DNA methylation is an epigenetic mark involved in biological processes, including plant development, stress adaptation, and genome evolution. As a new source of genetic variation, DNA methylation has great potential to enhance plant disease resistance. The phenomenon of RNA-directed DNA methylation (RdDM) is an essential form of genomic epigenetic modification alterations, including methylation of cytosines, methylation, and deacetylation of histones occurring on DNA. The RdDM pathway is unique to plants, and the occurrence of RdDM in plants is closely related to the triad of RNAi, DNA methylation, and histone modification, which ultimately results in the silencing of genes. Lifeasible can help you investigate the critical role of RdDM in plants for many processes, such as chromosome rearrangement, resistance to viral infection, regulation of gene expression, and development through genome-wide methylation sequencing and analysis of differentially methylated regions (DMRs).

Whole genome methylation sequencing (WGBS-seq) takes advantage of the ability of bisulfite to convert unmethylated Cs to Ts by sequencing the genome after treatment with bisulfite. We can calculate the methylation rate based on the ratio of the number of reads not converted to C not converted to T at a single C locus to the number of all covered reads.

WGBS-seq library construction process

WGBS-seq information analysis process

• Quality control of raw downstream data

Raw downstream data contains junctions and low-quality bases introduced during library construction, which will result in fewer reads compared to the genome, leading to less information to be obtained, and therefore need to be filtered. We used software to perform quality control steps on the raw data, such as removing splice sequences and low-quality bases.

• Sequence alignment

We used the software to align the QC reads to the reference genome based on sequence similarity. To perform the alignment, the position of the C base on the reference genome is used as a guide, and the T in the reads corresponding to the position of the C base in the reference genome is labeled as C. At the same time, the other T remains unchanged so that the reads can be directly aligned to the reference genome.

• Methylation level calculation

We can calculate the methylation level based on the ratio of C not converted to T to C converted to T in the reads and then use the software to count the methylation level.

• DMR identification and statistics

Applications

• Plant phenotypes (anthocyanin deposition, etc.)
• Abiotic stresses (temperature, drought, salt, heavy metals, etc.)
• Biotic stresses (pathogens, microbial-plant interactions, etc.)
• Environmental evolution

Lifeasible helps you perform analysis of overall genome-wide methylation changes, including average methylation level changes, methylation level distribution changes, dimensionality reduction analysis, clustering analysis, correlation analysis, and so on. In addition, we can also perform methylation difference level analysis to screen specific difference genes, including DMC / DMR / DMG identification, DMC / DMR distribution on genomic elements, TF binding analysis of DMC / DMR, analysis strategy of time-series methylation data, and functional analysis of DMG. Eventually, we can analyze methylation genomics and transcriptomics associations, including meta genes overall associations, DMG-DEG correspondence associations, network associations, and so on. Please feel free to contact us to submit your requirements.

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For research or industrial use.

Related Services

• Restriction Endonuclease-Based DNA Methylation Detection
• Bisulfite-Based DNA Methylation Detection
• Immunoprecipitation of Methylated DNA
• SMRT Sequencing for Direct Detection of DNA Methylation
• Single Molecule Nanopore Dependent Methylation Sequencing
• RNA Methylation
• DNA Hydroxymethylation