Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry

Discovery and characterization of a novel carlavirus in Ligularia jaluensis plants

Ligularia jaluensis is an important medicinal and ornamental plant in China. However, the viruses capable of infecting Ligularia jaluensis remains unknown. Here, we identified a novel carlavirus, tentatively named ligularia jaluensis carlavirus (LJCV), as well as a known iris severe mosaic virus (ISMV), in L. jaluensis plants displaying chlorosis and yellow ring spot symptoms, using RNA-seq analysis. The LJCV genome consists of an 8497 ​nt positive-sense, single-stranded RNA [excluding the poly(A) tail], and contains six open reading frames (ORFs). Phylogenetic analyses based on the full-length genome and RNA-dependent RNA polymerase (RdRp) amino acid (aa) sequences revealed that LJCV clusters within an evolutionary branch alongside known viruses in the Carlavirus genus. The RdRp protein encoded by ORF1 of LJCV shared 45.38%-67.41% identity with the corresponding proteins of eight closely related carlaviruses. ORFs 2-4 constitute the triple gene block (TGB), with TGBp1 and TGBp3 localized in the endoplasmic reticulum (ER), while TGBp2 is localized at plasmodesmata (PD) and facilitates viral intercellular movement, as demonstrated by its ability to complement the potato virus X with movement-deficient mutant (PVX-Δp25-GFP). Additionally, ORF6 encodes a cysteine-rich protein (CRP) that is localized in the chloroplast and functions as a viral pathogenicity factor, inducing severe viral symptoms in the heterologous PVX expression system. Furthermore, we successfully constructed an infectious cDNA clone of LJCV, and found that it can infect Nicotiana benthamiana plants through mechanical inoculation or agrobacterium-mediated infiltration of the LJCV infectious clone. These findings enhance our understanding of the characteristics and host range of carlaviruses, as well as the viruses capable of infecting L. jaluensis.

Genomic characterization and survey of a second luteovirus infecting blueberries

New and emerging viral problems may be contributing to blueberry decline. In this research we described a new virus detected in Oregon blueberry production field and surveyed the region for its potential spread. The complete genome sequence of a putative new member of the genus Luteovirus was obtained from blueberry (Vaccinium corymbosum L.) by high throughput sequencing and 5'/3'-RACE. The new virus was tentatively named blueberry virus M (BlVM). Its genome is 5,018 nt long with four putative open reading frames. Similarly to some recently discovered luteoviruses, BlVM does not possess any movement protein (MP). Phylogenetic analysis confirmed clustering of BlVM with the group of non-MP luteoviruses, showing blueberry virus L as the most similar species. Through a small-scale high throughput sequencing survey we obtained 14 additional near complete genomic sequences. A larger survey of 2,654 samples by RT-PCR in Oregon and Washington (USA) found 52 BlVM-positive plants collected from four locations in Oregon. These findings will facilitate monitoring virus distribution and assessment of potential disease associated with this new and emerging blueberry virus.

Engineering a robust infectious clone and gene silencing vector from blackberry yellow vein associated virus

Criniviruses are emerging pathogens responsible for significant disease outbreaks worldwide. Among them, blackberry yellow vein-associated virus (BYVaV) is prevalent in blackberry-producing areas of the United States and, when present in the blackberry yellow vein disease complex with other viruses, can lead to substantial crop losses. To better understand BYVaV biology and its role in virus complex disease development, we developed a BYVaV-derived infectious clone and a virus-induced gene silencing (VIGS) vector. The infectious clone successfully induced systemic infection and symptom development in Nicotiana benthamiana. Additionally, transmission of the recombinant virus to indicator plants was confirmed using the whitefly vector Trialeurodes vaporariorum. The infectious clone was subsequently modified into a VIGS vector, with the foreign insert remaining stable for the length of the study. This work provides essential tools for advancing the study of BYVaV biology and conducting genomic studies in its natural hosts.

Development and application of an infectious clone and gene silencing vector derived from blackberry chlorotic ringspot virus

Blackberry chlorotic ringspot virus (BCRV) was described about 20 years ago and since then there have been several publications of the virus infecting rosaceous hosts including blackberry, raspberry, rose and apple at high rates. Still the effect of the virus on disease development is poorly understood. Aiming to bridge this knowledge gap, we developed a BCRV infectious clone and virus-induced gene silencing vector (VIGS). The infectious clone can induce systemic infection with the transmissibility of the recombinant virus evaluated through mechanical transmission. The VIGS induced silencing using two different inserts, proving the versatility of the construct. The products of this work can be used to study disease development and control as well as functional genomics studies of BCRV hosts.

Complete genome sequence of vaccinium-associated virus C, a new member of the family Totiviridae from Vaccinium floribundum

Blueberries (Vaccinium sp.) are a major crop grown in the Pacific Northwest region. Currently, there are at least 17 known viruses that infect blueberry plants, and some of them cause a wide range of symptoms and economic losses. A new virus, vaccinium-associated virus C (VaVC) (family Totiviridae, genus Totivirus) was identified in an imported blueberry accession from the USDA-ARS National Clonal Germplasm Repository in Corvallis, Oregon. The complete genomic sequence of VaVC was determined, but the biological significance of VaVC is unknown and requires further study. Additional Vaccinium sp. accessions should be screened to investigate the incidence of this new virus.

Genomic analyses of a widespread blueberry virus in the United States

Screening of blueberry accessions using high throughput sequencing revealed the presence of a new virus. Genomic structure and sequence are similar to that of nectarine stem pitting associated virus (NSPaV), a member of the genus Luteovirus, family Tombusviridae. The full genome of the new luteovirus, tentatively named blueberry virus L (BlVL), was characterized and analyzed. Similar to NSPaV, BlVL does not contain readily identifiable movement proteins in any of the seven isolates sequenced. More than 600 samples collected from five states were screened and 79% were found infected, making BlVL the most widespread blueberry virus in the United States.

Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China

Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5'-untranslated region (UTR) and a 76-nt 3'-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1.