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

SUMMARY

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.