Distinct classes of 21 and 24-nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development
PhasiRNAs (phased small interfering RNAs) are a major class of plant small RNAs known to be key regulators in male reproductive development of maize and rice (Oryza sativa), among other plants. Earlier research focused primarily on premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNAs, while new studies uncovered a premeiotic class of 24-nt phasiRNAs. The biogenesis and function of these phasiRNAs remains unclear. We conducted an integrative analysis combining small RNA sequencing and transcriptomic profiling of small RNA-associated genes across Kitaake rice anther developmental stages to map associations between sRNA-related genes and phasiRNA classes. We identified new classes of postmeiotic 21-nucleotide and postmeiotic 24-nucleotide phasiRNA-producing loci and characterized their unique accumulation patterns. Our findings reveal distinct differences in nucleotide composition and register accumulation among the phasiRNA classes, suggesting the presence of diverse mechanisms of biogenesis and function. Our results provide new insights into the regulatory complexity of phasiRNAs, establishing a foundation for further functional studies and advancing our understanding of their roles in anther development and their underlying mechanisms. Overall design: Anthers of rice WT kitaake plants at 10 different sizes (0.4mm, 0.6mm, 0.8mm, 1.0mm, 1.2mm, 1.4mm, 1.6mm, 1.8mm, 2.0mm, and 2.5mm) were collected. For each anther size there were 3 biological replicates.