Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case-study on rainbow trout spermatozoa

El Kamouh, Marina; Brionne, Aurélien; Sayyari, Amin; Lallias, Delphine; Labbé, Catherine; Laurent, Audrey

doi:10.1007/s10695-024-01326-5

Cited by 3 publications

(1 citation statement)

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“…Furthermore, as our primary interest is on DNA methylation divergence between taxa, integrating two metrics of taxonomic divergence (i.e., parental comparisons in two experiments and hybrid index in another) will identify sites verifiably corresponding to taxonomic divergence. While financial constraints may cause our study to miss small-effect DNA methylation loci due to sample size limitations, our sample size within each experiment matches those in other WGBS [72][73][74][75][76] and RRBS [77][78][79][80][81] studies. Our multiexperimentally validated approach offers a novel framework to assess both inter-experimental batch effects and repeatability in a conservative framework, and our preferred approach in contrast to an approach which maximizes DMP discovery at the cost of false positives.…”

Section: Fig 2)mentioning

confidence: 75%

The contribution of epigenetic variation to evolution in crows

Merondun,

Wolf

2024

Preprint

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Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation to evolution we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone we show that 5mC methylation variation was almost exclusively explained by genome properties and ontogenetic program of the organism. Evidence for an environmental contribution was minor, and all methylation variation of potential importance to speciation clustered in intergenic space within a genomic region of elevated genetic differentiation encoding the diagnostic color-contrast between taxa. We conclude that methylation variation may aid in phenotypic translation of genetic polymorphism, but provides little scope for an autonomous contribution to evolution in this system.

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