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Rhizophagus irregularis gene regulation in response to rice root exudates

ABSTRACT: 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 root exudates from rice wild-type and osnope1 (no perception candidate - mutant unable to host arbuscular mycorrhizal fungi) Methods: Spores of R. irregularis were treated with root exudates and collected at 1 hour, 24 hours and 7 days after addition. To monitor fungal gene regulation, control conditions were also prepared at T0, 1h, 24h and 7d. mRNA were sequenced by HiSeq Illumina. Reads were mapped on the Rhizophagus irregularis genome assembly (Gloin1 - Tisserant et al., PNAS, 2013) using CLCworkbench suite. Results: -At 1h, a set of 92 fungal genes were found up-regulated in response to wt root exudates (92), not to osnope1 root exudates, many of them being involved in cell signaling. -At 24h and 7d, numerous genes putatively involved in primary metabolism were up-regulated in response to wt root exudates, not in response to osnope1 root exudates -Several vital genes involved in cell development are repressed in response to osnope1 RE compared to wt RE. Conclusions: these results argue for a high metabolic activity induced by wt root exudates, not by osnope1 root exudates.

ORGANISM(S): Rhizophagus irregularis

PROVIDER: GSE65595 | GEO | 2017/02/04

SECONDARY ACCESSION(S): PRJNA274445

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.

Project description:Purpose: we here adress the gene regulation of G.rosea in response to plant signals in the switch from asymbiotic to presymbiotic growth. Methods: -Strigolactone response: Spores of G.rosea were treated with GR24 (a synthetic strigolactone analog) and collected at 2 days after treatment. Control conditions: spores treated with solvent (M medium acetone 0.1%. Assay and control were performed in triplicates. -Root exsudate response: a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 10 days later. Control conditions: spores were spotted on cellophane membrane directly deposited on solid M medium. Assay and control were performed in triplicates. -Fungal gene expression were analyzed on mRNA were sequenced by Illumina HiSeq. sequencing Reads were firstly used in the de novo assembly of Gigaspora rosea Non Redundent Virtual Transcript and then mapped on the assembled transcriptome using CLC genomics workbench. Results: while GR24 triggered the regulation of only few genes which includes 32 genes upregulated (fold chang >2; FDR<0,05, experiment difference>10) and 61 downregulated (fold change < -2; FDR<0,05,experiment difference>10) genes, root exudates regulated several times more genes. A total of 390 genes were up-regulated by root exudates and 442 genes were down-regulated. Moreover, a majority of the genes (23 of 32 upregulated and 25 of 61 downregulated genes) regulated by GR24 were also regulated by root exudates. This is in consistant with the fact that strigolactones secreted from plant root are already characterized as a group of plant signals during AM symbiosis. The result that a large part of genes were differentialy expressed in reponse to root exudates but not GR24 suggested the presence of other plant signals than strigolactones. Conclusions: as a key player during the switch from asymbiotic to presymbiotic growth of G.rosea, plant root secreted signals - including but not limited to striglactones - significantly modified the expression of many G.rosea genes. The genes differentially expressed are mainly involved in oxidation-redution and metabolic processes that might contribute to prepare G.rosea for the following steps of symbiotic association with the host plant.

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Rhizophagus irregularis gene regulation in response to rice root exudates

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