Identification and Pathway Association of Abiotic Stress-Responsive Long Noncoding RNAs in Populus trichocarpa

We identified stress-responsive, tissue-specific lncRNAs, and characterized potential pathways that they could be involved in. We analyzed 81 RNA-seq samples in Populus trichocarpa from leaf, root, and xylem under control treatment or either short or prolonged heat, cold, salt, and drought stresses. First, we created a de novo transcriptome assembly, and through a multi-stage process we removed transcripts with any signs of protein-coding potential. We further divided up transcripts based on whether they overlapped transposable element annotations. The remaining transcripts were evaluated as candidate stress-responsive lncRNAs. We identified tissue-specific lncRNAs based on their combined expression across all treatments for a given tissue relative to other tissues. We further identified significantly differentially expressed lncRNAs as candidate stress-responsive transcripts. Transcripts were then analyzed to identify those with significant correlation with protein-coding transcripts, and then compared to pathways by for a significant number of correlated mRNAs belonging to a particular pathway. We then validated a number of these transcripts with digital droplet PCR (ddPCR). Taken together, these data support the hypothesis that lncRNAs with tissue-specific stress-responsive roles exist in Populus trichocarpa.

Funding for the project provided in part by U.S. Department of Energy, award # DE-SC0008570 and the Oregon State University.