Pig and quail CpG methylation datasets from short and long read sequencing technologies

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• CpG methylation is a crucial epigenetic mark regulating gene expression, development, and biological processes.
• Traditional Whole-Genome Bisulfite Sequencing (WGBS) for CpG methylation analysis causes significant DNA degradation.
• Enzymatic Methyl-seq (EM-seq) offers DNA integrity preservation but has limited downstream analysis compatibility.

Purpose of the Study:

• To present a comprehensive dataset combining long- and short-read sequencing data for CpG methylation analysis.
• To establish a benchmark for evaluating emerging sequencing technologies in epigenome research.
• To provide a resource for training and improving methylation calling algorithms.

Main Methods:

• Combined long-read (Oxford Nanopore Technologies, PacBio) and short-read (EM-seq, WGBS) sequencing.
• Data generation for two agronomically relevant species: pig (Sus scrofa) and quail (Coturnix japonica).
• Comprehensive data quality evaluation, including nucleotide quality scores and alignment rates.

Main Results:

• High nucleotide quality scores were observed for PacBio and short reads.
• Long reads demonstrated robust alignment rates.
• Inter-method correlations in CpG methylation calling ranged from 0.76 to 0.99.
• The dataset represents the first combined methylation data for pig and quail.

Conclusions:

• The generated dataset is a valuable resource for training methylation callers.
• This work provides an essential benchmark for assessing novel sequencing technologies for epigenome analysis.
• The findings support the utility of integrating diverse sequencing approaches for comprehensive epigenomic studies.