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Series GSE109094 Query DataSets for GSE109094
Status Public on Aug 16, 2018
Title Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [I]
Organism Fusarium graminearum
Experiment type Expression profiling by high throughput sequencing
Summary Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. A large fraction of the lncRNAs were found to be antisense to mRNAs, forming 300 sense–antisense pairs. Although small RNAs were produced from these overlapped loci, most of the antisense lncRNAs appeared not to be involved in gene silencing pathways. Rather, the expression of antisense lncRNA and sense mRNA pairs tended to be induced in parallel as the perithecium matured. To identify regulatory components for lncRNA expression, we analyzed mutants defective in the nonsense-mediated decay (NMD) pathway. A subset of lncRNAs was specifically targeted by NMD, suggesting a suppressive role of NMD in lncRNA expression during vegetative growth. This study provides comprehensive resources for studying developmental lncRNA that may be important for laying out the multicellular fruiting body plan.
 
Overall design Time-series mRNA profiles during the perithecial development for the Fusarium graminearum wild-type strain PH-1 were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 system. Also, sexual_stage0 and sexual_stage4 data for xrn1-deletion mutant (∆xrn1) were generated using the Illumina HiSeq 4000 system.
 
Contributor(s) Kim W, Trail F
Citation(s) 30108170, 38085094
Submission date Jan 11, 2018
Last update date Feb 14, 2024
Contact name Wonyong Kim
E-mail(s) apbiomol@gmail.com
Organization name Michigan State University
Department Plant Biology
Lab Trail, Frances
Street address 612 Wilson Road, Room 166
City East Lansing
State/province Michigan
ZIP/Postal code 48824
Country USA
 
Platforms (2)
GPL24501 Illumina HiSeq 2500 (Fusarium graminearum)
GPL24502 Illumina HiSeq 4000 (Fusarium graminearum)
Samples (24)
GSM2931587 sexual_stage0 rep1_WT
GSM2931588 sexual_stage0 rep2_WT
GSM2931589 sexual_stage0 rep3_WT
This SubSeries is part of SuperSeries:
GSE109095 Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum
Relations
BioProject PRJNA429633
SRA SRP128905

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109094_FgRM_filt_lcpm.tab.gz 1.4 Mb (ftp)(http) TAB
GSE109094_FgRM_stringtie_merged_gene_loci.gtf.gz 374.0 Kb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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