Genome-wide identification and characterization of long non-coding RNA in barley roots in response to Piriformospora indica colonization

Currently, there is very limited information about long noncoding RNAs (lncRNAs) found in barley. It remains unclear whether barley lncRNAs are responsive to Piriformospora indica (P. indica) colonization.We found that barley roots exhibited fast development and that large roots branched after P. indica colonization. Genome-wide high-throughput RNA-seq and bioinformatic analysis showed that 4356 and 5154 differentially expressed LncRNAs (DELs) were found in response to P. indica at 3 and 7 days after colonization (dai), respectively, and 2456 DELs were found at 7 dai compared to 3 dai. Based on the coexpression correlation of lncRNA-mRNA, we found that 98.6% of lncRNAs were positively correlated with 3430 mRNAs at 3 dai and 7 dai. Further GO analysis showed that 30 lncRNAs might be involved in the regulation of gene transcription; 23 lncRNAs might participate in cell cycle regulation. Moreover, the metabolite analysis indicated that chlorophyll a, sucrose, protein, gibberellin, and auxin were in accordance with the results of the transcriptome, and the respective lncRNAs were positively correlated with these target RNAs. Gene silencing suggested that lncRNA TCONS_00262342 is probably a key regulator of GA3 synthesis pathway, which participates in P. indica and barley interactions. We concluded that acting as a molecular material basis and resource, lncRNAs respond to P. indica colonization by regulating metabolite content in barley and coordinate the complex regulatory process of higher life by constructing highly positive correlations with their target mRNAs.