Abstract
BackgroundRoles of microRNAs (miRNAs) and short interfering RNAs (siRNAs) in biotic stress responses, e.g., viral infection, have been demonstrated in plants by many studies. Tomato yellow leaf curl China virus (TYLCCNV) is a monopartite begomovirus that can systemically infect Solanaceae plants, and induces leaf curling, yellowing and enation symptoms when co-inoculated with a betasatellite (TYLCCNB). The released genome sequence of Nicotiana benthamiana provides an opportunity to identify miRNAs and siRNAs responsive to begomovirus-associated betasatellite in N. benthamiana.ResultsmiRNAs were identified in three small RNA libraries generated using RNA isolated from N. benthamiana plants systemically infected with TYLCCNV (Y10A) alone, co-infected with Y10A and its betasatellite TYLCCNB (Y10β) or a TYLCCNB mutant (Y10mβ) that contains a mutated βC1, the sole betasatellite-encoded protein. A total of 196 conserved miRNAs from 38 families and 197 novel miRNAs from 160 families were identified. Northern blot analysis confirmed that expression of species-specific miRNAs was much lower than that of conserved miRNAs. Several conserved and novel miRNAs were found to be responsive to co-infection of Y10A and Y10β but not to co-infection of Y10A and Y10mβ, suggesting that these miRNAs might play a role unique to interaction between Y10β and N. benthamiana. Additionally, we identified miRNAs that can trigger the production of phased secondary siRNAs (phasiRNAs).ConclusionsIdentification of miRNAs with differential expression profiles in N. benthamiana co-infected with Y10A and Y10β and co-infected with Y10A and Y10mβ indicates that these miRNAs are betasatellite-responsive. Our result also suggested a potential role of miRNA-mediated production of phasiRNAs in interaction between begomovirus and N. benthamiana.
Highlights
Roles of microRNAs and short interfering RNAs in biotic stress responses, e.g., viral infection, have been demonstrated in plants by many studies
We identified N. benthamiana miRNAs based on the draft genome and our previously generated small RNA datasets using N. benthamiana plants infected with begomovirus, and found a number of miRNAs, including a few putative phasiRNA triggers, were responsive to co-infection of Tomato yellow leaf curl China virus (TYLCCNV) and TYLCCNV and its associated betasatellite (TYLCCNB) but not to TYLCCNV and a mutated TYLCCNB in N. benthamiana
Identification of miRNAs in N. benthamiana The N. benthamiana plant leaves systemically infected with TYLCCNV (Y10A) alone (P1), or co-infected with TYLCCNV and its betasatellite TYLCCNB (Y10β; P2) or a TYLCCNB mutant (Y10mβ; P3) were harvested for RNA extraction and small RNA sequencing [30]
Summary
Roles of microRNAs (miRNAs) and short interfering RNAs (siRNAs) in biotic stress responses, e.g., viral infection, have been demonstrated in plants by many studies. Roles of miRNAs and siRNAs in biotic and abiotic stress responses, Plant miRNAs can trigger the production of phased secondary siRNAs (phasiRNAs) from either non-coding (e.g., TAS) or protein-coding genes (e.g. NBS-LRR genes). Trans-acting siRNAs (tasiRNAs) are distinctive siRNAs, which are generated from TAS transcripts in 21nucleotide (nt) phases in relative to the miRNA cleavage site They act in trans to regulate gene expression at the posttranscriptional level. Recent studies demonstrated that plant genomes are rich in phased siRNA (phasiRNA)-producing loci, or PHAS genes [16,17,18,19], and may harbor hundreds of these loci in protein-coding genes [15,20,21,22,23]. Biogenesis of phasiRNAs and their roles in posttranscriptional regulation have been well discussed in a recent review [24]
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