GSE131206
Spontaneous mutations in FgSAD1 suppress the growth defect of the Fgprp4 mutant by affecting tri-snRNP stability and its docking in Fusarium graminearum
Purpose: For detecting splicing defects in wild type PH-1 and sector S139 and transformant D10. Our results showed that S139 and D10 had similar intron retention levels (un-spliced introns). The intron retention levels in S139 were significantly higher than those in PH-1 (P<0.001,t-test). For the 15,211 introns in the 6,995 genes expressed across two strains, approximately 25% of them had an over 2-fold intron retention rate in comparison with the intron retention rate in PH-1, indicating splicing defects in S139 and D10. Overall design: The vegetative hyphae of the PH-1, S139, and D10 were harvested from 16h liquid YEPD cultures. Total RNAs was extracted using RNeasy Mini Kit (QIAGEN, US) following the manufacturer's instructions. Library construction and sequencing with an Illumina Hiseq 2000 sequencer were performed at Shanghai Biotechnology Corporation (Shanghai, China). At least 25 Mb high-quality reads were obtained for each sample. The resulting RNA-seq reads were mapped onto the reference genome of F. graminearum strain PH-1 with the Tophat2 program (ccb.jhu.edu/software/tophat/index.shtml). The intron retention rate was defined as the number of reads that aligned to the predicted intron divided by the number of reads aligned to the corresponding transcript.