Tools and applications for integrative analysis of DNA methylation in social insects.
Details
Serval ID
serval:BIB_A51C5FD58AD1
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Tools and applications for integrative analysis of DNA methylation in social insects.
Journal
Molecular ecology resources
ISSN
1755-0998 (Electronic)
ISSN-L
1755-098X
Publication state
Published
Issued date
05/2022
Peer-reviewed
Oui
Volume
22
Number
4
Pages
1656-1674
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Publication Status: ppublish
Abstract
DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole-genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analysing several publicly available social insect WGBS data sets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.
Keywords
Animals, CpG Islands/genetics, DNA Methylation, Epigenomics/methods, High-Throughput Nucleotide Sequencing/methods, Insecta/genetics, Sequence Analysis, DNA/methods, Whole Genome Sequencing/methods, BS-seq, DNA methylation, arthropods, reproducibility, workflow
Pubmed
Web of science
Create date
11/12/2021 12:42
Last modification date
04/11/2023 7:07