GSE131517
Comparative de novo mRNA transcriptome analysis of Oryza sativa cv. IR-64 under control and fluoride stress
Purpose: The goal of this study was to identify the differentially expressed genes (DEGs) in the fluoride susceptible indica rice cultivar IR-64 in response to prolonged fluoride stress. The genes exhibiting high significance of relative expression were further analyzed by RT-PCR. Results: De novo transcriptome assembly by Trinity v2.8.3 led to the identification of 158411 transcripts. The Percent GC was 49.67, contig N50 was 1327, Median contig length was 422, average contig was 768.66 and total assembled bases were 121764099. After refinement and open reading frame detection with TransDecoder 70578 transcripts were retained. Among them, 68009 transcripts had at least one hit from Uniref100, Uniprot or Pfam. Differential expression analysis identified 1303 genes to be overexpressed and 93 genes to be down regulated in response to fluoride stress. After filtering, the transcripts with absolute log2 fold change 2 or more and p-value < 0.05 were considered as significantly differentially expressed. A total of 1396 transcripts with differential expression (majority overexpressed and some down regulated) were considered for further analysis. Next, PCR analysis with gene-specific primers was performed with some of the significant DEGs associated with transport, cytoskeletal organization and signaling to identify the genes/transcripts that are involved in stress Overall design: Comparative mRNA transcriptome profile of total seedlings of Oryza sativa cv. IR-64 under control conditions and under 25 day long fluoride stress.