Differential expression of novel microRNAs in response to the infection of a TMV mutant with an internal poly(A) tract in N. benthamiana

•A total number of 181 novel microRNAs (miRNAs) were identified from TMV and TMV-43A-infected Nicotiana benthamiana through an improved miRNAs analysis pipeline.•The expression of those novel miRNAs differed between TMV and TMV-43A-infected plants.•Virally induced miRNAs were associated with predicted mRNAs related to host defense.

We first constructed small RNA libraries of TMV- and TMV-43A-infected N. benthamiana for high throughput sequencing. A total number of 181 novel microRNAs (miRNAs) were identified through an improved miRNAs analysis pipeline. We were able to identify consistent miRNA expression changes induced in TMV and TMV-43A-infected plants, as well as differences associated with the UPD substitution in the TMV-43A viral genome. Virally induced miRNAs are associated with distinct processes and functions of predicted mRNA targets, including relation to host target defense. This study suggests an approach for functional genomics miRNAs in incompletely assembled genomes. These findings provide valuable information for further characterization of miRNAs by two genomic similar viruses, and provide clues to the study of TMV-UPD to find potential defense-related host genes targeted by miRNAs (126 words).