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| Status |
Public on Nov 03, 2021 |
| Title |
Genetic determinants of endophytism in the Arabidopsis root mycobiome |
| Organisms |
Arabidopsis thaliana; Macrophomina phaseolina; Truncatella angustata; Halenospora varia; Paraphoma chrysanthemicola; Phaeosphaeria sp.; Chaetomium sp.; Chaetomium sp. MPI-CAGE-AT-0009; Phaeosphaeria sp. MPI-PUGE-AT-0046c |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
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| Overall design |
We report the transcriptomes of six root mycobiota members in interaction in mono-association with their host Arabidopsis thaliana in gnotobiotic system. The six fungal strains used in this experiment were isolated from the roots of healthy Arabidopsis plants in the wild (Duran et al. 2018). To identify the genes they express in planta, we conducted a RNA-sequencing experiment. A. thaliana sterile seeds were inoculated with mycelium, then cultivated for 28 days on a phosphate-deficient agar-based medium. Roots were harvested and crushed, then total RNA was extracted and sequenced. As control conditions, mycelia were grown on the same plant culture medium and fungal RNA was extracted with the same method, after 28 days in culture. With this experiment, we identified a core set of genes - mostly composed of genes encoding carbohydrate active enzymes - which are over-expressed by all six fungi in the roots of A. thaliana. We believe they constitute a toolbox for root colonization and the endophytic lifestyle.
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| Contributor(s) |
Mesny F, Hüttel B, Hacquard S |
| Citation(s) |
34893598 |
| |
| Submission date |
Mar 25, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Fantin Mesny |
| E-mail(s) |
mesny@mpipz.mpg.de
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Department |
Plant-Microbes interaction
|
| Lab |
Hacquard group
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
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| Platforms (13)
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| GPL21179 |
Illumina HiSeq 3000 (Arabidopsis thaliana) |
| GPL29923 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Chaetomium sp.) |
| GPL29924 |
Illumina HiSeq 3000 (Paraphoma chrysanthemicola) |
| GPL29925 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Paraphoma chrysanthemicola) |
| GPL29927 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Phaeosphaeria sp.) |
| GPL29928 |
Illumina HiSeq 3000 (Truncatella angustata) |
| GPL29929 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Truncatella angustata) |
| GPL29930 |
Illumina HiSeq 3000 (Macrophomina phaseolina) |
| GPL29931 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Macrophomina phaseolina) |
| GPL29932 |
Illumina HiSeq 3000 (Halenospora varia) |
| GPL29933 |
Illumina HiSeq 3000 (Arabidopsis thaliana; Halenospora varia) |
| GPL29945 |
Illumina HiSeq 3000 (Chaetomium sp. MPI-CAGE-AT-0009) |
| GPL29946 |
Illumina HiSeq 3000 (Phaeosphaeria sp. MPI-PUGE-AT-0046c) |
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| Samples (39)
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| Relations |
| BioProject |
PRJNA717244 |
| SRA |
SRP312149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE169629_Cs_fungalTranscriptome.csv.gz |
743.3 Kb |
(ftp)(http) |
CSV |
| GSE169629_Cs_plantTranscriptome.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
| GSE169629_Hv_fungalTranscriptome.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE169629_Hv_plantTranscriptome.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSE169629_Mp_fungalTranscriptome.csv.gz |
919.9 Kb |
(ftp)(http) |
CSV |
| GSE169629_Mp_plantTranscriptome.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSE169629_Pc_fungalTranscriptome.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
| GSE169629_Pc_plantTranscriptome.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSE169629_Ps_fungalTranscriptome.csv.gz |
849.3 Kb |
(ftp)(http) |
CSV |
| GSE169629_Ps_plantTranscriptome.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
| GSE169629_Ta_fungalTranscriptome.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
| GSE169629_Ta_plantTranscriptome.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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