# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 4 Discussion  
Here, we detected a diverse set of potential plant viruses from 29 weed samples by deep transcriptomic sequencing. We identified 12 complete or nearly complete genome sequences of the potential plant viruses, 11 of which are previously undescribed, and all the potential plant viruses are positive-sense RNA viruses (Table S6). We also detected one known viruses, Sedum sarmentosum crinivirus. It was notable that this virus was firstly discovered in weeds. Of the potential plant viruses, most of them were detected in weeds at high abundance, indicating that weeds are the main hosts of these viruses. However, rice virus was not detected from the weed samples. Potyvirus and geminivirus, the most abundant plant virus species, were not identified in the collected weed samples [56; 57]. Similar results were also obtained in tomato fields. Broad bean wilt virus 1 was found  
Figure 6: ML phylogenetic analysis of the family _Partitiviridae_. Phylogenetic trees were constructed using the aligned sequences of RdRp. The names of new viruses discovered in this study are marked in red, the names of known viruses discovered in this study are marked in blue, the reference virus serial numbers and names are marked in black and the genera of viruses (and branches in minimized trees) in this study are marked in bold. The red box represents the clade of the virus identified in this study. The grey triangle represents the enlarged part of the red box. only in nightshade when there are numerous indications that this virus should be able to infect tomato [4]. The expected transfer is not observed for viral exchange between crops and weed plants, likely as a consequence of unforeseen biological or ecological barriers. Metatranscriptomics approaches have been successfully implemented to discover highly diverse and novel viruses from rice, citrus, sunflower and pear samples [14; 58; 59; 60; 61]. To the best of our knowledge, this is the first comprehensive high-throughput survey of viral sequences associated with weeds. Bacteriophages are the most abundant and diverse biological entities on the planet; they can even outnumber bacteria by approximately ten-fold in some ecosystems [62]. Bacteriophages can modulate the composition of microbial communities and maintain high levels of diversity, and they play important roles in the evolution, ecology and functions of microbial communities [63; 64; 65]. Bacteria have been described in a wide range of crop plant species [66; 67]. For examples, indica and japonica varieties recruit large numbers of bacteria in rice fields [68]. Bacteriophage in Nicotiana benthamiana plants produce endolysin, which exhibits antimicrobial activity [69] Bacteriophage ACPWH in melon plants inhibits the progression of bacterial fruit both [70]. In addition, bacteriophages play an important role in regulating the diversity of bacterial populations in plants [71]. In this study, we discovered 79 RNA bacteriophages in 29 different weeds, and our results show that 41% of the collected weeds harbor RNA bacteriophages, indicating that RNA bacteriophages may be common in weeds. However, the role of RNA bacteriophages in weed plants remains unknown. More studies are necessary to determine the potential functional roles of RNA bacteriophages in weeds. Fungi harbor various viruses and interact with different plants. Viruses could infect fungi at the incidence rates from 3% to over 90%, and multiple viruses often coinfect fungal hosts, occasionally altering their phenotypes [72]. Fungi can inhabit plants in many different ways. Plants and fungi can be symbiotic or mutualistic. Endophytic fungi have been widely reported for their ability to aid in the defense of their host plants, and plant responses upon endophytic fungi colonization are also good for the immune system of the plant [73]. However, fungi can also be pathogenic to their plant hosts [74]. To date, there are few reports of mycoviruses being associated with weeds.