Genome Sequence of Strawberry Pallidosis-associated Virus Isolated in China

doi:10.16420/j.issn.0513-353x.2019-0989

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (1): 146-152.doi: 10.16420/j.issn.0513-353x.2019-0989

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Genome Sequence of Strawberry Pallidosis-associated Virus Isolated in China

CHEN Dao, ZHANG Jie, WU Zujian, DING Xinlun^*()

State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops,Key Laboratory of Plant Virology of Fujian Province,Institute of Plant Virology,Fujian Agriculture and Forestry University,Fuzhou 350002,China

Received:2020-09-13 Revised:2020-12-11 Online:2021-01-25 Published:2021-01-29
Contact: DING Xinlun E-mail:dingxinlun@163.com

Abstract

Abstract:

Strawberry pallidosis-associated virus（SpaV）belongs to the genus Crinivirus of the family Closteroviridae,which causes strawberry diseases. It was first reported in China in 2017. In this study,high-throughput sequencing,RACE and RT-PCR techniques were used to obtain the full length of SPaV China isolate（FJ）. The virus contains two positive-sense single,stranded genome RNA1 and RNA2,RNA1 is composed of 8 048 nt and contains three open reading frames（ORFs）,encoding ORF 1a/1b fusion protein and p9 protein,flanked by 5′ and 3′ untranslated regions of 264 nt and 197 nt,respectively. RNA2 is composed of 7 977 nt and contains eight ORFs,encoding HSP70h,CPh,CP,CPm and other four unknown function proteins（p7,p6,p9 and p28）,flanked by 5′ and 3′ untranslated regions of 248 and 186 nt,respectively. RNA1 and RNA2 share 98.5% and 99.0% nucleotide sequence identity with that of M1 isolate（USA）,respectively. Phylogenetic analysis showed that SPaV China isolate （FJ）was clustered in a separate branch. The analysis of sRNA derived from SPaV showed that the dominant sizes were 21 nt and 22 nt.

Key words: Fragaria × ananassa, strawberry pallidosis-associated virus, NGS, RT-PCR, viral genome sequence

CLC Number:

S668.4

CHEN Dao, ZHANG Jie, WU Zujian, DING Xinlun. Genome Sequence of Strawberry Pallidosis-associated Virus Isolated in China[J]. Acta Horticulturae Sinica, 2021, 48(1): 146-152.

Figures/Tables 5

References 11

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引物名称 Primer name	引物序列（5′-3′） Primer pair
RNA1-1	F:GTAATGAAGTCGTCGAGACCA;R:GAATAGACTACTTCGCCATGTCTG	47
RNA1-2	F:GAGACGATAACGATGTGCGAC;R:TCGACAGTTGAGAGTCGTGAC	52
RNA1-3	F:TCTAAATTTAAGAGTTTGCTGTTTAA;R:ATAGCTCTAGAGGCTCTAGCATT	57
RNA1-4	F:TGCGTATCAGTATGTCACCAC;R:CATGGCCAAGGTCACCAGAGT	56
RNA1-5	F:TCTTATAATATTCATACCCTTGAAC;R:CGGGAATTTATTGTAAATCATAC	58
race1-3	ACACTGGAGTTAAAGTCTGAAACTCTAAATTTAAGAGTTTAG	57
race1-5	TTTAAAAGTAACTGATACATCTTCAGGCAGACATAATCTCT	61
RNA2-1	F:CCAAAGATAAATAACAAACAATCAA;R:ATATCTTCCCGCATACGAATTTATCAA	57
RNA2-2	F:GGGCAGATCAAAGAACAACTTGTT;R:CATTGATCGTTCCACTCAATTTGAAA	60
RNA2-3	F:ATGACGTCGCAAATGATAGTGCTTTC;R:CTTCCAACTCTCTGCTCGGTAACTT	55
RNA2-4	F:CTTGATAAACGTGACAAATCAAACCT;R:GGGGTCAGCTCTTTCAAAGCTTGA	57
RNA2-5	F:CTTTTTATTAGCGTCAATCTTAGCTTT;R:TTTCTCGGTCAATCGATCGAACTCTGA	58
RNA2-6	F:CAAGAATAATGGATTGGAGGATATGCCTT;R:TCACCAGGGGATTGCTTTCCAACTT	56
race2-3	GATTACGCCAAGCTTTGCTACCTCCTATACCAATGCGGA	67
race2-5	ACCTCCCAAACGAATTTATCAATCTCATAAGGTAAAGTGTT	65

引物名称 Primer name	引物序列（5′-3′） Primer pair
RNA1-1	F:GTAATGAAGTCGTCGAGACCA;R:GAATAGACTACTTCGCCATGTCTG	47
RNA1-2	F:GAGACGATAACGATGTGCGAC;R:TCGACAGTTGAGAGTCGTGAC	52
RNA1-3	F:TCTAAATTTAAGAGTTTGCTGTTTAA;R:ATAGCTCTAGAGGCTCTAGCATT	57
RNA1-4	F:TGCGTATCAGTATGTCACCAC;R:CATGGCCAAGGTCACCAGAGT	56
RNA1-5	F:TCTTATAATATTCATACCCTTGAAC;R:CGGGAATTTATTGTAAATCATAC	58
race1-3	ACACTGGAGTTAAAGTCTGAAACTCTAAATTTAAGAGTTTAG	57
race1-5	TTTAAAAGTAACTGATACATCTTCAGGCAGACATAATCTCT	61
RNA2-1	F:CCAAAGATAAATAACAAACAATCAA;R:ATATCTTCCCGCATACGAATTTATCAA	57
RNA2-2	F:GGGCAGATCAAAGAACAACTTGTT;R:CATTGATCGTTCCACTCAATTTGAAA	60
RNA2-3	F:ATGACGTCGCAAATGATAGTGCTTTC;R:CTTCCAACTCTCTGCTCGGTAACTT	55
RNA2-4	F:CTTGATAAACGTGACAAATCAAACCT;R:GGGGTCAGCTCTTTCAAAGCTTGA	57
RNA2-5	F:CTTTTTATTAGCGTCAATCTTAGCTTT;R:TTTCTCGGTCAATCGATCGAACTCTGA	58
RNA2-6	F:CAAGAATAATGGATTGGAGGATATGCCTT;R:TCACCAGGGGATTGCTTTCCAACTT	56
race2-3	GATTACGCCAAGCTTTGCTACCTCCTATACCAATGCGGA	67
race2-5	ACCTCCCAAACGAATTTATCAATCTCATAAGGTAAAGTGTT	65

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Genome Sequence of Strawberry Pallidosis-associated Virus Isolated in China

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