Résumé
Paspalum notatum is a perennial grass native to South America with variations in ploidy levels and reproductive modes. The diploid cytotype (2n=2x=20) reproduces sexually, while the tetraploid cytotype (2n=4x=40)reproduces through aposporous apomixis. In this species, apomixis is governed by a single genetic region known as the Apomixis Controlling Locus (ACL). The ACL is a complex genomic structure enriched in both coding and non-coding sequences, repetitive elements, and strong cytosine methylation. It is also characterized by a distorted segregation ratio and suppressed recombination. Emerging evidence implicates small interfering RNAs and RNA-directed DNA methylation (RdDM) in apomictic regulation, and cytosine demethylation in Paspalum simplex has been shown to impair parthenogenesis. To investigate epigenetic variation associated with the reproductivemode and ploidy level, we characterized DNA methylation patterns of four genotypes from Oxford Nanopore Technologies (ONT) long read sequencing data generated with the Dorado base caller and the Modkit softwarefor base modification analysis. One diploid sexual (PnR1), one tetraploid sexual (Q4188), and two tetraploid apomictic genotypes (Q4117, obligate, and Q3664, facultative) were analyzed. Our results revealed that, in thecontext CG, Q4117 showed 10% less methylation (~54%) than Q4188 and Q3664 (~64%), while PnR1 displayed an intermediate level (~57%). In the CHH context, Q3664 and PnR1 had more than 10% less methylation than theother genotypes. Meanwhile, methylation levels in the CHG context were similar across genotypes, ranging from 82% to 89%. Additionally, Q4117 exhibited the fewest methylated genes in CHG context, while it presented thehigher rRNA methylated in contexts CG and CHG. These findings demonstrate the usefulness of Oxford Nanopore technology in revealing variability in methylation landscapes between genotypes, representing a significant steptowards identifying epigenetics associated with ploidy levels and reproductive modes.