RESUMEN
A new positive-strand RNA virus genome was discovered in Camellia japonica plants. The complete genome of the virus is 12,570 nt in size, excluding the poly(A) tail, and contains one large open reading frame (ORF1) and two small open reading frames (ORF2, ORF3). ORF1 and ORF2 are homologous to sequences of waikaviruses, while ORF3 has no relatives in the databases. ORF1 encodes a putative polyprotein precursor that is putatively processed into eight smaller proteins, as in typical waikaviruses. Comprehensive analysis, including BLAST searches, genome organization and pairwise sequence comparisons, and phylogeny reconstructions, invariably placed the virus with the waikaviruses. Furthermore, due to lower amino acid sequence identity to known waikaviruses than the threshold species demarcation cutoff, this virus may represent a new species in the genus Waikavirus, family Secoviridae, and we have tentatively named it "camellia virus A" (CamVA). Finally, a field survey was conducted to assess the occurrence of CamVA in camellias and its associated symptoms.
Asunto(s)
Camellia/virología , Genoma Viral , Filogenia , Waikavirus/genética , Sistemas de Lectura Abierta , Proteínas Virales/genética , Waikavirus/aislamiento & purificación , Secuenciación Completa del GenomaRESUMEN
A novel dsRNA virus was identified by high-throughput sequencing from tea oil trees in China. Its complete genome of 4714 bp contains two open reading frames (ORFs). ORF1 encodes a putative coat protein (CP) of 702 amino acids (aa), and ORF2 codes for an RNA-dependent RNA polymerase (RdRp) of 855 aa. The virus shares the highest aa sequence identity of 45.21% in RdRp with taro-associated totivirus L (MN_119621), a member of the genus Totivirus in the family Totiviridae. Phylogenetic analysis of the aa sequences of the RdRp places the new virus in a group with other totiviruses, suggesting that this virus, which is provisionally named "tea-oil camellia-associated totivirus 1", should be considered a member of the genus Totivirus.
Asunto(s)
Camellia/virología , Enfermedades de las Plantas/microbiología , Totivirus/clasificación , Secuenciación Completa del Genoma/métodos , Tamaño del Genoma , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Homología de Secuencia de Aminoácido , Totivirus/genética , Totivirus/aislamiento & purificaciónRESUMEN
A new badnavirus was identified in an ornamental camellia tree with yellow mottle symptom. The complete circular double-stranded DNA genome of this virus was found to consist of 8,203 bp. Its genome organization is typical of badnaviruses, containing three open reading frames (ORFs). ORFs 1 and 2 encode putative proteins with unknown functions. ORF3 encodes a large polyprotein that contains almost all of the conserved domains of badnaviruses. The virus shares 55-62% nucleotide sequence identities with other badnaviruses in the RT+RNase H region. Phylogenetic analyses placed it in group I of the genus Badnavirus. Therefore, this virus, which is tentatively named "camellia Lemon Glow virus", should represent a new species of the genus Badnavirus. This virus was found to be present in approximately a quarter of camellia trees tested.
Asunto(s)
Badnavirus/genética , Badnavirus/aislamiento & purificación , Camellia/virología , Enfermedades de las Plantas/virología , Badnavirus/clasificación , Badnavirus/fisiología , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Proteínas Virales/genéticaRESUMEN
Camellia japonica plants manifesting a complex and variable spectrum of viral symptoms like chlorotic ringspots, necrotic rings, yellowing with necrotic rings, yellow mottle, leaves and petals deformations, and flower color-breaking have been studied since 1940, mainly by electron microscopic analyses; however, a strong correlation between the symptoms and one or more well-characterized viruses was never verified. In this work, samples collected from symptomatic plants were analyzed using the next-generation sequencing technique, and a complex virome composed of members of the Betaflexiviridae and Fimoviridae families was identified. In particular, the genomic fragments typical of the emaravirus group were organized in the genomes of two new emaraviruses species, tentatively named Camellia japonica-associated emaravirus 1 and 2. They are the first emaraviruses described in camellia plants and found in symptomatic plants. At the same time, in both symptomatic and asymptomatic plants, five betaflexivirus isolates were detected that, based on amino acid sequence comparisons, can be considered two new isolates of the recently characterized camellia ringspot-associated virus 1 and 2 (CRSaV-1/2). These recently identified betaflexiviruses associated with C. japonica disease show an unusual hyper-conservation of the coat protein at the amino acid level. The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are MN385581, MN532567, MN532565, MN385582, MN532566, MN385573, MN385577, MN385574, MN385578, MN385575, MN385579, MN385576, MN385580, MN557024, MN557025, MN557026, MN557027, and MN557028.
