IdHydMili
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB85208 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR14224663_1.fastq.gz | Fastqsanger.gz | |||
| ERR14224663_2.fastq.gz | Fastqsanger.gz | |||
| ERR14209189.fastq.gz | Fastqsanger.gz | |||
| ERR14209190.fastq.gz | Fastqsanger.gz |
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Project description:Hydrotaea militaris, genomic and transcriptomic data
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Project description:Genome-wide analysis of DNA methylation for asexual and sexual stages of Cordyceps militaris DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes; however, its function underlying the sexual development of fungi remains unclear. Cordyceps militaris, readily performing sexual reproduction, provides a remarkably rich model for understanding epigenetic processes in sexual development. The methylome was surveyed to assess DNA methylation patterns of the nascent fruiting body in C. militaris at single-base resolution by genomic bisulfite sequencing (BS-Seq). The results showed that around 0.4 % of cytosines are methylated, and that there is no difference compared with the DNA methylation level (0.39 %) during asexual development. However, 225 differentially methylated regions (DMRs) were identified between the stages. Moreover, RNA-Seq analysis indicated that the DMRs have no direct relation with the genes for fungal sexual development in C. militaris. DNA methylation regions from the BS-Seq show a striking correspondence to regions predicted to be repetitive and repeat-induced point mutation (RIP) mutated, suggesting that DNA methylation functions as a genome defense mechanism in sexual development. These results provide a comprehensive characterization of DNA methylation in the sexual development of C. militaris, which will contribute to future investigations of epigenetics in fungi. Bisulphite converted genomic DNA from the mycelium and fruitingbody of Cordyceps militaris
2016-05-13 | E-GEOD-66919 | biostudies-arrayexpress
Project description:Cordyceps militaris and Cordyceps sinensis belong to belong to the same genus, but the different species, with immunity improvement, antibacterial, and antihypertensive effect, and the studies on the functions of Cordyceps militaris mainly focus on those of its polysaccharides and polypeptides. The latest studies have found that some of the polypeptides with immunomodulatory effect can widely regulate immune functions at multiple levels, improve immunity, and enhance immune functions to ensure the healthy body, showing an important significance. Cordyceps militaris polypeptide prepared with the enzymolysis method was taken as the research object in this study. The differentially expressed genes and the related cell signal transduction pathway were screened by mRNA expression microarray. STEM 1.3.6 software was used for the clustering of the gene functions, and David and KEGG database were applied for the analysis of the related functions. 1748 differentially expressed genes were selected finally and three of them were validated by qPCR. The results showed that gene Hist1h2bp, Ctsg, and Elane were involved in the regulation of Cordyceps militaris on the immune activity of mice. Gene Hist1h2bp, Ctsg and Elan may be the potential targets of Cordyceps militaris polypeptide, which may provide an important theory basis for the further research and development of Cordyceps militaris polypeptide.
2019-05-01 | GSE81389 | GEO
Project description:Genome-wide analysis of DNA methylation for asexual and sexual stages of Cordyceps militaris DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes; however, its function underlying the sexual development of fungi remains unclear. Cordyceps militaris, readily performing sexual reproduction, provides a remarkably rich model for understanding epigenetic processes in sexual development. The methylome was surveyed to assess DNA methylation patterns of the nascent fruiting body in C. militaris at single-base resolution by genomic bisulfite sequencing (BS-Seq). The results showed that around 0.4 % of cytosines are methylated, and that there is no difference compared with the DNA methylation level (0.39 %) during asexual development. However, 225 differentially methylated regions (DMRs) were identified between the stages. Moreover, RNA-Seq analysis indicated that the DMRs have no direct relation with the genes for fungal sexual development in C. militaris. DNA methylation regions from the BS-Seq show a striking correspondence to regions predicted to be repetitive and repeat-induced point mutation (RIP) mutated, suggesting that DNA methylation functions as a genome defense mechanism in sexual development. These results provide a comprehensive characterization of DNA methylation in the sexual development of C. militaris, which will contribute to future investigations of epigenetics in fungi.
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Project description:The RNA-Seq technique was used to investigate the differentially transcribed genes of the caterpillar fungus Cordyces militaris. It was calculated that >63% of total annotated genes were expressed, including >55% of putative pathogen-host interaction genes. Overall, the fruiting-body development and mycelium growth by C. militaris activated high expression levels of genes in association with translation and post-translational modifications. Otherwise, there were many differentially expressed genes when the fungus was grown on insect pupae to different stages or in liquid medium. In general, the transcriptional profiles were more similar with each other during fungal fruiting-body developmental stages than during growth in a liquid culture. Examination of differential gene expressions by Cordyceps militaris during fruiting-body developments on silkmoth pupae and growth in a liquid medium.
2011-11-08 | E-GEOD-28001 | biostudies-arrayexpress
Project description:The high frequency strain degeneration during subculture seriously restrict the large-scale production of Cordyceps militaris and industrialized process. In the current study, the high-throughput Illumina sequencing was performed on 6 passages subculture C. militaris strains to obtain the divergence of transciptomes in degeneration progress. Then various statistical comparison analysis was further conducted based on the HQ reads to better understand their difference. Over 9015 unigenes and 731 new genes were formed by initial sequence splicing and showed a perfect coverage;3737 ends in 3695 genes were optimized, 2010 at 5’ end (1847 genes ≥ 50 bps) and 1727 at 3’ end (1485 genes ≥ 50 bps); 134783 variants including 126923 SNP variants and 7860 InDelvariants were detected;more than 11304 RNA editing events occurred in total, which yielded 2950 nonsynonymous SNV, 6 stoploss, 5 stopgain and 8343 synonymous SNV; Compared with the first passage strain, the third passage strain exhibited 2498 differentially expressed genes (DEGs) including 1729 up-regulated genes and 769 down-regulated genes, which was higher than other samples. Seventeen enriched gene ontology (GO) terms were identified by GO enrichment analysis and twenty seven enriched pathways were identified by KEGG enrichment analysis, which might be mainly associated with the processing of degeneration. The findings revealed the DEGs involved into the degeneration progress of C. militaris and yielded insights into molecular mechanism of degeneration, which provide the reference for efficiently and artificially producing C. militaris.
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