Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection
Abstract Background Paulownia 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 respo...
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5609-1 |
| _version_ | 1818491090399920128 |
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| author | Lijun Yan Guoqiang Fan Xiaoyu Li |
| author_facet | Lijun Yan Guoqiang Fan Xiaoyu Li |
| author_sort | Lijun Yan |
| collection | DOAJ |
| description | Abstract Background Paulownia 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. Results Here, 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. Conclusions Taken 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. |
| first_indexed | 2024-12-10T17:25:39Z |
| format | Article |
| id | doaj.art-956601b30024441285850a593eaba9c4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T17:25:39Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-956601b30024441285850a593eaba9c42022-12-22T01:39:51ZengBMCBMC Genomics1471-21642019-03-0120111410.1186/s12864-019-5609-1Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infectionLijun Yan0Guoqiang Fan1Xiaoyu Li2Institute of Paulownia, Henan Agricultural UniversityInstitute of Paulownia, Henan Agricultural UniversityInstitute of Paulownia, Henan Agricultural UniversityAbstract Background Paulownia 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. Results Here, 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. Conclusions Taken 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.http://link.springer.com/article/10.1186/s12864-019-5609-1PaWBEpigeneticsHistone modificationsChIP-Seq |
| spellingShingle | Lijun Yan Guoqiang Fan Xiaoyu Li Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection BMC Genomics PaWB Epigenetics Histone modifications ChIP-Seq |
| title | Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection |
| title_full | Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection |
| title_fullStr | Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection |
| title_full_unstemmed | Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection |
| title_short | Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection |
| title_sort | genome wide analysis of three histone marks and gene expression in paulownia fortunei with phytoplasma infection |
| topic | PaWB Epigenetics Histone modifications ChIP-Seq |
| url | http://link.springer.com/article/10.1186/s12864-019-5609-1 |
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