Biogenesis, features, and functions of coding transcripts-derived siRNAs in plants

Plant small RNAs (sRNAs) are pivotal regulators of development, genome stability, and environmental adaptation. In plants, endogenous sRNAs are broadly grouped into microRNAs (miRNAs) and small interfering RNAs (siRNAs). siRNAs can be further subdivided into those derived from noncoding transcripts, such as transposable elements and long noncoding RNAs, and those generated from protein-coding transcripts. Among these, coding transcript-derived siRNAs (ct-siRNAs) represent a critical link between RNA quality control (RQC) and post-transcriptional gene silencing. When RNA decay and RQC pathways are genetically impaired or attenuated by environmental and biotic stresses, aberrant protein-coding mRNAs can be converted into ct-siRNAs, with 22-nt species efficiently triggering secondary siRNA amplification. ct-siRNA production is highly selective, concentrating at hotspot loci whose transcripts are shaped by characteristic RNA features, translational status, and contributes to enhanced stress resistance by modulating defense- and metabolism-related gene networks. ct-siRNAs bridge mRNA surveillance and growth defense trade-offs, acting as endogenous danger signals to expand post-transcriptional regulation and improve crop resilience. This review summarizes recent advances in endogenous sRNA biology with a particular focus on ct-siRNAs, detailing their biogenesis, regulatory properties, and biological functions. We further discuss their physiological significance and highlight key open questions and future directions in this emerging field.