In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants

Rice viruses seriously threaten rice cultivation and cause significant economic losses, but they have not yet been systematically identified, with only 20 rice-infecting viruses reported. Here, we perform a large-scale analysis of 17,115 RNA-seq libraries spanning 24 Oryza species across 51 countries. Using de novo assembly and homology-based methods, we identify 810 complete or near-complete viruses, including 276 known viruses and 534 novel viruses. Given the high divergence and atypical genome organizations of novel viruses, more than a half of them are tentatively assigned to 1 new order, 61 new families, and at least 104 new genera. Utilizing homology-independent approaches, we additionally identify 49 divergent RNA-dependent RNA polymerases (RdRPs), which are confirmed by protein structural alignment. Furthermore, we analyze the metadata of related Sequence Read Archive (SRA) libraries and estimated viral abundance in each library, leading to the screening of 427 viruses closely associated with rice plants. Overall, our study vastly expands the viral diversity in rice plants, providing insights for the prevention and control of viral disease.