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

BMC Genomics

Research Article

Sang-Min Kim¹  Sun-Lim Kim¹  Bong Choon Lee¹  Hoseong Choi²  Yeonhwa Jo²  Won Kyong Cho³ 

[1] Crop Foundation Division, National Institute of Crop Science, RDA, 55365, Wanju, South Korea;Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;The Taejin Genome Institute, Gadam-gil 61, 25239, Hoeongseong, Republic of Korea;

关键词: Apple stem grooving virus;    De novo;    Recombination;    RNA-Seq;    Single nucleotide variation;    Transcriptome;   

DOI  :  10.1186/s12864-016-2994-6

 received in 2016-04-28, accepted in 2016-08-03,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2016