The epigenetic hypothesis of doubly uniparental inheritance of mitochondria: unveiling the mtDNA methylation toolkit in the blue mussel Mytilus edulis

Mitochondrial epigenetics, particularly mtDNA methylation, is a flourishing field of research. MtDNA methylation appears to play multiple roles, including regulating mitochondrial transcription, cell metabolism and mitochondrial inheritance. In animals, bivalves with doubly uniparental inheritance (DUI) of mitochondria are the exception to the rule of maternal mitochondrial inheritance since DUI also involve a paternal mtDNA transmitted from the father to sons. The mechanisms underlying DUI are still unknown, but mtDNA methylation could play a role in its regulation. Here, we investigated mtDNA methylation levels and machinery in gonads of the mussel Mytilus edulis using methods based on antibodies, enzymatic cleavage and methylome sequencing. Our results confirm the presence in mitochondria of methylated cytosines and adenines and methyltransferases and unveil a more variable cytosine methylation state among males than females. Also, spermatid mtDNA is always methylated, while only few..., DNA extractions : DNA extractions used for enzymatic digestions were performed on 9 male and 9 female of Mytilus edulis gonad samples with phenol-chloroform following a protocol adapted to molluscan tissues (Sokolov, 2000). DNA extractions used for methylome sequencing were performed on gonad tissues of 5 males and 3 females of M. edulis following the DNeasy blood & tissue kit (QIAGEN) protocol. DNA samples were then digested to linearize mtDNA using SwaI restriction enzyme (New England BioLabs), following the manufacturer’s protocol. Linearized mtDNA (and digested nuclear DNA) was then purified with a QIAquick PCR purification kit (QIAGEN) according to the manufacturer’s protocol.
Enzymatic digestions : DNA samples were digested with the cytosine methyl-sensitive restriction enzyme (MSRE) HpaII and its insensitive isoschizomer restriction enzyme MspI, as well as with an adenine MSRE, DpnI, and its methyl-insensitive isoschizomer DpnII. Digestions were performed separately for each ..., , # The epigenetic hypothesis of doubly uniparental inheritance of mitochondria: unveiling the mtDNA methylation toolkit in the blue mussel Mytilus edulis

[https://doi.org/10.5061/dryad.cvdncjtc5](https://doi.org/10.5061/dryad.cvdncjtc5)

## Description of the data and file structure

The dataset comprises text files of enzymatic digestion levels (labelled \"ratios.merged.MF.txt\", \"ratios.enzymes.txt\" and \"ratios_enzymes_diff.txt.\") of *Mytilus edulis* DNA samples (**available on Zenodo**), which can be used in the R code (see below). Digestion levels were calculated using ImageJ software program following the DNA band quantification protocol from Davarinejad (2015).

The dataset also comprises fastqsanger files of paired-end sequencing data (R1 and R2) from *M. edulis* DNA samples (**available on Dryad)**, as well as text files of the processed reads (**available on Zenodo**), labelled \"*SampleNumber_RefGenome*_seq.txt\" (Sample number = M1 to M5 male samples and F3, F5, F6 for female sam...