Genome-wide epigenetic variation among ash trees differing in susceptibility to a fungal disease

• Published in: BMC genomics 2018-06, Vol.19 (1), p.502-15, Article 502
• Main Authors: Sollars, Elizabeth S A, Buggs, Richard J A
• Format: Article
• Language: English
• Subjects: Ascomycota - pathogenicity; Ash dieback; Bioinformatics; Biological evolution; Cloning; Cytosine; Deciduous trees; Deoxyribonucleic acid; Dieback; Disease Susceptibility; DNA; DNA Methylation; DNA, Plant - chemistry; DNA, Plant - isolation & purification; DNA, Plant - metabolism; Dosage compensation; Epigenetics; Epigenomics; Fraxinus - genetics; Fraxinus excelsior; Fraxinus mandshurica; Fungal diseases; Fungi; Gene dosage; Gene Duplication; Gene expression; Gene Silencing; Genes; Genetic aspects; Genetic Variation; Genome, Plant; Genomes; Genomics; Genotype; Genotypes; Hymenoscyphus fraxineus; Infections; Mycoses; Nucleotide sequence; Plant Diseases - genetics; Plant Diseases - microbiology; Principal Component Analysis; Reproduction (copying); Sequence Analysis, DNA; Tomatoes; Trees; Variability; Whole genome duplication
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-4874-8

European ash trees (Fraxinus excelsior) are currently threatened by ash dieback (ADB) caused by the fungus Hymenoscyphus fraxineus but a small percentage of the population possesses natural low susceptibility. The genome of a European ash tree has recently been sequenced. Here, we present whole genome DNA methylation data for two F. excelsior genotypes with high susceptibility to ADB, and two genotypes with low susceptibility, each clonally replicated. We also include two genotypes of Manchurian ash (F. mandshurica), an ash species which has co-evolved with H. fraxineus and also has low susceptibility to ADB. In F. excelsior, we find an average methylation level of 76.2% in the CG context, 52.0% in the CHG context, and 13.9% in the CHH context; similar levels to those of tomato. We find higher methylation in transposable elements as opposed to non-mobile elements, and high densities of Non-Differentially Methylation Positions (N-DMPs) in genes with housekeeping functions. Of genes putatively duplicated in whole genome duplication (WGD) events, an average of 25.9% are differentially methylated in at least one cytosine context, potentially indicative of unequal silencing. Variability in methylation patterns exists among clonal replicates, and this is only slightly less than the variability found between different genotypes. Of twenty genes previously found to have expression levels associated with ADB susceptibility, we find only two of these have differential methylation between high and low susceptibility F. excelsior trees. In addition, we identify 1683 significant Differentially Methylated Regions (DMRs) (q-value