RESUMEN
Severe mottling symptoms were observed on Carica papaya L. in Koyonzo, Kakamega County, Kenya. Total RNA was sequenced via an RNAtag-seq workflow. Assembled contigs indicated the presence of a divergent strain of Moroccan watermelon mosaic virus (genus Potyvirus) with a complete genome length of 9,733 nt (GenBank accession no. MN418119). Additionally, the complete genome sequence of a novel member of the viral genus Allexivirus was determined (GenBank accession no. MN418120). The genome contains six open reading frames (ORFs) that show varying degrees of sequence similarity to members of the genus Allexivirus; however, it appears to lack an ORF encoding a nucleic-acid-binding homolog. The tentative name "papaya virus A" (PaVA) has been proposed for this virus.
Asunto(s)
Carica/virología , Flexiviridae/clasificación , Flexiviridae/aislamiento & purificación , Metagenoma , Enfermedades de las Plantas/virología , Potyvirus/clasificación , Potyvirus/aislamiento & purificación , Coinfección/virología , Flexiviridae/genética , Genoma Viral , Kenia , Sistemas de Lectura Abierta , Filogenia , Potyvirus/genética , ARN Viral/genética , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
RNAtag-seq of maize samples collected in Tanzania revealed the presence of a previously undescribed nucleorhabdovirus, tentatively named "Morogoro maize-associated virus" (MMaV), in three samples. The MMaV genome is 12,185-12,187 nucleotides long and shares a 69-70% nucleotide sequence identity with taro vein chlorosis virus. Annotation of the genomes showed a typical nucleorhabdovirus gene organization. PCR was unable to detect the same virus in the remaining 35 samples collected in the region.
Asunto(s)
Enfermedades de las Plantas/virología , Rhabdoviridae/genética , Análisis de Secuencia de ARN/métodos , Zea mays/virología , Tamaño del Genoma , Genoma Viral , Anotación de Secuencia Molecular , Sistemas de Lectura Abierta , Filogenia , Hojas de la Planta/virología , Rhabdoviridae/clasificación , Rhabdoviridae/aislamiento & purificación , TanzaníaRESUMEN
Typically associated with fungal species, members of the viral family Totiviridae have recently been shown to be associated with plants, including important crop species, such as Carica papaya (papaya) and Zea mays (maize). Maize-associated totivirus (MATV) was first described in China and more recently in Ecuador, where it has been found to co-occur with other viruses known to elicit maize lethal necrosis disease (MLND). In a survey for maize-associated viruses, 35 samples were selected for Illumina HiSeq sequencing, from the Tanzanian maize producing regions of Mara, Arusha, Manyara, Kilimanjaro, Morogoro and Pwani. Libraries were prepared using an RNA-tag-seq methodology. Taxonomic classification of the resulting datasets showed that 6 of the 35 samples from the regions of Arusha, Kilimanjaro, Morogoro and Mara, contained reads that were assigned to MATV reference sequences. This was confirmed with PCR and Sanger sequencing. Read assembly of the six MATV-associated datasets yielded partial MATV genomes, two of which were selected for further characterization, using RACE. This yielded two full-length MATV genomes, one of which is divergent from other available MATV genomes.
Asunto(s)
Variación Genética , Enfermedades de las Plantas/virología , Totivirus/genética , Zea mays/virología , China , Genoma Viral/genética , Filogenia , Enfermedades de las Plantas/genética , Totivirus/patogenicidad , Zea mays/genéticaRESUMEN
Citrus tristeza virus (CTV) is present in almost all of the major citrus production areas where it continues to reduce the profitability of citriculture. The accurate characterisation of CTV populations, which are usually made up of a number of disparate strains, requires the use of robust PCR protocols. Mismatches between primers and their corresponding binding sites may introduce primer-associated bias during amplification. The primer-associated bias of four sets of CTV specific primers, targeting the A and F regions and the p33 and p23 genes, were evaluated. This was done through the amplification of defined templates followed by their characterisation using the sequencing of multiple clones, as well as Illumina next generation sequencing. High levels of bias were found to be associated with the primer pairs targeting the A and F regions. The p33 gene primers were found to be biased against two genotypes and suggestions for preventing this apparent bias are discussed. The primer pair targeting the conserved p23 gene was found to have very little associated bias. Primers should undergo rigorous screening before being used to characterize virus populations that are known to exhibit high levels of variation, especially within primer binding sites.
Asunto(s)
Closterovirus/genética , Variación Genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Reacción en Cadena de la Polimerasa , Sitios de Unión , Citrus/virología , Cartilla de ADN , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/normas , Filogenia , Enfermedades de las Plantas/virología , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/normasRESUMEN
We report here the complete genome sequence of "Candidatus Liberibacter africanus" strain PTSAPSY. The 1,192,232-bp genome with 34.5% G+C content comprises 1,017 open reading frames, 44 tRNAs, and three complete rRNAs in a circular chromosome.