Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization

Abstract

Leptosphaeria maculans ‘brassicae’ (Lmb) and Leptosphaeria maculans ‘lepidii’ (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.

Local Rather than Global H3K27me3 Dynamics Are Associated with Differential Gene Expression in Verticillium dahliae

“…The global fraction of genes that are located in H3K27me3 domains in V. dahliae is similar to what has been reported for the ascomycete Podospora anserina ( 28 ) but higher than those for N. crassa , Zymoseptoria tritici , Leptosphaeria maculans , and Magnaporthe oryzae (9 to 16% of genes in H3K27me3 domains) ( 20 , 30 , 32 , 50 ). Previous reports showed that H3K27me3 represses the transcription of secondary metabolite clusters in Fusarium spp.…”

A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes

“…As noticed when having cloned the first avirulence gene of L. maculans more than a decade ago (Gout et al, 2006 ), all of them are “lost in the middle of nowhere” genes isolated in large AT‐rich blocks of degenerated transposable elements (for a review, see Rouxel & Balesdent, 2017 ). In relation to this genome location we also found recently that all AvrLm genes are enriched in H3K9me3 (trimethylation of lysine 9 of histone H3) marks, usually regarded as characteristic of constitutive heterochromatin in other organisms (Soyer et al, 2021 ). Being associated with this repressive mark, none of the AvrLm genes are expressed during vegetative growth (Soyer et al, 2021 ), but all of them show the same kinetics of expression when the fungus is inoculated onto cotyledons of B. napus , with a strong peak of overexpression 5–9 days postinoculation before symptoms are expressed (Figure 3 ) (Gay et al, 2021 ).…”

“…In relation to this genome location we also found recently that all AvrLm genes are enriched in H3K9me3 (trimethylation of lysine 9 of histone H3) marks, usually regarded as characteristic of constitutive heterochromatin in other organisms (Soyer et al, 2021 ). Being associated with this repressive mark, none of the AvrLm genes are expressed during vegetative growth (Soyer et al, 2021 ), but all of them show the same kinetics of expression when the fungus is inoculated onto cotyledons of B. napus , with a strong peak of overexpression 5–9 days postinoculation before symptoms are expressed (Figure 3 ) (Gay et al, 2021 ). Additionally, all of them encode small secreted proteins, often but not always enriched in cysteine residues, and showing no or few matches in databases, no recognizable domain, and no postulated function.…”

“…Exploitation of RNA‐Seq data (Dutreux et al, 2018 ) pointed to expression kinetics typical of known avirulence genes for this candidate, with a low level of expression in axenic conditions and a strong overexpression upon cotyledon infection 5–9 days postinoculation (dpi) followed by a drastically reduced expression level at later time points (Figure 3 ). In addition to its location within a large transposable element (TE)‐rich genome region, examination of data generated by Soyer et al ( 2021 ) also showed that Lmb_JN3_05547 was strongly enriched in the heterochromatin mark H3K9me3. RACE‐PCR was used to confirm the improved gene annotation obtained in Dutreux et al ( 2018 ) and refine it.…”

A devil's bargain with transposable elements in plant pathogens

“…Recognition by the host activates the host immune response, including the deployment of antimicrobial compounds, pH change, and programmed cell death at the infection site [23][24][25]. To successfully hijack host cells, effector expression is orchestrated by alterations in the chromatin state leading to waves of expression changes [26][27][28]. In concert with effector expression, TEs are derepressed during the early infection phase [7] (Figure 1A), thus weakening the genome's control of TEs.…”