Non canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia.

The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of transposable elements, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable to mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC which signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC regarding its counterpart. This fact is shared with 5mC resembling dosage compensation. Colocalization showed higher correlation between 5mC and 5fC than with 5hmC, suggesting no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex biased TEs gathered on a clear sex-dependent clustering. Together, these findings unveil a hypothetical role of oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.