Function and mechanism of double-stranded RNA-binding protein 1 in small RNA metabolism in tomato

Tomato is an important vegetable crop that is rich in genetic variation, but published high-quality tomato reference genomes are limited. Small RNAs play ubiquitous roles in plants, but their biogenesis in tomatoes is not well studied. We assembled a high-quality chromosome-level reference genome for the tomato cultivar Ailsa Craig 57 (A57) and generated CRISPR mutants deficient in double-stranded RNA-binding protein 1 (SlDRB1) in this cultivar. Mutations in SlDRB1 led to severely abnormal development (e.g., loss of leaf polarity, pollen abortion, and infertility). High-throughput sRNA sequencing analysis revealed that SlDRB1, similar to its Arabidopsis ortholog Hyponastic Leaves 1 (HYL1), is required for the biogenesis of most miRNAs. Interestingly, SlDRB1 is also required for the accumulation of a large population of small RNAs derived from rRNAs and negatively regulates miR6026, which is dependent on DCL2 instead of DCL1. Comprehensive protein-protein interaction studies between SlDRB1 and SlDCL1 uncovered detailed interaction mechanisms involving subdomains of these two proteins. Their potential role in miRNA biogenesis is discussed.