subject | Dual RNAseq | en_ZA |
dc.title | The transcriptome of Pinus pinaster under Fusarium circinatum challenge | en_ZA |
dc.type | Article | en_ZA |