Abstract
BackgroundPaulownia withes’-broom (PaWB) disease caused by phytoplasma is a serious infectious disease for Paulownia. However, the underlying molecular pathogenesis is not fully understood. Recent studies have demonstrated that histone modifications could play a role in plant defense responses to pathogens. But there is still no available genome-wide histone modification data in non-model ligneous species infected with phytoplasma.ResultsHere, we provided the first genome-wide profiles of three histone marks (H3K4me3, H3K36me3 and H3K9ac) in Paulownia fortunei under phytoplasma stress by using chromatin immunoprecipitation sequencing (ChIP-Seq). We found that H3K4me3, H3K36me3 and H3K9ac were mainly enriched in the genic regions in P. fortunei with (PFI) and without (PF) phytoplasma infection. ChIP-Seq analysis revealed 1738, 986, and 2577 genes were differentially modified by H3K4me3, H3K36me3 and H3K9ac marks in PFI under phytoplasma infection, respectively. The functional analysis of these genes suggested that most of them were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction. In addition, the combinational analysis of ChIP-Seq and RNA-Seq showed that differential histone methylation and acetylation only affected a small subset of phytoplasma-responsive genes.ConclusionsTaken together, this is the first report of integrated analysis of histone modifications and gene expression involved in Paulownia-phytoplasma interaction. Our results will provide the valuable resources for the mechanism studies of gene regulation in non-model plants upon pathogens attack.
Highlights
Paulownia withes’-broom (PaWB) disease caused by phytoplasma is a serious infectious disease for Paulownia
Genome-wide patterns of histone modifications in Paulownia under phytoplasma stress To investigate whether histone modifications (H3K4me3, H3K36me3 and H3K9ac) are implicated in the responses of Paulownia to phytoplasma, we applied chromatin immunoprecipitation (ChIP)-Seq to determine the changes of histone modifications between P. fortunei without phytoplasma infection (PF) and P. fortunei with (PFI) at the whole genome level
Correlation analysis of histone modification alterations with differential gene expression in response to phytoplasma in Paulownia In our previous study, we have investigated the transcriptional changes in P. fortunei under phytoplasma stress, and significantly differentially expressed genes (DEGs) responsive to phytoplasma infection were identified by using the criteria of |log2 ratio| ≥ 1 and FDR < 0.001 [63]
Summary
Paulownia withes’-broom (PaWB) disease caused by phytoplasma is a serious infectious disease for Paulownia. Ayyappan et al [21] conducted genome-wide analysis of changes on histone modification (H3K9me and H4K12ac) and gene expression in Phaseolus vulgaris under rust pathogen (Uromyces appendiculatus) stress, and found that the methylation and acetylation patterns of P. vulgaris altered in response to rust pathogen, affecting a large proportion of defense-related genes expression, including plant resistant (R) genes, detoxifying enzymes and genes associated with ion flux and cell death. Ding et al [22] demonstrated that the expression level of HDT701, a member of the plant-specific HD2 subfamily of histone deacetylases (HDACs) in rice, altered after infection with fungal pathogen Magnaporthe oryzae It negatively regulates innate immunity of rice by modulating the levels of histone H4 acetylation of pattern recognition receptor (PRR) and defense-related genes. Information about histone marks in plants infected with phytoplasma is still lacking
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