FAIRification of DMRichR Pipeline: Advancing Epigenetic Research on Environmental and Evolutionary Model Organisms

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Authors

Wassim Salam, Marcin Wlodzimierz Wojewodzic, Dagmar Frisch 

Abstract

Bioinformatics tools often prioritize humans or human-related model organisms, overlooking the requirements of environmentally relevant species, which limits their use in ecological research. This gap is particularly challenging when implementing existing software, as inadequate documentation can delay the innovative use of environmental models for modern risk assessment of chemicals that can cause aberration in methylation patterns. The establishment of fairness in ecological and evolutionary studies is already constrained by more limited resources in these fields of study, and an additional imbalance in tool availability further hinders comprehensive ecological research. To address these gaps, we adapted the DMRichR package, a tool for epigenetic analysis, for use with custom, non-model genomes. As an example we here use the crustacean Daphnia, a keystone grazer in aquatic ecosystems. This adaptation involved the modification of specific code, computing three new species-specific packages (BSgenome, TxDb, and org.db), and computing a CpG islands track using the makeCGI package. Additional adjustments to the DMRichR package were also necessary to ensure proper functionality. The developed workflow can now be applied not only to different Daphnia species that were previously unsupported, but also to any other species for which an annotated reference genome is available.

DOI

https://doi.org/10.32942/X2J32C

Subjects

Bioinformatics, Computational Biology, Environmental Public Health, Life Sciences, Other Ecology and Evolutionary Biology

Keywords

ecology, Epigenetics, Daphnia pulex, DMRichR, Methylation, Non-model organism, risk assessment

Dates

Published: 2024-11-05 11:22

License

CC BY Attribution 4.0 International

Additional Metadata

Language:
English

Conflict of interest statement:
None

Data and Code Availability Statement:
Open data/code are not available. Code and data will be made available after peer review, upon publication in github and Zenodo.