GSE123811
The Blue-Light Photoreceptor Sfwc-1 Gene Regulates the Phototropic Response and Fruiting-Body Development in the Homothallic Ascomycete Sordaria fimicola
Purpose: The goal of this stufy is to elucidate the transcriptional regulatory network in response to light in S. fimicola. We analyzed blue-light-induced genome-wide transcriptional responses by high-throughput RNA-seq to determine the transcriptional profiles between the wild type and Sfwc-1(?lov) mutant. Untreated mycelia (constant darkness sample) and mycelia treated with blue light for 15 and 45 min were used to explore. Method: the S. fimiocla wild type and Sfwc-1(?lov) mutant were grown on malt extract agar I in constant dark for 2 days. The drak grown  samples were exposed to blue light for 15 and 45 min. The cDNA was synthesized from mRNA by using the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)and then sequencing involved using Illumina NextSeq 500. The clean RNA-seq reads were then de novo assembled into a transcript sequence by using the Trinity platform and the jaccard_clip option. The quantified gene and isoform abundances (transcript abundance estimation) were obtained by using RNA-seq by expectation-maximization (RSEM) software with the default setting of Bowtie. Then differentially expressed genes (DEGs) were identified by using the EdgeR Bioconductor package in Trinity platform. The normalized RSEM-estimated abundances weighted by Trimmed Mean of M values (TMM) method counted by EdgeR was used for pairwise comparison of each of the sample pairs. Conclusion: Our study represents  the transcription regulatory nextwork existing in S. fmicola, generated by RNA-seq technology. The data analysis  has been providing a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and contribute the understanding of biologic functions in S. fimicola. Overall design: The mRNA profile of S. fimiocla Wild Type and Sfwc-1(?lov) illuminated by light for 15 and 45 min were generated by using Illumina NextSeq 500. Please note that  feature Ids like “TR4637|c0_g1” (in the processed data files) are generated in this study (de novo transciptome assembly: SF_denovo_trinity.fasta) and the corresponding public gene Id was included in the last column (https://www.ncbi.nlm.nih.gov/bioproject/13841). However, as the species Sordaria fimicola and the reference Neurospora crassa OR74A genome (used for annotation) are closely related but different species, there are 26 out of 53,338 transcripts which do not  match to the reference genome.