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Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

BACKGROUND: Next-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 availab...

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Autores principales: Jo, Yeonhwa, Choi, Hoseong, Kim, Sang-Min, Kim, Sun-Lim, Lee, Bong Choon, Cho, Won Kyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977635/
https://www.ncbi.nlm.nih.gov/pubmed/27507588
http://dx.doi.org/10.1186/s12864-016-2994-6
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author Jo, Yeonhwa
Choi, Hoseong
Kim, Sang-Min
Kim, Sun-Lim
Lee, Bong Choon
Cho, Won Kyong
author_facet Jo, Yeonhwa
Choi, Hoseong
Kim, Sang-Min
Kim, Sun-Lim
Lee, Bong Choon
Cho, Won Kyong
author_sort Jo, Yeonhwa
collection PubMed
description BACKGROUND: Next-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. RESULTS: We 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. CONCLUSIONS: Taken 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-49776352016-08-10 Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus Jo, Yeonhwa Choi, Hoseong Kim, Sang-Min Kim, Sun-Lim Lee, Bong Choon Cho, Won Kyong BMC Genomics Research Article BACKGROUND: Next-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. RESULTS: We 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. CONCLUSIONS: Taken 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users. BioMed Central 2016-08-09 /pmc/articles/PMC4977635/ /pubmed/27507588 http://dx.doi.org/10.1186/s12864-016-2994-6 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Jo, Yeonhwa
Choi, Hoseong
Kim, Sang-Min
Kim, Sun-Lim
Lee, Bong Choon
Cho, Won Kyong
Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title_full Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title_fullStr Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title_full_unstemmed Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title_short Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus
title_sort integrated analyses using rna-seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for apple stem grooving virus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977635/
https://www.ncbi.nlm.nih.gov/pubmed/27507588
http://dx.doi.org/10.1186/s12864-016-2994-6
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