Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

Abstract The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in compact plant genomes. Because the small genome size of the carnivorous plant Utricularia gibba we investigate the noncoding RNA landscape and global DNA methylation in a compact genome. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of noncoding RNAs and reduced global DNA methylation levels, as determined by a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, reduced DNA methylation correlates with lack of a functional RdDM pathway, as U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs lost key domains required for complete function. Our findings unveil that lack of a functional DCL3 in U. gibba correlates with a decreased proportion of 24-nt small-interfering RNAs, low genome methylation levels, and developmental abnormalities during female gametogenesis that are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of apomixis in compact genomes.