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

Abstract

Nodaviruses are small bipartite RNA viruses and are considered animal viruses. Here, we identified two novel noda-like viruses (referred to as rice-associated noda-like virus 1 (RNLV1) and rice-associated noda-like virus 2 (RNLV2)) in field-collected rice plants showing a dwarfing phenotype through RNA-seq. RNLV1 genome consists of 3335 nt RNA1 and 1769 nt RNA2, and RNLV2 genome consists of 3279 nt RNA1 and 1525 nt RNA2. Three conserved ORFs were identified in each genome of the two novel viruses, encoding an RNA-dependent RNA polymerase, an RNA silencing suppressor, and a capsid protein, respectively. The results of sequence alignment, protein domain prediction, and evolutionary analysis indicate that these two novel viruses are clearly different from the known nodaviruses, especially the CPs. We have also determined that the B2 protein encoded by the two new noda-like viruses can suppress RNA silencing in plants. Two reverse genetic systems were constructed and used to show that RNLV1 RNA1 can replicate in plant cells and RNLV1 can replicate in insect Sf9 cells. We have also found two unusual peptidase family A21 domains in the RNLV1 CP, and RNLV1 CP can self-cleave in acidic environments. These findings provide new knowledge of novel nodaviruses.

Molecular characterization of a novel chlorotic leaf curl-associated foveavirus infecting prune trees

“…1a). To identify the potential viruses in collected leaves, RNA-seq was performed as described previously [1,6,7]. Brie y, the EASYspin Plus Complex Plant RNA Kit (Aidlab Biotech, Beijing, China) was used to extract total RNA from the sampled leaf tissues.…”

Discovery and Characterization of a Novel Umbravirus from Paederia scandens Plants Showing Leaf Chlorosis and Yellowing Symptoms

“…The RNA-seq and de novo assembly was performed as previously described [21][22][23]. Briefly, total RNA was extracted from the sampled leaf tissues using the EASYspin Plus Complex Plant RNA Kit (Aidlab Biotech, Beijing, China).…”

“…With the development of highthroughput RNA sequencing (RNA-seq) technique and bioinformatics, many novel viruses infecting different organisms have been identified [18,19]. For example, using the RNA-seq technique, our laboratory has identified several novel viruses in field-collected plants such as rice curl dwarf-associated picornavirus [20], rice-associated noda-like virus 1 and 2 [21], rice dwarf-associated bunya-like virus [22], and wheat yellow stunt-associated betaflexivirus [23].…”

The Identification of Viral Pathogens in a Physostegia virginiana Plant Using High-Throughput RNA Sequencing

“…For example, its throughput is very high, only a small number of samples are required, the genomic characteristic of the virus is not necessary to be known in advance, and the detection accuracy is up to a single base [ 7 ]. Using the RNA-seq technique, numerous new viruses were identified [ 8 , 9 , 10 , 11 ].…”