Fraxinus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA79687 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR058827.fastq.gz | Fastqsanger.gz |
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Project description:A new genome of Fraxinus excelsior was assembled using a hybrid approach combining Nanopore and Illumina data (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ). Methylation was also assessed in the genome. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214553 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214554 | GEO
Project description:An updated de novo transcriptome for green ash (Fraxinus pennsylvanica)
| PRJNA898644 | ENA
Project description:Transcriptome profiling of Fraxinus excelsior clones challenged by Emerald ash borer
| PRJDB15336 | ENA
Project description:<p><strong>INTRODUCTION:</strong> Larvae of the invasive emerald ash borer [EAB, <em>Agrilus planipennis</em> Fairmaire (Coleoptera: Buprestidae)], kill over 99% of green ash (<em>Fraxinus pennsylvanica</em> Marshall) trees they infest, yet a small percentage of green ash (“lingering ash”) survive years of heavy EAB attack. In the face of an ongoing invasion that threatens multiple North American <em>Fraxinus</em> species with extinction, any evidence for reproducible defensive responses in the native species merits investigation.</p><p><strong>METHODS: </strong>We evaluated the capacity of 3 families of green ash F1 progeny to kill EAB larvae when challenged in greenhouse studies by infestation with a uniform density of EAB eggs followed by dissection 8 weeks post-infestation and comparison of the host metabolomic profiles.</p><p><strong>RESULTS:</strong> The mean proportions of host-killed larvae in the 2 families of F1 progeny from lingering ash parents were significantly higher than that of host-killed larvae in the family of F1 progeny from susceptible ash parents (<em>p</em> < 0.001). Untargeted metabolomics comparing F1 progeny in the quartile with the highest percent host-killed larvae (HHK) to F1 progeny in the quartile with the lowest percent host-killed larvae (LHK) and to the uninfested F1 progeny within each family revealed evidence for induced biochemical responses to EAB. Infested trees produced significantly higher levels of select secoiridoids than uninfested trees, and LHK progeny produced significantly higher levels of select secoiridoids than the HHK progeny. HHK progeny produced significantly higher abundances of 3 metabolites annotated as aromatic alkaloids than the LHK and uninfested individuals.</p><p><strong>DISCUSSION: </strong>Based on these results, we hypothesize that green ash responds to EAB infestation. However, only certain trees have the genetic capacity to tailor a response that kills enough EAB larvae to prevent lethal damage to the vascular system. Rigorous tests of this hypothesis will require 15–20 years of additional crossing, phenotyping, and omics analyses. The results of this investigation will encourage the establishment and continuation of breeding programs that, in concert with biocontrol and management, could provide trees that slow, if not halt, the decimation of the <em>Fraxinus</em> gene pool. At the same time, ongoing work on host-insect interaction will contribute to our understanding of how forest trees recognize and defend themselves against phloem-feeding insects.</p>
2024-02-08 | MTBLS7999 | MetaboLights
Project description:DNA was extracted from two ash tree samples, one tolerant and one susceptible to ash dieback. The DNA was sequenced using Nanopore technologies and the methylation was called against the new genome (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ) to identify differentially methylated regions between both samples. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214552 | GEO
Project description:A new genome of Fraxinus excelsior (PRJNA865134) was assembled using a hybrid approach combining Nanopore and Illumina data. The gene expression of a 182 Danish tree panel (Harper et al. 2016) was assessed using the new genome as reference (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ).Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214551 | GEO
Project description:Hymenoscyphus fraxineus, the causal agent of Ash Dieback (ADB), has been introduced to eastern Europe in the 1990s from where it spread causing decline in European ash populations. However, the genetic basis of the molecular response in tolerant and susceptible ash trees to this disease is still largely unknown. We performed RNA-sequencing to study the transcriptomic response to the disease in four ash genotypes (ADB-tolerant FAR3 and FS36, and ADB-susceptible UW1 and UW2), during a time-course of 7, 14, 21, and 28 days post-inoculation, including mock-infected trees as control samples for each sampling time point. The analysis yielded 395 and 500 Differentially Expressed Genes (DEGs) along the response for ADB-tolerant FAR3 and FS36, respectively, while ADB-susceptible UW1 and UW2 revealed 194 and 571 DEGs, respectively, with most DEGs found exclusively in just one of the genotypes. DEGs shared between tolerant genotypes FAR3 and FS36, included genes involved in the production of phytoalexins and other secondary metabolites with roles in plant defense. Moreover, we identified an earlier expression of genes involved in both pattern- and effector-triggered immunity (PTI and ETI) in ADB-tolerant genotypes, while in ADB-susceptible genotypes both responses were delayed (late response). Overall, these results revealed different transcriptomic expression patterns not only between ADB-tolerant and ADB-susceptible genotypes, but also within these two groups. This hints to individual response in the natural tolerance to ADB, possibly revealing diversified strategies across ash genotypes.
2025-01-29 | GSE278637 | GEO