Asunto(s)
Camellia/virología , Flexiviridae/clasificación , Genoma Viral , Enfermedades de las Plantas/virología , Virus ARN/clasificación , Viroma , Flexiviridae/aislamiento & purificación , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia , Hojas de la Planta/virología , Virus ARN/aislamiento & purificaciónRESUMEN
One large contig with high sequence similarity to Asian prunus virus 2 was identified by high-throughput sequencing from a camellia (Camellia japonica) tree with ringspot symptoms. The complete genome of this new virus was determined to be 8829 nucleotides long, excluding the 3' poly(A) tail. Its genome organization resembles that of known foveaviruses but contains an additional open reading frame in the 3'-terminal region. Phylogenetic analysis also places this virus with members of the genus Foveavirus in the family Betaflexiviridae in the same subgroup. The virus, which is provisionally named "camellia ringspot-associated virus 4â³, shares 50-56% nucleotide sequence identity with other foveaviruses and should represent a new species in the genus.
Asunto(s)
Camellia/virología , Flexiviridae/aislamiento & purificación , Enfermedades de las Plantas/virología , Flexiviridae/clasificación , Flexiviridae/genética , Tamaño del Genoma , Genoma Viral , Sistemas de Lectura Abierta , FilogeniaRESUMEN
Three viral contig sequences, which represented complete genome of a novel virus with three dsRNAs of 1,712 nucleotides (nt) (dsRNA1), 1,504 nt (dsRNA2) and 1,353 nt (dsRNA3), were found in tea-oil camellia plants by high-throughput sequencing analysis. The three dsRNAs were re-sequenced by RT-PCR cloning. The largest dsRNA, dsRNA1, had a single open reading frame (ORF) that encoded a putative 52.7-kDa protein of a putative viral RNA-dependent RNA polymerase (RdRp). DsRNA2 and dsRNA3 were predicted to encode putative capsid proteins (CPs) of 40.47 kDa and 40.59 kDa, respectively. The virus, which is provisionally named "tea-oil camellia deltapartitivirus 1", shared amino acid sequence itentities of 36.09-69.18% with members of the genus Deltapartitivirus on RdRp. Phylogenetic analysis based on RdRp also placed the new virus and other deltapartitiviruses together in a group, suggesting that this virus should be considered a new member of the genus Deltapartitivirus.
Asunto(s)
Camellia/virología , Virus ARN/genética , Secuenciación Completa del Genoma/métodos , Mapeo Contig , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Sistemas de Lectura Abierta , Filogenia , Virus ARN/clasificación , ARN Bicatenario/genéticaRESUMEN
Foliar chlorotic and necrotic ringspots of different sizes were observed in many ornamental camellia (Camellia spp.) species and cultivars with or without variegation symptoms. In this study, flexuous, filamentous virions of approximately 680-780â¯nm long were observed by electron microscopy in sap of camellia trees with chlorotic ringspots. Five large viral contigs were identified by high-throughput sequencing technology, and complete genome sequences of them were determined. Sequence analyses show that these five isolates represent three novel viruses, two in the genus Prunevirus, one in the genus Capillovirus. The genome organization of the two camellia pruneviruses resembles that of pruneviruses but does not contain the nucleic acid-binding protein (NABP) at the 3'-terminal region. They share 66.5-66.8% with each other and 51.9-58.6% with the known pruneviruses at the genome sequence level. The genome of the camellia capillovirus contains an additional NABP at the 3'-terminus when compared to those of Capillovirus. The genomes of the two capillovirus variants are 72.7% identical to each other and 42.1-48.4% to the known capilloviruses. Phylogenetic analyses support these viruses are new members of either Prunevirus or Capillovirus. The two pruneviruses are tentatively named as camellia ringspot associated virus 1 (CRSaV-1) and CRSaV-2, and the capillovirus is named as CRSaV-3. Infections of these viruses were common in camellia species, cultivars and hybrids. The viruses were also detected in seedlings from seeds collected from two camellia trees, indicating that they are seed transmissible.
Asunto(s)
Camellia/virología , Flexiviridae/clasificación , Flexiviridae/genética , Enfermedades de las Plantas/virología , Flexiviridae/ultraestructura , Genoma Viral , Genómica/métodos , Fenotipo , Filogenia , Semillas/virología , Virión/genética , Virión/ultraestructura , Secuenciación Completa del GenomaRESUMEN
Next-generation sequencing of small RNAs and PCR amplification with two pairs of back-to-back primers, followed by cloning and sequencing, allowed identification of a novel geminivirus isolate provisionally named camellia chlorotic dwarf-associated virus (CaCDaV). The complete genome sequence of CaCDaV comprises 3,687 nucleotides (nts) and six open reading frames (ORFs). The genome and putative proteins of CaCDaV were most closely related to those of two unclassified geminiviruses: citrus chlorotic dwarf-associated virus (CCDaV, 3,640 nt) and mulberry mosaic dwarf-associated virus (MMDaV, 2,952 nt). Phylogenetic analysis revealed a distinct clade for CaCDaV, CCDaV and MMDaV, supporting their inclusion in a new genus within the family Geminiviridae. Because CaCDaV and CCDaV shared a high genome nucleotide sequence identity (54.8%), we propose that the CaCDaV should be included as a member in this new genus.