Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

Liu, Mao-Yan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

doi:10.1007/s00705-015-2691-9

Cited by 18 publications

(13 citation statements)

References 32 publications

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“…Both emerging and known plant viruses can be easily discovered by high-throughput sequencing [ 21 ]. Liu et al [ 22 ] determined the whole genome sequence of a Chinese isolate of Pepper vein yellows virus using deep sequencing of small RNAs. Bejerman et al [ 23 ] discovered a new enamovirus and obtained genome sequences from alfalfa plants that showed dwarfism symptoms by de novo sequencing, which was confirmed by the Sanger method.…”

Section: Discussionmentioning

confidence: 99%

Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China

et al. 2016

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The genome sequences of Apple chlorotic leaf spot virus (ACLSV) isolates from three accessions of hawthorns (Crataegus pinnatifida) grown at Shenyang Agricultural University were determined using Illumina RNA-seq. To confirm the assembly data from the de novo sequencing, two ACLSV genomic sequences (SY01 and SY02) were sequenced using the Sanger method. The SY01 and SY02 sequences obtained with the Sanger method showed 99.5% and 99.7% nucleotide identity with the transcriptome data, respectively. The genome sequences of the hawthorn isolates SY01, SY02 and SY03 (GenBank accession nos. KM207212, KU870524 and KU870525, respectively) consisted of 7,543, 7,561 and 7,545 nucleotides, respectively, excluding poly-adenylated tails. Sequence analysis revealed that these hawthorn isolates shared an overall nucleotide identity of 82.8–92.1% and showed the highest identity of 90.3% for isolate YH (GenBank accession no. KC935955) from pear and the lowest identity of 67.7% for isolate TaTao5 (GenBank accession no. EU223295) from peach. Hawthorn isolate sequences were similar to those of ‘B6 type’ ACLSV. The relationship between ACLSV isolates largely depends upon the host species. This represents the first comparative study of the genome sequences of ACLSV isolates from hawthorns.

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Section: Discussionmentioning

confidence: 99%

Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China

et al. 2016

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“…A total of 36,430,754 (a: 17,322,690, b: 11,735,694 and c: 7,372,370) paired-end reads were obtained, and 432,848 contigs (a: 143,689, b: 113,012 and c: 176,147) were generated de novo and compared with sequences in the GenBank nt using BLASTn, and 7 contigs were identi ed with E-values of zero. Contig_62 was 5992 nt long and had high identities (>87.5%) to the genome of PeVYV-3 (Pepper vein yellows virus 3) (KP326573; [3]) and the other contigs were matched with Chilli ringspot virus (ChiRSV, 3 contigs), Chilli veinal mottle virus (ChiVMV, 1 contig), Tomato zonate spot virus (TZSV, 1 contig) and Cucumber mosaic virus (CMV, 1 contig).…”

Section: Main Textmentioning

confidence: 99%

“…Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae and are currently classi ed into six species (International Committee on Taxonomy of Viruses [ICTV] 2019 release), named Pepper vein yellows virus 1 to 6 [1][2][3][4][5][6]. They have 86.2-94.6% nucleotide identity between them.…”

Section: Introductionmentioning

confidence: 99%

Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China

Zhao

Yin

Hua

et al. 2021

Preprint

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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.

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“…The total RNAs were sent for next-generation sequencing. De novo assembly generated 7 contigs, one of which was 5992 nt long and had high identities (>87.5%) to the genome of PeVYV-3 (Pepper vein yellows virus 3) (KP326573; [3] ). Primers designed from this sequence were then used to amplify a coat protein (CP) fragment of the virus (PeVYV-CP f: 5′-ATGAATACGGGAGGAGTTAGG -3′, PeVYV-CP r: 5′-CTATTTGGGGTTGTGCAGTTG -3′).…”

Section: Main Textmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pod Pepper Vein Yellows Virus, a New Recombinant Polerovirus Infecting Pod Pepper in Yunnan Province, China

Zhao¹,

Yin²,

Hua³

et al. 2020

Preprint

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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 (94% 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 (88.8% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event at nucleotide positions 4126 to 5192 nt, with TVDV and PeVYV-3 as the minor and major parents, respectively. 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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Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

Cited by 18 publications

References 32 publications

Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China

Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China

Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China

Pod Pepper Vein Yellows Virus, a New Recombinant Polerovirus Infecting Pod Pepper in Yunnan Province, China

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