Genome-wide maps of H3K9me3, H3K27me3 and H3K4me2 in two species of Leptosphaeria maculans during vegetative growth

ABSTRACT: In plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in the interaction(s) with the host plant. Two closely-related phytopathogenic species, Leptosphaeria maculans ‘brassicae’ (Lmb) and L. maculans ‘lepidii’ (Lml) exhibit a large conservation of genome synteny but contrasted genome structure. Lmb has undergone massive invasion of its genome by transposable elements summing up one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has a low amount of repeats (3% of the genome). Previous information also showed that the TE-rich regions of Lmb host a few species-specific effector genes, expressed during plant infection, with main incidence on the adaptive potential of the fungus. The distinct genome organisation between Lmb and Lml thus provides us with a model of choice for the comparison of the epigenomic organization in two closely related phytopathogenic fungi, in order to investigate pathogenicity/effector gene landscape with respect to the chromatin landscape. To address this, we performed chromatin immunoprecipitation, targeting either histone modifications typical for heterochromatin or euchromatin, during axenic culture, combined with transcriptomic analysis to analyse the influence of the chromatin organisation on gene expression. Our data comfort in both species the postulate that facultative heterochromatin landscapes, associated with H3K27me3 domains, are enriched in genes with no annotation, including numerous candidate effector and species-specific genes. Notably orthologous genes located in the same H3K27me3 domains are enriched in genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in vegetative growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb has the particularity to have large H3K9me3-domains within chromosomal arms, strongly associated to TEs, and hosting numerous species-specific effector-encoding genes. These two distinct heterochromatin landscapes hosting genes involved in interaction with the host now questions their involvement in regulation of pathogenicity, the dynamics of the domains during plant infection, and the selective advantage for the fungus to host effector genes in H3K9me3 or H3K27me3 domains.

ORGANISM(S): Plenodomus lingam/Leptosphaeria maculans 'brassicae' group Plenodomus lingam/Leptosphaeria maculans 'lepidii' group

PROVIDER: GSE150125 | GEO | 2021/06/02

REPOSITORIES: GEO