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 performed 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 identified 809 complete or near-complete viruses, including 274 known viruses and 535 novel viruses. Given the high divergence and atypical genome organizations of novel viruses, more than a half of novel viruses were tentatively assigned to new genera, new families and even new orders. Utilizing homology-independent approaches, we additionally identified 49 divergent RdRPs, which were confirmed by protein structural prediction and comparison. Furthermore, we analyzed the metadata of related SRA libraries from other organisms, and estimated viral abundance in each library, leading to the screening of rice-infecting viruses and rice associated viruses. Our further analysis shows that these viruses distributed in various plants, including wild rice plants, other crops and weeds, highlighting the potential threats of these plants on cultivated rice via virus transmission. Overall, our study vastly expended the viral diversity in rice plants, providing new insights for the prevention and control of viral disease.