ArticleBMC genomics2016
Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Virome analysis of field-collected chilli samples reveals diverse viruses.Virology journal · 2025Article
- Genomic diversity of Capillovirus uniheveae (Betaflexiviridae) infecting Hevea brasiliensis Muell. Arg. in Hainan, China.BMC genomics · 2025Article
- Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran.Viruses · 2024Article
- Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.Nature communications · 2023Article
- Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered FernGenes · 2023Article
- Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage.Frontiers in microbiology · 2022Article
- Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes.Scientific reports · 2020Article
- Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine (Frontiers in microbiology · 2020Article
- Detection of disease inPeerJ · 2019Article
- Article
- RNA viromes of the oriental hybrid lily cultivar "Sorbonne".BMC genomics · 2018Article
- Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies.Viruses · 2018Review
- Peach RNA viromes in six different peach cultivars.Scientific reports · 2018Article
- Diverse, Novel Mycoviruses From the Virome of a HypovirulentFrontiers in plant science · 2018Article
- Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine.Genome announcements · 2017Article
- Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine.Genome announcements · 2017Article
- Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.Frontiers in plant science · 2017Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study.
resultsWe de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes.
conclusionsTaken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination.
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