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
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
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.
Project description:European common ash, Fraxinus excelsior L., is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus we performed untargeted metabolomic profiling on leaves from selected F. excelsior individuals showing strong tolerance or susceptibility to H. fraxineus. We identified sets of "features" [small molecules] that enabled strong discrimination between tolerant or susceptible genotypes of F. excelsior. Strikingly, tolerant F. excelsior lines exhibited low levels of iridoid glycosides, known anti-feeding deterrents. As Europe is threatened by Emerald Ash Borer (Agrilus planipennis), an invasive wood boring beetle native to East Asia that has devastated North American ash, our study raises the question whether selection for resistance to H. fraxineus leads to ecological trade-offs that result in susceptibility to emerging pests such as emerald ash borer.
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
Project description:A de novo 454-Illumina whole genome sequence for a self-pollinated progeny of a Fraxinus excelsior tree growing in woodland in Gloucestershire, UK
