Pig and quail CpG methylation datasets from short and long read sequencing technologies
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.
Authors
- Christine Gaspin (ORCID: https://orcid.org/0000-0003-0304-5186)
- Carole Iampietro (ORCID: https://orcid.org/0000-0002-8148-4785)
- Denis Milan (ORCID: https://orcid.org/0000-0002-8062-5072)
- Katia Fève (ORCID: https://orcid.org/0000-0003-3287-1604)
- Michèle Bonnet
- Cécile Donnadieu (ORCID: https://orcid.org/0000-0002-5164-3095)
- Paul Terzian (ORCID: https://orcid.org/0000-0002-7092-3906)
- Claire Kuchly (ORCID: https://orcid.org/0000-0001-8994-550X)
- Joanna Lledo (ORCID: https://orcid.org/0000-0001-7239-2259)
- Céline Vandecasteele (ORCID: https://orcid.org/0000-0002-5262-0709)
- Christophe Klopp (ORCID: https://orcid.org/0000-0001-7126-5477)
- Julie Demars (ORCID: https://orcid.org/0000-0003-2451-0059)
- Nathalie Iannuccelli (ORCID: https://orcid.org/0000-0002-7822-3250)
- Frédérique Pitel
- Jules Sabban (ORCID: https://orcid.org/0000-0001-6780-5362)
- Sophie Leroux (ORCID: https://orcid.org/0000-0003-2840-5109)
- Rémy-Félix Serre
Institutions
- École Nationale Vétérinaire de Toulouse (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Laboratoire de Microbiologie et Génétique Moléculaires (FR)
- Génétique Physiologie et Systèmes d'Elevage (FR)
Publication Details
- Journal
- Scientific Data
- Published
- 2025-04-01
- DOI
- https://doi.org/10.1038/s41597-025-04769-4
- Citations
- 1
- Primary Topic
- Epigenetics and DNA Methylation
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- European Commission
- Région Occitanie Pyrénées-Méditerranée
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement