DNA Methylation In Genomic Evolution And Tissue-specific Gene Expression Differences In Polyploid Sugarcane

DNA methylation is a stable,conserved,reversible,and heritable epigenetic modification widely found in plants and animals,plants,and microbiology,which can regulate gene expression and inhibit transposon activity.Compared to other epigenetic modifications,DNA methylation is the most extensively and thoroughly studied.In plants,DNA methylation is involved in the development,fruit ripening,stress response,etc.In addition,DNA methylation plays an important role in polyploid subgenomic differentiation and the formation of important agronomic traits.Therefore,DNA methylation has broad application prospects in crop breeding and variety improvement.Sugarcane is an important subtropical cash crop.The high ploidy and high complexity of the sugarcane genome have led to slow progress in sugarcane genomics,gene function mining,and multi-omics association analysis.There are few reports on the sugarcane epigenome,especially on DNA methylation.The regulatory role of DNA methylation in the expression of homologous alleles and tissue-specific genes in sugarcane remains unclear.The publication of the sugarcane AP85-441 genome and the identification of homologous alleles provide an opportunity for researching DNA methylation in sugarcane genome evolution and gene expression regulation.This study intends to conduct genome-wide methylation and transcriptome sequencing of different tissues(leaves,roots,rinds,and piths)of "Zhongzhe 1",we investigated the role of DNA methylation in the expression bias of homologous alleles;analyzed the functions of expression-biased alleles regulated by DNA methylation;explored the distribution and characteristics of DNA methylation in sugarcane;revealed the regulatory role of DNA methylation on gene expression in sugarcane and its effects on gene functions and trait formation of important agronomic traits.We expect to uncover valuable genetic resources that will provide a theoretical basis for functional studies of sugarcane genes as well as breeding efforts.This study compares the genomics,epigenomics,and transcriptomics of different tissues of sugarcane.The significance of DNA methylation in sugarcane genome evolution was explored by analyzing the expression levels,genetic variation,and DNA methylation variation among homologous alleles in sugarcane.In addition,the analysis of DNA methylation patterns and levels between different tissues and the correlations between DNA methylation and gene expression was performed to investigate the differences in DNA methylation in sugarcane tissuespecific gene expression.The main findings are as follows.1)There is no bias or subgenome dominance in the expression of allelic genes among sugarcane subgenomes(|Fold-change| > 2).However,thousands of homologous allele pairs were differentially expressed,which means that one homologous allele is highly expressed,and the other allele is lowly expressed.The expression bias pattern of alleles was conservative across different tissues.In addition,the dominantly expressed genes in the allele are subject to strong purifying selection during evolution.2)We found that DNA methylation changes and genetic variation between dominant and suppressed alleles are closely associated with allelic expression bias.More importantly,differentially expressed alleles regulated by DNA methylation have important biological functions and are involved in biological pathways related to important agronomic traits,such as response to stress and sugar transport.3)DNA methylation patterns were similar among the different sugarcane tissues,whereas DNA methylation levels differed.Pith tissue showed the highest DNA methylation levels,followed by the rind,root,and leaf.We found that gene-enriched regions showed low CG and CHG methylation levels,while TE-(Transposable element)enriched regions had high methylation levels.The DNA demethylation pathway plays a critical role in methylation level changes across the four tissues.4)CG methylation in gene body was positively correlated with gene expression,and methylation near TSS(Transcription start site)or TES(Transcription end site)was negatively correlated with gene expression,while gene expression was positively correlated with CHH methylation in upstream regions.DNA methylation was involved in gene expression regulation.DNA methylation of different genic regions and sequence contexts played different roles in gene expression.5)Differences in methylation among tissues resulted in many differentially methylated regions(DMRs)between tissues,particularly CHH DMRs.Genes overlapping with DMRs tended to be differentially expressed(DEGs)between tissues,and these DMR-associated DEGs were enriched in biological pathways related to tissue function,such as photosynthesis,sucrose synthesis,stress response,transport,and metabolism.More importantly,differentially expressed genes regulated by DNA methylation have important biological functions,such as SPS,SWEET,NAPDH,and FBPase.6)We observed many DNA methylation valleys(DMVs),which always overlapped with transcription factors(TFs)and sucrose-related genes,such as WRKY,b ZIP,WOX,and Pectate lyase.In conclusion,Through comparative genomics,DNA methylation,and association analysis of transcriptome,Through comparative genomics,DNA methylation,and transcriptome association analysis,we constructed a genome-wide map of DNA methylation in sugarcane,revealing the effects of DNA methylation on sugarcane subgenomic differentiation and allele function,deepening the understanding of the intricate interplay between DNA methylation and gene expression,and resolving the epigenetic regulatory pathways of sucrose-related genes in sugarcane,which contributes to the This provides unique epigenetic insights into the transcriptional regulation of homologous alleles and provides a theoretical basis for the use of epigenetics in breeding and variety improvement of highyield,high-sugar and high-resistance sugarcane,which is beneficial for epigenetic studies of other polyploid crops.