Complete genome sequence of tobacco virus 1, a closterovirus from Nicotiana tabacum

Complete genome sequence of cnidium closterovirus 1, a novel member of the genus Closterovirus infecting Cnidium officinale

The genome of a novel virus identified in Cnidium officinale is composed of a monopartite ssRNA of 16,755 nucleotides that shares 68.73% (query coverage, 20%) sequence identity with carrot yellow leaf virus (CYLV, accession no. FJ869862.1). It contains 11 putative open reading frames and has an organization typical of closteroviruses. It shares 30-50% nucleotide sequence identity with other closteroviruses. The heat shock protein 70-like protein (HSP70), putative RNA-dependent RNA polymerase (RdRp), and coat protein (CP) show 39-66%, 16-60%, and 24-41% amino acid sequence identity, respectively, to the homologous proteins of previously identified closteroviruses. Molecular and HSP70-based phylogenetic analysis of the genome and encoded protein sequences suggested that this virus is a novel member of the genus Closterovirus in the family Closteroviridae, which we have tentatively named "cnidium closterovirus 1" (CnClV1).

Complete genome sequence of platycodon closterovirus 1, a novel putative member of the genus Closterovirus

A new member of the genus Closterovirus was detected in Platycodon grandiflorus using high-throughput RNA sequencing analysis. The complete genome sequence of this new virus isolate, tentatively named "platycodon closterovirus 1" (PlaCV1), comprises 16,771 nucleotides with nine predicted open reading frames (ORFs) having the typical closterovirus genome organization. PlaCV1 shares 37%-50% nucleotide sequence identity with other known closterovirus genome sequences. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70-like protein (HSP70h), viral heat shock protein 90-like protein (HSP90h), minor coat protein (CPm), and coat protein (CP) show 47-68%, 39-66%, 24-52%, 21-57%, and 16-35% amino acid sequence identity, respectively, to homologous proteins in previously identified closteroviruses, suggesting that it represents a distinct, new species in the genus. Phylogenetic analysis of HSP70h sequences places PlaCV1 alongside other members of the genus Closterovirus in the family Closteroviridae. To our knowledge, this study is the first report of the complete genome sequence of PlaCV1 infecting P. grandiflorus in the Republic of Korea.

Identification of rehmannia virus 1, a novel putative member of the genus Closterovirus, from Rehmannia glutinosa

Transcriptome sequencing analysis of a symptomatic Rehmannia glutinosa plant revealed a virome containing two known RNA viruses and one novel virus. In this study, we examined the molecular and biological characteristics of the novel virus. The complete genome of the novel virus is composed of monopartite single-stranded RNA of 15,322 nucleotides with 69% nucleotide sequence identity (with 68% coverage) to tobacco virus 1. Its genome organization is typical of the members of the genus Closterovirus, containing nine putative open reading frames. Molecular and phylogenetic analyses of the genome and encoded protein sequences strongly support that the identified virus is a new species of the genus Closterovirus in the family Closteroviridae. The name rehmannia virus 1 (ReV1) is proposed for this novel virus.

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

BACKGROUND

The invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs.

METHODS

Survey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses.

RESULTS

Twenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell.

CONCLUSION

This study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.