Long noncoding RNA s responsive to F usarium oxysporum infection in A rabidopsis thaliana

Summary Short noncoding RNA s have been demonstrated to play important roles in regulation of gene expression and stress responses, but the repertoire and functions of long noncoding RNA s ( l nc RNA s) remain largely unexplored, particularly in plants. To explore the role of l nc RNA s in disease resistance, we used a strand‐specific RNA ‐sequencing approach to identify l nc RNA s responsive to F usarium oxysporum infection in A rabidopsis thaliana . Antisense transcription was found in c . 20% of the annotated A . thaliana genes. Several noncoding natural antisense transcripts responsive to F . oxysporum infection were found in genes implicated in disease defense. While the majority of the novel transcriptionally active regions ( TAR s) were adjacent to annotated genes and could be an extension of the annotated transcripts, 159 novel intergenic TAR s, including 20  F . oxysporum ‐responsive l nc TAR s, were identified. Ten F . oxysporum ‐induced l nc TAR s were functionally characterized using T ‐ DNA insertion or RNA ‐interference knockdown lines, and five were demonstrated to be related to disease development. Promoter analysis suggests that some of the F . oxysporum ‐induced l nc TAR s are direct targets of transcription factor(s) responsive to pathogen attack. Our results demonstrated that strand‐specific RNA sequencing is a powerful tool for uncovering hidden levels of transcriptome and that Inc RNA s are important components of the antifungal networks in A . thaliana .