Research On The Histone Modifications Of Methylation And Acetylation Related To Paulownia Witches’ Broom

Paulownia fortunei,which belongs to Scrophulariaceae,is native to China and has important economic and social values to humans and the environment.However,P.fortunei may be infected with phytoplasma,which leads to Paulownia witches’ broom(Pa WB).P.fortunei with Pa WB is characterized with witches’ broom,short internodes,and etiolated and smaller leaves.Pa WB can disrupt the growth and development of P.fortunei,leading them to death eventually.It may bring the serious economic losses to the production of agroforestry,and obstruct the development of P.fortunei in the world.Therefore,it becomes important to reveal the pathogenesis and molecular mechanism of Pa WB.In this study,chromatin immunoprecipitation sequencing(ChIP-seq)was applied to genome-wide investigate the level of histone modifications(H3K4ME3,H3K9 AC,and H3K36ME3)in 0 mg·L-1 and 60 mg·L-1 methyl methane sulfonate(MMS)-treated healthy P.fortunei and P.fortunei with Pa WB.Then a correlation analysis between RNA sequencing(RNA-seq)and ChIP-seq was conducted to detect the relationship between gene expression and histone modification.This study will lay the foundation for better understanding the mechanisms of Pa WB in the future.The results of this study were as follows:(1)In this study,54604426 raw reads,48953870 clean reads with 7151337384 bases,and36.93% G+C content in average samples were acquired by ChIP-seq.And 41189460(84.32%)clean reads were mapped to genome of P.fortunei.(2)After analyzing the length,number,and distribution of peak in three histone modifications(H3K4ME3,H3K9 AC,and H3K36ME3),we found these histone modifications were enriched in promoter and coding sequences,mostly in transcription start site.(3)Different genes can have a variety of histone modification.According to the scheme analysis,1158 H3K4ME3 peaks in 919 genes,752 H3K36ME3 peaks in 558 genes,and 1059H3K9 AC peaks in 783 genes were acquired.Amonge them,49 genes were modified with H3K4ME3 and H3K36ME3,37 genes were modified with H3K36ME3 and H3K9 AC,81 genes were modified with H3K4ME3 and H3K9 AC,and 11 genes were modified with all of them.(4)In the correlation analysis of RNA-seq and ChIP-seq,there were 387 H3K4ME3 peaks in374 genes,352 H3K36ME3 peaks in 341 genes,and 422 H3K9 AC peaks in 410 genes.Amonge them,29 genes were modificated with H3K4ME3 and H3K36ME3,20 genes were modificated with H3K36ME3 and H3K9 AC,38 genes were modificated with H3K4ME3 and H3K9 AC,and 4genes were modificated with all of them.It was found that only a part of gene expressions were affected by histone modifications,and mostly with positive correlation.(5)The results showed that Pa WB-related genes were associated with phytohormones and plant-pathogen interactions.It indicated that phytoplasma may disturb the balance of phytohormones,which lead to morphology changes in P.fortunei.Meantime,phytohormones could participate in defense system to resist the invasion of phytoplasma.