草莓病毒1山东分离物全基因组分析

doi:10.16420/j.issn.0513-353x.2021-0934

摘要/Abstract

摘要：

草莓病毒1（strawberry virus 1，StrV-1）属于弹状病毒科（Rhabdoviridae）细胞质弹状病毒属（Cytorhabdovirus），可侵染草莓。利用高通量测序（high-throughput sequencing，HTS）结合RT-PCR和RACE技术从采自山东省烟台市乳山市草莓种植基地的草莓品种‘全明星’上获得了StrV-1山东分离物（StrV-1-CN）的基因组全长（GenBank登录号:MW795715）。该分离物基因组全长为14 051 nt，3'和5'非编码区序列分别为181和767 nt，其负义链含有9个开放阅读框（open reading frame，ORF），从3'到5'端分别编码N、P'、P、P3、M、G、P6、P7和L等9个蛋白。序列分析表明，StrV-1-CN与已报道的StrV-1分离物基因组全长核苷酸序列一致性为77% ~ 88%。系统发育分析结果表明，StrV-1-CN与捷克分离物B和1/2017聚在一个分支，亲缘性最近。

关键词: 草莓, 草莓病毒1, 基因组全长, 高通量测序

Abstract:

Strawberry virus 1（StrV-1，genus Cytorhabdovirus，family Rhabdoviridae）was a new pathogen that infecting strawberry. The complete genome sequence of StrV-1 identified in strawberry （Fragaria ananassa Duch.‘All Star’）from Shandong Province，China（StrV-1-CN）was determined and submitted to the GenBank database under accession No. MW795715. In the negative strand，the 14 051-nucleotide-long viral genome with 181 and 767 nt in the 3' and 5' UTR，and contains nine open reading frames（ORFs）in the canonical order 3'-N-P'-P-P3-M-G-P6-P7-L-5'. Pairwise comparisons showed that StrV-1-CN shared 77%-88% sequence identity with StrV-1 isolates. Phylogenetic analysis based on the complete genome sequence of StrV-1 isolates showed that StrV-1-CN grouped with StrV-1 isolate B and isolate 1/2017 in a subcluster.

Key words: strawberry, strawberry virus 1, complete genome sequence, HTS

中图分类号:

S668.4

何成勇, 赵晓丽, 许腾飞, 高德航, 李世访, 王红清. 草莓病毒1山东分离物全基因组分析[J]. 园艺学报, 2023, 50(1): 153-160.

HE Chengyong, ZHAO Xiaoli, XU Tengfei, GAO Dehang, LI Shifang, WANG Hongqing. Genome Sequence Analysis of Strawberry Virus 1 from Shandong Province，China[J]. Acta Horticulturae Sinica, 2023, 50(1): 153-160.

图/表 6

表1 本研究中使用的引物

Table 1 Primers used in this study

扩增片段 Fragment	引物名称 Primer name	引物序列（5′-3′） Primer sequence	引物位置 Position
F1	StrVp1	F:CATTACTGAAGCATTCCGTG R:AGATATCACGCACAGTGAC	98 ~ 117 1 259 ~ 1 241
F2	StrVp2	F:TTGCGCGAAGCGGATGTCCG	7 864 ~ 7 883
		R:GGCTGCCAGAGCGTTGGATG	9 368 ~ 9 387
F3	StrVp3	F:ATCGCAGAGACTTGTCGAT	11 677 ~ 11 695
		R:GACTTGGCATACTCTATTCC	12 275 ~ 12 256
F4	StrVp4	F:CAGAAGAGACAAGAGAACCG	13 070 ~ 13 089
		R:ATCTCTTTTTCGGAGTGCG	13 495 ~ 13 477
3'RACE	StrVp5	R:GTCGGCAGTTCCATCCGAATCAGGG	513 ~ 489
5'RACE	StrVp6	F:GGCACCAGGACATCCCAAACCGCCG	13 583 ~ 13 607

图1 田间样品疑似病毒病症状

Fig. 1 Virus-like symptoms on naturally infected strawberry plants

图2 StrV-1分离物5'RACE（A）、3'RACE（B）扩增结果及全长序列一致率分布（C）

Fig. 2 Amplification results of 5' RACE（A），3' RACE（B）and distribution of pairwise identity scores of the complete sequences of Strv-1 isolates（C）

图3 StrV-1基因组结构示意图（A）和3'和5'末端互补结构（B）箭头表示预测的ORF；F1 ~ F4:RT-PCR产物；contig1 ~ contig5:高通量测序组装的片段。

Fig. 3 Schematic representation of the genome organization of StrV-1（A）and complementary structure between the 3' and 5' termini in the genome（B） Arrows indicate predicted open reading frames；F1-F4:RT-PCR products；contig1-contig5:de novo assembly contigs from HST.

图4 基于StrV-1及其他细胞质弹状病毒N蛋白核苷酸序列构建系统发育树菱形表示本研究中获得的分离物。下同。

Fig. 4 Phylogenetic tree calculated based on the N protein amino acid sequences of StrV-1 and representative members of the genus Cytorhabdovirus The diamond represents the isolate obtained in this study. The same below.

图5 基于StrV-1及其他细胞质弹状病毒L蛋白核苷酸序列构建系统发育树

Fig. 5 Phylogenetic tree calculated based on the L protein amino acid sequences of StrV-1 and representative members of the genus Cytorhabdovirus

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