Two mutually exclusive evolutionary scenarios for allexiviruses that overcome host RNA silencing and autophagy by regulating viral CRP expression

The role of cysteine-rich protein in enhancing mandarivirus infectivity and pathogenicity

Mandariviruses pose a significant threat to the citrus industry due to their diverse transmission modes and high pathogenicity. However, the pathogenicity mechanisms of mandariviruses remain largely unknown, especially as there is a complete lack of understanding regarding the function of the cysteine-rich proteins (CRPs) encoded by mandariviruses during infection. In this study, ectopic expression of two mandarivirus CRPs from citrus yellow mottle-associated virus (CiYMaV) and citrus yellow vein clearing virus (CYVCV) using a potato virus X vector resulted in severe symptoms and increased viral accumulation in Nicotiana benthamiana. CiYMaV CRP induced cell death in N. benthamiana leaves, with the zinc finger motif identified as the critical region responsible for this induction. CYVCV CRP functioned as a suppressor to inhibit local gene silencing induced by single-stranded GFP, but not double-stranded GFP. Furthermore, mutational analysis of the infectious clones of CiYMaV and CYVCV revealed that their respective CRPs are essential for disease symptom development and viral accumulation in citrus plants. In summary, our findings indicate that CiYMaV and CYVCV CRPs act as pathogenicity determinants, thereby enhancing our understanding of the functional repertoire within the mandariviruses proteome and providing a target for citrus hosts to defend against mandariviruses.

IMPORTANCE

Mandariviruses, infecting a wide range of citrus varieties, cause serious epidemics in Pakistan, India, Turkey, China, Iran, Italy, and America. However, little information is available about pathogenicity mechanisms of mandariviruses. Here, we confirmed the importance of two mandarivirus CRPs of citrus yellow mottle-associated virus (CiYMaV) and citrus yellow vein clearing virus (CYVCV) in disease symptom development and viral accumulation in citrus plants. Our study first provides evidence that CiYMaV and CYVCV CRPs, nonstructural proteins, act as pathogenicity determinants with multiple functions. This offers a broad understanding of functional repertoire within the mandariviruses proteome. Further investigation of the underlying mechanisms of how CRP, as a virulence factor, modulates plant immunity may suggest a possible new strategy for combating mandarivirus infection in the field.

Alphaflexiviridae in Focus: Genomic Signatures, Conserved Elements and Viral-Driven Cellular Remodeling

The family Alphaflexiviridae comprises plant- and fungus-infecting viruses with single-stranded, positive-sense RNA genomes ranging from 5.4 to 9 kb. Their virions are flexuous and filamentous, measuring 470-800 nm in length and 12-13 nm in diameter. The family includes 72 recognized species, classified into six genera: Allexivirus, Lolavirus, Platypuvirus, Potexvirus (plant-infecting), and Botrexvirus and Sclerodarnavirus (fungus-infecting). The genus Potexvirus is the largest, with 52 species, including Potexvirus ecspotati (potato virus X), an important crop pathogen and plant virology model. The genera are distinguished by genome organization and host range, while species differentiation relies on nucleotide and protein sequence identity thresholds. In this review, we summarize the current knowledge on the genomic structure, conserved genes, and phylogenetic relationships within Alphaflexiviridae, with a particular focus on the replicase and coat protein genes as signature markers. Additionally, we update the model of cellular remodeling driven by the triple gene block proteins, which are essential for virus movement, among other viral functions. Beyond their biological significance, alphaflexiviruses serve as valuable models for studying virus-host dynamics and hold potential applications in plant disease control and biotechnology. This review provides an updated framework for understanding Alphaflexiviridae and their broader impact on plant virology.

Elucidating the genetic basis of bulb-related traits in garlic (Allium sativum) through genome-wide association study

The genetic architecture of garlic bulb related traits were still not well elucidated due to its big and complex genome. In this study, genotyping-by-sequencing (GBS) in 163 garlic accessions mainly from China were conducted. All the 163 garlic accessions were divided into three subpopulations, and largely consistent with geographic origins. Genome-wide association study (GWAS) was conducted for 5 garlic bulb related traits across four environments. Totally, 26 significantly loci were identified in two or more environments and located within or near 431 genes, and explain 14.0-31.7 % of the phenotypic variances. Among these, qBW5.1 was nearly with the qBH5.1. Four loci were reported previously, whereas the remaining 22 are likely to be new. Gene ontology enrichment analysis showed that the candidate genes were significantly enriched in metabolic process, biosynthetic process and catalytic activity. Nine candidate genes encode the zinc finger domain-containing protein, serine/threonine-protein kinase, peroxygenase, auxin-induced protein, ethylene-responsive transcription and E3-Ubiquitin protein ligases were identified and validated. Additionally, a meaningful achievement is one kompetitive allele-specific PCR marker, Kasp_chr7_BW for bulb weight were successfully developed and validated in a diverse panel. These results uncover the genetic mechanism of garlic bulb related traits and provide accessions and KASP markers for further garlic molecular breeding.

An Inexpensive System for Rapid and Accurate On-site Detection of Garlic-Infected Viruses by Agarose Gel Electrophoresis Followed by Array Assay

Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.