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<p>CpG methylation, a key epigenetic mark involved in gene regulation, development, and other biological processes, is commonly analyzed using Whole-Genome Bisulfite Sequencing (WGBS). However, bisulfite treatment causes significant DNA degradation. Enzymatic Methyl-seq&#xa0;(EM-seq) offers a short-read alternative that preserves DNA integrity but requires conversion steps, limiting its compatibility with downstream analyses. Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and PacBio, enable direct detection of DNA modifications without altering the DNA, providing simultaneous genome and epigenome information. This work presents a comprehensive dataset combining long- and short-read sequencing data, including ONT, PacBio, Enzymatic Methyl-seq, and WGBS, for two agronomically relevant species: pig (<i>Sus scrofa</i>) and quail (<i>Coturnix japonica</i>). Data quality evaluation reveals high nucleotide quality scores for PacBio and short reads, robust alignment rates for long reads, and inter-method correlations in CpG methylation calling ranging from 0.76 to 0.99. This dataset is a valuable resource for training methylation callers and represents the first combined methylation dataset for these species, providing an essential benchmark for assessing emerging sequencing technologies.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年4月1日

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  • Paul Terzian,
  • Céline Vandecasteele,
  • Joanna Lledo,
  • Rémy-Félix Serre,
  • Jules Sabban,
  • Claire Kuchly,
  • Frédérique Pitel,
  • Sophie Leroux,
  • Julie Demars,
  • Nathalie Iannuccelli,
  • Katia Fève,
  • Michèle Bonnet,
  • Christine Gaspin,
  • Denis Milan,
  • Carole Iampietro,
  • Christophe Klopp,
  • Cécile Donnadieu

摘要

CpG methylation, a key epigenetic mark involved in gene regulation, development, and other biological processes, is commonly analyzed using Whole-Genome Bisulfite Sequencing (WGBS). However, bisulfite treatment causes significant DNA degradation. Enzymatic Methyl-seq (EM-seq) offers a short-read alternative that preserves DNA integrity but requires conversion steps, limiting its compatibility with downstream analyses. Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and PacBio, enable direct detection of DNA modifications without altering the DNA, providing simultaneous genome and epigenome information. This work presents a comprehensive dataset combining long- and short-read sequencing data, including ONT, PacBio, Enzymatic Methyl-seq, and WGBS, for two agronomically relevant species: pig (Sus scrofa) and quail (Coturnix japonica). Data quality evaluation reveals high nucleotide quality scores for PacBio and short reads, robust alignment rates for long reads, and inter-method correlations in CpG methylation calling ranging from 0.76 to 0.99. This dataset is a valuable resource for training methylation callers and represents the first combined methylation dataset for these species, providing an essential benchmark for assessing emerging sequencing technologies.