Abstract
Grapevine red blotch virus (GRBV) is type member of the newly identified genus Grablovirus. It possesses a single-stranded circular DNA genome of around 3200 nucleotides encoding three open reading frames (ORFs) in both the virion sense, the V1 (CP), V2 and V3, and complementary sense, C1 (RepA), C2 and C3. As shown for members of the genus Mastrevirus, the C1 and C2 ORFs are predicted to fuse through splicing to form a replication-associated protein (Rep). Data obtained using high-throughput sequencing (RNA-Seq) of three RNA-enriched populations, extracted from GRBV-infected grapevine (Vitis vinifera), confirmed the presence of the predicted C1-C2 intron (nts 2288-2450), but in addition identified a larger virion-sense intron (nts 251-589) spanning the V2 ORF. Evidence for both introns in a number of isolates was supported by bioinformatic analysis of publicly available datasets (n=20). These observations were further supported by RT-PCR analyses in both GRBV-infected grapevine and transient expression assays where GRBV genome segments were agro-inoculated onto Nicotiana benthamiana. The donor site of the virion-sense intron is located within two small ORFs, V0 and V02, while the acceptor site is two-thirds along the V2 ORF. Splicing at these positions is predicted to delete the N terminus of the encoded V2 protein. Comparative analyses of full-length GRBV sequences and the related tentative grabloviruses Prunus geminivirus A and wild Vitis virus 1 support the existence of both introns and V0. The probable regulatory role of these introns in the GRBV infection cycle is discussed.
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Claims 8
Claim · model-written summary
RNA sequencing of infected grapevine confirmed the predicted GRBV C1-C2 intron.
- Taxon
- grapevine (Vitis vinifera)
Vitis viniferae0 - Interactor
- GRBVe0pathogen
- Gene
- C1-C2 introne0
- Outcome
- presence of the predicted C1-C2 introne0
- Value
- nts 2288-2450e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Data obtained using high-throughput sequencing (RNA-Seq) of three RNA-enriched populations, extracted from GRBV-infected grapevine (Vitis vinifera), confirmed the presence of the predicted C1-C2 intron (nts 2288-2450)”
Claim · model-written summary
RNA sequencing identified a larger GRBV virion-sense intron spanning V2.
- Taxon
- grapevine (Vitis vinifera)Vitis viniferae1
- Interactor
- GRBVe1pathogen
- Gene
- V2 ORFe0
- Outcome
- larger virion-sense introne0
- Value
- nts 251-589e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“identified a larger virion-sense intron (nts 251-589) spanning the V2 ORF”
e1“GRBV-infected grapevine (Vitis vinifera)”
Claim · model-written summary
Public datasets supported both GRBV introns across isolates.
- Taxon
- grapevine (Vitis vinifera)Vitis viniferae1
- Interactor
- GRBVe1pathogen
- Outcome
- Evidence for both intronse0
- Value
- n=20e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Evidence for both introns in a number of isolates was supported by bioinformatic analysis of publicly available datasets (n=20)”
e1“GRBV-infected grapevine (Vitis vinifera)”
Claim · model-written summary
RT-PCR supported both introns in infected grapevine.
VitisOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These observations were further supported by RT-PCR analyses in both GRBV-infected grapevine”
Claim · model-written summary
Transient expression in Nicotiana benthamiana supported the intron observations.
- Taxon
- Nicotiana benthamiana
Nicotiana benthamianae0 - Interactor
- GRBVe0pathogen
- Outcome
- transient expression assayse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“transient expression assays where GRBV genome segments were agro-inoculated onto Nicotiana benthamiana”
Claim · model-written summary
The GRBV virion-sense donor site lies within V0 and V02 and the acceptor lies in V2.
- Taxon
- grapevine (Vitis vinifera)Vitis viniferae1
- Interactor
- GRBVe1pathogen
- Gene
- V0 and V02e0
- Outcome
- donor site of the virion-sense introne0
- Qualifier
- acceptor site is two-thirds along the V2 ORFe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The donor site of the virion-sense intron is located within two small ORFs, V0 and V02, while the acceptor site is two-thirds along the V2 ORF”
e1“GRBV-infected grapevine (Vitis vinifera)”
Claim · model-written summary
Splicing is predicted to remove the V2 protein N terminus.
- Taxon
- grapevine (Vitis vinifera)Vitis viniferae1
- Interactor
- GRBVe1pathogen
- Gene
- V2 proteine0
- Outcome
- delete the N terminus of the encoded V2 proteine0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Splicing at these positions is predicted to delete the N terminus of the encoded V2 protein”
e1“GRBV-infected grapevine (Vitis vinifera)”
Claim · model-written summary
Comparative sequences support both introns and V0.
- Taxon
- grapevine (Vitis vinifera)Vitis viniferae1
- Interactor
- GRBVe0pathogen
- Gene
- V0e0
- Outcome
- existence of both introns and V0e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Comparative analyses of full-length GRBV sequences and the related tentative grabloviruses Prunus geminivirus A and wild Vitis virus 1 support the existence of both introns and V0”
e1“GRBV-infected grapevine (Vitis vinifera)”