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Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

ABSTRACT: Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE76204 | GEO | 2016/07/20

SECONDARY ACCESSION(S): PRJNA306627

REPOSITORIES: GEO

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Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control. Examination of arbuscular mycorrhiza responsive miRNAs in tomato through high-throughput small RNA sequencing of roots with Rhizophagus irregularis and that without Rhizophagus irregularis

2016-07-20 | E-GEOD-76204 | biostudies-arrayexpress

responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-Physiological and molecular responses of maize to the arbuscular mycorrhizla fungus 5AMF) Rhizophagus irregularis mitigate nitrogen deficiency stress.

Project description:ngs2021_19_rhizophagus-responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-What is the impact of Rhizophagus irregularis on maize transcriptome under different N nutrition conditions, what is the impact of N on R. irregularis transcriptome in maize roots.-After 4 days of germination, maize seeds were sown in pots filled with sterile mix 1:1 clay beads:unfertilized peat. Inoculation performed in 3 times with Rhizohphagus irregularis spores purchased at Agronutrition. First inoculation perfomed with 500 spores/plant at sowing. Two other incoulations performed the following week and 2 weeks later with 100 spore per plant each.

2023-12-13 | GSE235654 | GEO

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

Project description:Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Characterising the epigenomic status of R. irregularis provides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.

2022-02-17 | PXD025245 | Pride

Rhizophagus irregularis gene regulation in response to rice root exudates

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 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.

2017-02-04 | GSE65595 | GEO

Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis

Project description:Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, 1) within the genomic regions lacking annotated genes in the Populus genome and 2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments.

2019-04-09 | GSE117158 | GEO

Rhizophagus irregularis

Project description:Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

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Transcription profiling of Physcomitrella patens response to fungal exudates

Project description:Physcomitrella patens gametophores were treated with exudates from the arbuscular mycorrhiza fungi (AMF) Rhizophagus irregularis (formerly known as Glomus intraradices) and Gigaspora margerita for one hour and 24 hours.

2014-11-10 | E-MTAB-3081 | biostudies-arrayexpress

Rhizophagus irregularis DAOM 181602=DAOM 197198

Project description:Improved genome sequencing of arbuscular mycorrhizal fungi, Rhizophagus irregularis

| PRJDB4945 | ENA

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Project description:Rhizophagus irregularis

| PRJNA268659 | ENA

Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis

Project description:The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AMfungi, and 108 genes were only expressed in non- mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AMcolonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AMfungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for under- standing the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.

2019-03-30 | GSE129059 | GEO

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