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Phylogenetic analysis of grapevine mitovirus 1 (GMV1) (Acc. No: PP803060) at amino-acid level with other RdRp protein sequences of mitoviruses. Phylogenetic tree was generated using the neighbour-joining method using MEGA-X with p-distance matrix and 1,000 bootstrap replicates (places at the nodes on the tree). The scale units (0.05) are substitutions per site
Source publication
Background
Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.
Methods and results
Here, we identify putative novel m...
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Citations
... The ribosomal RNA (rRNA)-depleted RNA sequence data generated from HTS using the NovaSeq 6000 sequencing platform from pooled sugarcane sample SP6 was retrieved from the Sequence Read Archive (SRA), which were submitted to the National Center for Biotechnology Information (NCBI) under accession number SRR29750383 in our previous study [25] and re-assembled using the CLC Genomic Workbench assembler (version 20.0.4) [26]. ...
Background
Sugarcane is cultivated globally and affected by more than 125 pathogens, which lead to various plant diseases. In recent years, high-throughput sequencing (HTS)-based genome analyses have been broadly adopted for the discovery of both characterized and un-characterized viruses from plant samples. In this study, the HTS data of sugarcane pooled sample retrieved from sequence read archive (SRA) were de novo re-assembled using CLC Genomic Workbench.
Methods and results
The genomic sequence of a novel dsRNA totivirus, 5,384 nucleotides (nt) long, excluding the 5’ untranslated region (UTR) and 3’ UTR, was discovered and named sugarcane totivirus 1 (STV 1). The genome contains two open reading frames (ORFs): a putative coat protein (CP) encoding 866 amino acids (aa) and RNA-dependent RNA polymerase (RdRp) encoding 824 aa. Phylogenetic studies based on the genomic sequences (nt), and the aa sequences of CP as well as RdRp regions revealed that STV 1 is closely related to other members of the genus Totivirus. Pairwise sequence identity of CP and RdRp aa sequences showed 30.0-51.5% and 26.3–47.2% similarity, respectively with other members of the family Totiviridae. The HTS results were further validated and confirmed through OneStep RT-PCR assay and Sanger sequencing.
Conclusion
A novel totivirus (STV 1) in the genus Totivirus, family Totiviridae has been identified. This is the first report of dsRNA totivirus STV 1 associated with sugarcane from India.
... High-throughput sequencing (HTS) is now recognized as a key tool for virus identification and characterization, as it offers advantages such as independence from prior knowledge of specific genome sequences, increased sensitivity, and the possibility of discovering novel sequences [10][11][12][13][14][15][16][17][18][19][20]. RNA-seq data from plant research frequently include sequences from RNA viruses, which could reveal novel plant RNA viruses including rhabdoviruses [13][14][15][16][17][18]. ...
... High-throughput sequencing (HTS) is now recognized as a key tool for virus identification and characterization, as it offers advantages such as independence from prior knowledge of specific genome sequences, increased sensitivity, and the possibility of discovering novel sequences [10][11][12][13][14][15][16][17][18][19][20]. RNA-seq data from plant research frequently include sequences from RNA viruses, which could reveal novel plant RNA viruses including rhabdoviruses [13][14][15][16][17][18]. In an earlier study, pear (Pyrus communis 'Bartlett') RNA-seq data were generated which led to identification of several known viruses [21]. ...
Novel viruses in plants can be detected through transcriptome data mining. In this study, a novel cytorhabdovirus, pear rhabdovirus 1 (PRV-1) was identified through reanalysis of RNA-seq data of pear (P. communis 'Bartlett'). The genomic RNA of PRV-1, with complete coding region, measured 15,628 nucleotides (nts) and encompassed six open reading frames (ORF). Homology analysis of PRV-1 genome showed sequence identity of 33.18-56.75% with the existing cytorhabdovirus sequences. Phylogenetic analysis based on genome sequences showed that PRV-1 clustered in the same clade of cytorhab-doviruses. Based on the sequence demarcation criteria, PRV-1 represents a newly discovered species within the Cytorhab-dovirus genus of the Rhabdoviridae family. Identification of a novel virus in pear will enhance our understanding on the diversity of plant cytorhabdoviruses.
