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Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5’ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3’-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126-5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.
Keywords
pepper vein yellows virus, recombination, Polerovirus, readthrough domain
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- 8.Fig.S1.jpg
Fig. S1 Symptoms of virus-infected Pod peppers from the field.
- 9.Fig.S2.jpg
Fig. S2 Pairwise nucleotide sequence comparisons of PoPeVYV with related reference viruses. Genome: the full genome sequence of viruses; 5’- half: sequence contain the 5’ NCR to P3; 3’- half: sequence from P3 readthrough domain to 3’ NCR. Multiple nucleotide sequences were aligned using MUSCLE, and pairwise nucleotide sequence comparisons were done using the SDT (Species Demarcation Tool) v1.2 program.
- 10.Fig.S3.jpg
Fig. S3 Phylogenetic tree of PoPeVYV. The enamovirus Pea enation mosaic virus 1 (PEMV-1, NC_003629.1) was used as an outgroup. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. Evolutionary analyses were conducted in MEGA X.
- 11.Fig.S4.jpg
Fig. S4 Structure of the cloning vector pCB301-MD. The 2x35S in pCB301-MD was originally from the vector pCass2[15], MCS- HDVRZ-NOS cassette was originally from the vector pHST40[16]. Transcription Start site and Ribozyme cleavage site were based on vectors of pCass2 and pHST40 in references.
- 12.Fig.S5.jpg
Fig. S5 The strategy for constructing the full-length infectious clone by homologous recombination. Two overlapped PCR products of PoPeVYV were amplified with primers (Inf-PoPeVYV-1 f/r, Inf-PoPeVYV-2 f/r) and recombined with the linearized binary vector pCB301-MD which was amplified with primers pair Vec-pCB301(Vec-pCB301 f/r).
- 3.TableS1.docx
- 13.RDP4files.rar
- 14.PoPeVYVMT188667.txt
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See the published version of this preprint at Virology Journal.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Short report
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at Virology Journal.
Version 2
Posted 26 Jan, 2021
No community comments so far
Editorial decision: Accept
On 02 Feb, 2021
Editor assigned
On 14 Jan, 2021
Submission checks complete
On 14 Jan, 2021
Editor invited
On 14 Jan, 2021
Version (no preprint)
Posted 28 Dec, 2020
Editor assigned
On 28 Dec, 2020
Submission checks complete
On 28 Dec, 2020
Editor invited
On 28 Dec, 2020
This version was not preprinted
Version (no preprint)
Posted 25 Dec, 2020
Editor assigned
On 25 Dec, 2020
Submission checks complete
On 25 Dec, 2020
Editor invited
On 25 Dec, 2020
This version was not preprinted
Version (no preprint)
Posted 23 Dec, 2020
Review #1 received
Received 23 Dec, 2020
Review #2 received
Received 22 Dec, 2020
Reviewer #2 agreed
On 17 Dec, 2020
Reviewer #1 agreed
On 16 Dec, 2020
Editor assigned
On 15 Dec, 2020
Reviewers invited
Invitations sent on 15 Dec, 2020
Submission checks complete
On 15 Dec, 2020
Editor invited
On 15 Dec, 2020
This version was not preprinted
No comments provided
Editorial decision: Major revision
On 22 Nov, 2020
Review #2 received
Received 21 Nov, 2020
Review #1 received
Received 09 Nov, 2020
Reviewer #2 agreed
On 07 Nov, 2020
Reviewer #1 agreed
On 05 Nov, 2020
Reviewers invited
Invitations sent on 05 Nov, 2020
Editor assigned
On 03 Nov, 2020
Submission checks complete
On 03 Nov, 2020
Editor invited
On 03 Nov, 2020
First submitted
On 29 Oct, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Virology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at Virology Journal.
Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5’ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3’-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126-5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- 8.Fig.S1.jpg
Fig. S1 Symptoms of virus-infected Pod peppers from the field.
- 9.Fig.S2.jpg
Fig. S2 Pairwise nucleotide sequence comparisons of PoPeVYV with related reference viruses. Genome: the full genome sequence of viruses; 5’- half: sequence contain the 5’ NCR to P3; 3’- half: sequence from P3 readthrough domain to 3’ NCR. Multiple nucleotide sequences were aligned using MUSCLE, and pairwise nucleotide sequence comparisons were done using the SDT (Species Demarcation Tool) v1.2 program.
- 10.Fig.S3.jpg
Fig. S3 Phylogenetic tree of PoPeVYV. The enamovirus Pea enation mosaic virus 1 (PEMV-1, NC_003629.1) was used as an outgroup. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. Evolutionary analyses were conducted in MEGA X.
- 11.Fig.S4.jpg
Fig. S4 Structure of the cloning vector pCB301-MD. The 2x35S in pCB301-MD was originally from the vector pCass2[15], MCS- HDVRZ-NOS cassette was originally from the vector pHST40[16]. Transcription Start site and Ribozyme cleavage site were based on vectors of pCass2 and pHST40 in references.
- 12.Fig.S5.jpg
Fig. S5 The strategy for constructing the full-length infectious clone by homologous recombination. Two overlapped PCR products of PoPeVYV were amplified with primers (Inf-PoPeVYV-1 f/r, Inf-PoPeVYV-2 f/r) and recombined with the linearized binary vector pCB301-MD which was amplified with primers pair Vec-pCB301(Vec-pCB301 f/r).
- 3.TableS1.docx
- 13.RDP4files.rar
- 14.PoPeVYVMT188667.txt
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