Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China
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.
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Fig. S1 Symptoms of virus-infected Pod peppers from the field.
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.
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.
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.
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).
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Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China
Posted 26 Jan, 2021
On 23 Feb, 2021
On 02 Feb, 2021
On 14 Jan, 2021
On 14 Jan, 2021
On 14 Jan, 2021
Posted 28 Dec, 2020
On 28 Dec, 2020
On 28 Dec, 2020
On 28 Dec, 2020
Posted 25 Dec, 2020
On 25 Dec, 2020
On 25 Dec, 2020
On 25 Dec, 2020
Posted 23 Dec, 2020
Received 23 Dec, 2020
Received 22 Dec, 2020
On 17 Dec, 2020
On 16 Dec, 2020
On 15 Dec, 2020
Invitations sent on 15 Dec, 2020
On 15 Dec, 2020
On 15 Dec, 2020
On 22 Nov, 2020
Received 21 Nov, 2020
Received 09 Nov, 2020
On 07 Nov, 2020
On 05 Nov, 2020
Invitations sent on 05 Nov, 2020
On 03 Nov, 2020
On 03 Nov, 2020
On 03 Nov, 2020
On 29 Oct, 2020
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.
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Figure 2
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Figure 4