title: Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors: Yeonhwa
authors: Y
authors: Jo
authors: Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors: Hoseong
authors: H
authors: Choi
authors: Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea.
authors: Sang-Min
authors: SM
authors: Kim
authors: Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea.
authors: Sun-Lim
authors: SL
authors: Kim
authors: Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea.
authors: Bong Choon
authors: BC
authors: Lee
authors: Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. wonkyong@gmail.com.|The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea. wonkyong@gmail.com.
authors: Won Kyong
authors: 0000-0002-8416-5173
authors: WK
authors: Cho
mesh_terms: D019295:Computational Biology / Q000379:methods; D052677:Flexiviridae / Q000145:classification* / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D027845:Malus / Q000235:genetics / Q000821:virology; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000821:virology; D010942:Plant Viruses / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D031989:Pyrus / Q000235:genetics; D012367:RNA, Viral; D011995:Recombination, Genetic; D059467:Transcriptome
chemical_list: D012367:RNA, Viral
keywords: Apple stem grooving virus; De novo genome assembly; RNA-Seq; Recombination; Single nucleotide variation; Transcriptome