Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq]

Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms. Overall design: Time-course RNAseq to identify differentially expressed lncRNAs using 3 biological replicates per time-point (0, 6, 12, 24 and 72 hours post inoculation with Pectobacterium carotovorum subsp brasiliense 1692)

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