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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #349796
Title: A virus in American blackcurrant (Ribes americanum) with distinct genome features reshapes classification in the Tymovirales

Author
item THEKKE-VEETIL, T - University Of Arkansas
item HO, T - University Of Arkansas
item Postman, Joseph
item Martin, Robert
item TZANETAKIS, I - University Of Arkansas

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2018
Publication Date: 7/26/2018
Citation: Thekke-Veetil, T., Ho, T., Postman, J.D., Martin, R.R., Tzanetakis, I.E. 2018. A virus in American blackcurrant (Ribes americanum) with distinct genome features reshapes classification in the Tymovirales. Viruses. 10(8):406. https://doi.org/10.3390/v10080406.
DOI: https://doi.org/10.3390/v10080406

Interpretive Summary: A novel virus with distinct genome features was discovered in a symptomatic blackcurrant plant by high throughput sequencing. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames (ORFs) were identified and the first codes for typical virus replicase that contains a methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four open reading frames code for putative proteins that exhibit no significant homology to other virus proteins in the databases. The arrangement of the genes downstream from the first ORF resembles that of members of the order Tymovirales, but with an unconventional triple gene block (TGB) protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae, but it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a new species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.

Technical Abstract: A novel virus with distinct genome features was discovered by large scale sequencing in a symptomatic blackcurrant plant. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames (ORFs) were identified with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four putative proteins exhibit no significant homology to other virus proteins. The genome organization downstream the first ORF resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae whereas it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.