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ABSTRACT: RNA-sequencing of single spore lines of R. irregularis Sc2

PROVIDER: PRJEB39188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4314410_1.fastq.gz	Fastqsanger.gz
	ERR4314410_2.fastq.gz	Fastqsanger.gz
	ERR4314420_1.fastq.gz	Fastqsanger.gz
	ERR4314420_2.fastq.gz	Fastqsanger.gz
	ERR4314430_1.fastq.gz	Fastqsanger.gz

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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.

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

Project description: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.

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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.

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Proteomic Comparison Between Hyphae and Spores Reveals Pathogenicity Diversity in Mucor Irregularis

Project description:Mucor irregularis poses significant clinical risks, including severe disfigurement, with hyphal forms being more commonly encountered in clinical settings compared to spore forms. However, the pathogenic differences between these forms at the protein level remain poorly understood. This study employed TMT-based quantitative proteomics to investigate the proteomic differences between spores and hyphae of Mucor irregularis. Our analysis revealed that differentially abundant proteins are predominantly expressed during the hyphal stage. Notably, key enzymes such as RhoGEF GTPase, Subtilisin-related Protease, Acyl-CoA Synthetase, and Ribonuclease T2 appear crucial for hyphal morphological development and pathogenic mechanisms. Additionally, myosins play a significant role not only in hyphal growth and virulence but also in influencing sensitivity to antifungal agents. These findings provide new insights into the morphogenesis, development, and metabolic processes of Mucor irregularis, laying a foundation for further research into its pathogenic mechanisms.

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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

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Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

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Project description:Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relative spore mRNA levels were determined by RNA-seq. Determination of RNA levels in single spores allowed calculation of RNA nt/spore, and assuming mRNA is 3% of spore RNA allowed calculation that only ~6% of spore mRNAs were present at ≥ 1/spore. Bacillus subtilis, Bacillus atrophaeus and Clostridioides difficile spores had 49, 42 and 51 mRNAs at >1/spore, respectively. Numbers of mRNAs at ≥1/spore were ~10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores, respectively, and ~ 4-fold higher in Bacillus megaterium spores. Notably, in all species: i) many of the 60 most abundant spore mRNAs were transcribed by RNA polymerase with forespore-specific s factors; ii) some to many of the most abundant spore mRNAs encoded orthologs of those encoded by abundant B. subtilis spore mRNAs and proteins present in dormant spores ; and iii) some spore mRNAs were likely transcribed in the mother cell compartment of the sporulating cell. Indeed , analysis of the coverage of RNA-seq reads on mRNAs from all six species suggested that abundant spore mRNAs were at least somewhat fragmented. This observation was confirmed by RT-qPCR analysis of three abundant mRNAs each from B. subtilis and C. difficile spores. These data add to a growing body of evidence indicating that the great majority of mRNAs in spores of Firmicutes are degradation and function as a ribonucleotide depot for new RNA synthesis when spores germinate.

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