Metatranscriptomic Sequencing Suggests the Presence of Novel RNA Viruses in Rice Transmitted by Brown Planthopper

Abstract

Viral pathogens are a major threat to stable crop production. Using a backcross strategy, we find that integrating a dominant brown planthopper (BPH) resistance gene Bph3 into a high-yield and BPH-susceptible indica rice variety significantly enhances BPH resistance. However, when Bph3-carrying backcross lines are infested with BPH, these BPH-resistant lines exhibit sterile characteristics, displaying panicle enclosure and failure of seed production at their mature stage. As we suspected, BPH-mediated viral infections could cause the observed sterile symptoms, and we characterized rice-infecting viruses using deep metatranscriptomic sequencing. Our analyses revealed eight novel virus species and five known viruses, including a highly divergent virus clustered within a currently unclassified family. Additionally, we characterized rice plant antiviral responses using small RNA sequencing. The results revealed abundant virus-derived small interfering RNAs in sterile rice plants, providing evidence for Dicer-like and Argonaute-mediated immune responses in rice plants. Together, our results provide insights into the diversity of viruses in rice plants, and our findings suggest that multiple virus infections occur in rice plants.

Seasonal activities of the phyllosphere microbiome of perennial crops

“…Our work is an untargeted bacterial metatranscriptomic work performed on the leaf phyllosphere of field-grown crops. Other recent leaf metatranscriptome studies have focused the viral communities of tomato and pepper 82 , soybean 83 , and rice 84 . A key strength of this work is the challenging integration of phyllosphere metagenome and metatranscriptome data, leveraging the higher coverage of the metagenomes with the activity information available from the metatranscriptomes.…”

Novel RNA Viruses Discovered in Weeds in Rice Fields

“…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.…”

“…Using metatranscriptomic approach, 1445 RNA viruses were discovered from over 200 invertebrate species sampled across nine animal phyla [13]. A total of 13 RNA viruses were detected from sterile rice plants [14]. Metatranscriptomics has advantages in terms of characterizing RNA viromes: (i) it can uncover entire viromes, including those from coinfected pathogens;…”

Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom

“…Moreover, some nodaviruses have been found in mammals or their fecal samples [21][22][23][24][25]. Although nodaviruses are currently considered to be animal viruses, some noda-like viruses have also been detected in plant samples through RNA-seq technologies [26,27].…”