As the energy powerhouses of the cell, mitochondria play a fundamental role in muscle growth, which is one of most important traits in aquaculture. There is increasing evidence that epigenetic mechanisms, and DNA methylation in particular, can regulate growth. Nevertheless , methylation changes in mitochondrial DNA (mtDNA ) and their potential impact on growth are currently not known in fish. Hence, the aim of this study was to determine the mitochondrial methylome in Nile tilapia (Oreochromis niloticus) .
We isolated and sequenced mtDNA from the liver of 5 full-sib Nile tilapia females. Similarly to other cichlids, the Nile tilapia mitogenome is 16,625 bp long and contains 13 protein-coding genes involved in oxidative phosphorylation, two rRNA genes, 22 tRNA genes and the control region D-loop. We prepared libraries for whole genome bisulfite sequencing on the NextSeq platform to determine the methylation rate within CHH, CHG and CpG contexts in mitochondrial genes . Our results revealed that methylation is present in the mitochondrial genome of Nile tilapia. U nlike the nuclear genome, cytosine methylation in mtDNA occurs predominantly within a non-CpG context . Also, methylation of mtDNA was found to be strand-specific , since 68% of methylated cytosines were located on the light (minus) strand , and some tRNA genes had high methylation levels.
This is the first methylation map of the mitochondrial genome in fish. In addition to providing novel insights into mitochondrial epigenetics, our results constitute an epigenetic toolbox that may be used to modulate growth in Nile tilapia.
Acknowledgements: This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements nos 683210 and 812986) and from the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20).