Abstract
Small RNA (sRNA) molecules are key factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed cross-kingdom RNA interference (ck-RNAi). Consistent with this recent knowledge, sRNAs and their double-stranded RNA precursor have been adopted to control diseases in crop plants, demonstrating a straight forward application of the new findings to approach agricultural problems. Despite the great interest in natural ck-RNAi, it is astonishing to find just a few additional examples in the literature since the first report was published in 2013. One reason might be that the identification of sRNA effectors is hampered both by technical challenges and lack of routine bioinformatics application strategies. Here, we suggest a practical procedure to find, characterize, and validate sRNA effectors in plant–microbe interaction. The aim of this review is not to present and discuss all possible tools, but to give guidelines toward the best established software available for the analysis.
Highlights
Natural cross-kingdom RNA interference is an emerging field of research in plant– microbe interactions and plant pathology (Cai et al, 2018)
RNAi is the process by which 21–24 nucleotide small RNA (sRNA) are used by ARGONAUTE (AGO) proteins to guide an RNA-Induced Silencing Complex (RISC) toward a complementary messenger RNA, resulting either in mRNA cleavage and degradation, or impairment of its transcription by acting as a physical block (Fire et al, 1998; Hamilton and Baulcombe, 1999)
Read length and sequencing depth selected can vary depending on the experimental design and resources available, but the mRNA sequences are primarily obtained from the large RNA fraction after polyA affinity selection, as more than 90% of total RNA is comprised of ribosomal RNA (Conesa et al, 2016)
Summary
Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions. Small RNA (sRNA) molecules are key factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed crosskingdom RNA interference (ck-RNAi). Consistent with this recent knowledge, sRNAs and their double-stranded RNA precursor have been adopted to control diseases in crop plants, demonstrating a straight forward application of the new findings to approach agricultural problems. We suggest a practical procedure to find, characterize, and validate sRNA effectors in plant–microbe interaction.
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