Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of CpMMV and factors shaping it were analyzed. Phylogeny and nucleotide composition analyses showed that isolates of different geography or hosts had very similar nucleotide compositions. Relative synonymous codon usage (RSCU) and neutrality analyses suggest that CpMMV prefers A/U-ending codons and natural selection is the dominative factor that affects its codon bias. Dinucleotide composition and codon adaptation analyses indicate that the codon pattern of CpMMV is mainly shaped by the requirement of escaping of host dinucleotide-associated antiviral responses and translational efficiency.

NONEXPRESSER OF PATHOGENESIS‐RELATED GENES 1 (NPR1), the receptor for salicylic acid (SA), plays a central role in the SA‐mediated basal antiviral responses. Recent studies have shown that two different plant RNA viruses encode proteins that suppress such antiviral responses by inhibiting its SUMOylation and inducing its degradation, respectively. However, it is unclear whether targeting NPR1 is a general phenomenon in viruses and whether viruses have novel strategies to inhibit NPR1. In the present study, we report that two different positive‐sense single‐stranded RNA (+ssRNA) viruses, namely, alfalfa mosaic virus (AMV) and potato virus X (PVX); one negative‐sense single‐stranded RNA (−ssRNA) virus (calla lily chlorotic spot virus, CCSV); and one single‐stranded DNA virus (beet severe curly‐top virus, BSCTV) that also encode one or more proteins that interact with NPR1. In addition, we found that the AMV‐encoded coat protein (CP) can induce NPR1 degradation by recruiting S‐phase kinase‐associated protein 1 (Skp1), a key component of the Skp1/cullin1/F‐box (SCF) E3 ligase. In contrast, the BSCTV‐encoded V2 protein inhibits NPR1 function, probably by affecting its nucleocytoplasmic distribution via the nuclear export factor ALY. Taken together, these data suggest that NPR1 is one of the central hubs in the molecular arms race between plants and viruses and that different viruses have independently evolved different strategies to target NPR1 and disrupt its function.

Cowpea mild mottle virus (CpMMV) is an important viral pathogen that seriously influences the yield and seed quality of soybeans worldwide. Resistance breeding is one of the most effective, economical, and environmentally safe strategies for controlling the disease caused by CpMMV. However, only few resistance genes have been identified in soybeans. In this study, the resistance of 169 soybean germplasms from Northeast China to a CpMMV strain isolated from soybean in China was evaluated, and a genome-wide association study (GWAS) was then performed to find possible resistance genes in these soybean germplasms. Nine resistant soybean germplasms were identified and two single nucleotide polymorphism sites (SNPs) were found to be closely associated with CpMMV resistance. A total number of 51 and 25 candidate genes neighboring the resistance-associated SNPs on chromosomes 6 and 12, respectively, were identified, among which one receptor-like kinase (RLK) on chromosome 6 and 2 toll-interleukin-1 receptor nucleotide-binding leucine-rich repeat receptors (TNLs) on chromosome 12 were recognized as the most probable resistance genes, respectively. Together, these data provide new insights on the resistance resources of soybeans to CpMMV, which will benefit the breeding of CpMMV-resistant soybean cultivars.

DNA methylation is an important epigenetic marker for the suppression of transposable elements (TEs) and the regulation of plant immunity. However, little is known how RNA viruses counter defense such antiviral machinery. In this study, the change of DNA methylation in turnip mosaic virus (TuMV)-infected cells was analyzed by whole genome bisulfite sequencing. Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells, the majority of differentially methylated regions (DMRs) in the CHH and CHG contexts were associated with hypermethylation. Gene expression analysis showed that the expression of two methylases (DRM2 and CMT3) and three demethylases (ROS3, DML2, DML3) was significantly increased and decreased in TuMV-infected cells, respectively. Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes. Finally, we found TuMV-encoded NIb, the viral RNA-dependent RNA polymerase, was able to induce the expression of DRM2. In conclusion, this study discovered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.

Positive-sense single-stranded RNA viruses replicate in virus-induced membranous organelles for maximum efficiency and immune escaping. The replication of potato virus X (PVX) takes place on the endoplasmic reticulum (ER); however, how PVX-encoded RNA-dependent RNA polymerase (RdRp) is associated with the ER is still unknown. A proline-kinked amphipathic α-helix was recently found in the MET domain of RdRp. In this study, we further illustrate that the first α-helix of the MET domain is also required for ER association. Moreover, we found that the MET domain forms multimers on ER and the first α-helix is essential for multimerization. These results suggest that the RdRp of PVX adopts more than one hydrophobic motif for membrane association and for multimerization.