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Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

ABSTRACT: We report polyA+ mRNA profiles in a developmental assay where R. irregularis spores were exposed to either medium containing rice root-derived exudates or a mock nutrient medium. We report small RNA repertoires produced from R. irregularis spores using two different isolation techniques. We report the application of single-molecule-based DNA sequencing for profiling of CG methylation in untreated R. irregularis. spores.

ORGANISM(S): Rhizophagus irregularis

PROVIDER: GSE172187 | GEO | 2021/09/16

REPOSITORIES: GEO

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Project description:Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here adress the gene regulation of R. irregularis in response to plant signals in the switch from asymbiotic to presymbiotic growth Methods: Spores of R. irregularis were treated with GR24 (strigolactone synthetic analog) and collected at 1 hour, 2 days, 7 days and 14 days after induction. To stimulate the fungus with root exudates, a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 14 days after. To monitor fungal gene regulation, control conditions were also prepared and mRNA were sequenced by HiSeq Illumina. Read were mapped on the genome assembly with CLCworkbench Results: At 1 hour, GR24 triggered the overexpression (fold change >2; FDR<0,05) of 123 genes and the repression (fold change < -2; FDR<0,05) of 17 genes. At 2 days, 33 genes were induced, 13 repressed ; at 7 days 106 genes were induced and 13 repressed and at 14 days 19 genes were induced and 10 repressed. Few genes overlap between the different time point. Root exudates induced 251 genes and repressed 63 genes. Few genes were regulated by both GR24 and root exudates. Conclusions: GR24 kinetic showed that fungal gene regulation is sequential, quick and involves hundreds of genes. Among those genes, a chitin synthase, involved either in fungal growth either in symbiotic signal production was strongly induced at 1hour, 7 days and 14 days. As few genes are regulated in response to root exudates and GR24, we propose that other plant signals play a role in ealy steps and trigger fungal gene regulation. Several genes coding for putative secreted peptides were induced in response to these plant signals. These genes might be effectors involved in early plant defense manipulation, then facilitating root entry. Thus, they are good candidates to investigate early steps of plant penetration.

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Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

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