Allele-specific methylation of MRP3 drives mating type determination in a marine diatom

Sex determination mechanisms exhibit remarkable diversity across eukaryotic lineages. In the pennate diatom Pseudo-nitzschia multistriata, sex is determined by MRP3, a gene with unknown function, which is monoallelically expressed in sexually competent mating type plus (MT+) cells and silenced in MT- cells. Here, we describe an allelic-specific methylation pattern at the sex locus, with a hypomethylated allele specific to the MT+ which is transcriptionally active, while the other hypermethylated MRP3 alleles are transcriptionally silent. In addition, the genome-wide methylation landscape remains stable throughout the life cycle. Treatment with a methylation inhibitor leads to MRP3 activation and partial sex reversal, suggesting an active role of DNA methylation in the sex determination mechanism. Long-read sequencing improved the MT-determining region resolution, highlighting a gene-poor, repeat-rich area that likely represents a primordial MT-determining locus. Our results provide insights into the mechanisms of sex determination and suggest that DNA methylation in diatoms has a more complex role than silencing repetitive regions.