# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 4 Discussion
In this study, our results showed that 85 viruses were clustered within the families of fungal virus species. We speculate that these mycoviruses may be derived from the fungi inhabiting weeds; however, we cannot exclude mycoviruses directly infecting weeds, especially those with high abundances. The relationship between mycoviruses and weeds remains relatively unexplored. More studies are necessary to survey the potential roles of mycoviruses in weeds. In the present study, we described the metatranscriptomic sequencing of 29 weed samples. We discovered 304 virus genomes belonging to 224 virus species, including bacteriophages, mycoviruses and plant viruses. Of the identified viruses, 211 were newly discovered virus species and 13 were known virus species. The newly identified viruses clustered within 18 single-stranded positive-stranded RNA virus families, 3 single-stranded negative-stranded RNA virus families and 1 double-stranded RNA virus family. Many newly identified viruses constitute potentially new viral families and genera. Compared to previous results, our analysis of deep meta-transcriptomic sequencing has resulted in a great increase in the number of RNA viruses in weeds, with some RNA viruses clustering within the genera of several plant virus species. Together, our meta-transcriptomic analysis reveals genetic diversity of RNA viruses in weeds. Our work also provides valuable information for developing efficient strategies to manage weeds. **Supplementary Materials:** The following supporting information can be downloaded at: [[https://www.mdpi.com/article/10.3390/v14112489/s1](https://www.mdpi.com/article/10.3390/v14112489/s1)]([https://www.mdpi.com/article/10.3390/v14112489/s1](https://www.mdpi.com/article/10.3390/v14112489/s1)), Figure S1: Overview of viral contigs in each weed species; Figure S2: ML phylogenetic analysis of the family _Dicistrovitidae_; Figure S3: Sequence properties of new solemoviruses identified in this study; Figure S4: ML phylogenetic analysis of the family _Astrovitidae_ (A) and _Marnaviridae_ (B); Figure S5: Sequence properties of new tombusviruses identified in this study; Figure S6: ML phylogenetic analysis of the family _Nodaviridae_ (A), _Virgaviridae_ (B) and _Closteroviridae_ (C); Figure S7: The conserved sequence and ML phylogenetic analysis of the family _Tymoviridae_; Figure S8: ML phylogenetic analysis of the family _Botourmiaviridae_; Figure S9: ML phylogenetic analysis of the family _Mitovididae_; Figure S10: Representative genome organizations and ML phylogenetic analysis of the family _Narnaviridae_; Figure S11: ML phylogenetic analysis of the family _Fusariviidae_; Figure S12: A fully labelled ML phylogeny for the class _Levivivixtetes_; Figure S13: Representative genome structure of viruses classified into the family _Partitividae_ and the order _Bumyaviridae_; Table S1: The informations on 29 weed plants collected from rice fields and sequencing libraries; Table S2: Data generated in this study and summary of the viruses; Table S3: Mycoviruses detected in weeks in rice field; Table S4: Bacteriophages identified in breeds in rice field; Table S5: Data generated in this study and summary of negative-sense RNA viruses; Table S6: Viruses infecting weeds in rice field. **Author Contributions:** Conceptualization, G.F. and S.C.; methodology, S.C., H.W. and G.F.; software, S.C. and H.W. ; validation, S.C., H.W., G.C. and L.C. ; formal analysis, S.C., H.W., C.M. and G.C. ; resources, S.C., S.Z., Y.H., F.Y., S.W., L.L. and L.C. ; writing--original draft preparation, G.F. and S.C.; writing--review and editing, G.F. and G.C. ; funding acquisition, G.F. All authors have read and agreed to the published version of the manuscript. **Funding:** This research was funded by the National Natural Science Foundation of China (Nos: 31972983 and 32072487), the Key Technology R & D Program of Zhejiang Province (No. 2021C02006) and the Central Public-interest Scientific Institution Basal Research Fund (No. CPSIBRF-CNRRI-202115). **Institutional Review Board Statement:** Not applicable.