Identification and expression analysis of long non-coding RNAs of rice induced during interaction with Rhizoctonia solani

The sheath blight caused by fungus Rhizoctonia solani K & uuml;hn AG1-IA (Teleomorph:Thanatephorus cucumeris (A. B. Frank) Donk.) is one among the most important rice diseases. The limited success towards achieving reliable and persistent resistance against this fungal pathogen is due to lack of knowledge of resistance mechanisms and gene regulation during host-fungal interaction. Long non coding RNAs (lncRNA) are a class of non-protein coding RNAs that play critical role in regulating gene expression through a variety of mechanisms. In this study, the RNA sequencing data of 4 rice genotypes including two sheath blight susceptible (TN1 and BPT5204) and two resistant (Tetep and Pankaj) genotypes was used for the identification of R. solani (AG1-IA) induced lncRNAs. After quality assessment of sequencing reads, a total of 522561 assembled transcripts were obtained from eight RNA sequencing libraries. Among them, a total of 855 putative lncRNAs were identified after filtering against stringent criteria and bioinformatics tools. The differential expression analysis of lncRNAs was done in 4 rice genotypes by analyzing the expression values before and after the R. solani (AG1-IA) infection, which suggested 17 differentially expressed lncRNAs commonly present in all 4 genotypes. Real time (RT-qPCR) analysis of lncRNAs indicated significant up-regulation of lncRNA (TCONS_00079033) in resistant genotype (Tetep). The co-expression and gene regulation network analysis suggested the critical role of TCONS_00079033 in regulation of defense proteins and molecular pathways associated with sheath blight resistance. This study will pave the way for better understanding the molecular interactions during sheath blight and devising effective strategies for resistance development.