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Article(id=1226956552532308767, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20250135, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1740326400000, receivedDateStr=2025-02-24, revisedDate=null, revisedDateStr=null, acceptedDate=1743523200000, acceptedDateStr=2025-04-02, onlineDate=1770458837874, onlineDateStr=2026-02-07, pubDate=1756915200000, pubDateStr=2025-09-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1770458837874, onlineIssueDateStr=2026-02-07, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1770458837874, creator=13701087609, updateTime=1770458837874, updator=13701087609, issue=Issue{id=1226956547847275311, tenantId=1146029695717560320, journalId=1192105938417971205, year='2025', volume='65', issue='9', pageStart='3821', pageEnd='4232', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1770458836757, creator=13701087609, updateTime=1770459153781, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1226957877613605816, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1226957877613605817, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=4029, endPage=4041, ext={EN=ArticleExt(id=1226956552863658796, articleId=1226956552532308767, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Isolation, identification, and genomic sequence analysis of datura yellow vein virus infecting Sauropus androgynus, columnId=1192149543992045670, journalTitle=Acta Microbiologica Sinica, columnName=Research Article, runingTitle=null, highlight=null, articleAbstract=

Sauropus androgynus has high medicinal and edible values. However, its growth is threatened by various viral diseases, which severely affect both the yield and quality of S. androgynus. Since research is limited regarding the viral diseases affecting S. androgynus in China. [Objective] To isotation, identifying the viral pathogens of S. androgynus in China. [Methods] The small RNA sequencing (sRNA-seq) data of S. androgynus leaves from our previous study were analyzed. RT-PCR was employed to detect the datura yellow vein virus (DYVV) in leaf samples of 10 different varieties of S. androgynus. With the total RNA of positive S4 leaves as a template, reverse transcription-polymerase chain reaction (RT-PCR), rapid amplification of cDNA ends (RACE), and Sanger sequencing were employed to determine the full-length genome sequence of the DYVV isolate from S. androgynus (named DYVV-sa). [Results] The analysis of the sRNA-seq data revealed the presence of DYVV in S. androgynus. RT-PCR detection of different varieties showed that only S4 and S12 tested positive for DYVV, and the full-length sequence of DYVV-sa was cloned based on S4. The genome of DYVV-sa was 13 185 nt in length and contained six open reading frames (ORFs). The DYVV-sa showed the identity as high as 95.8%-98.1% with the DYVV sequences isolated from Thunbergia alata. Moreover, the phylogenetic tree also demonstrated that DYVV-sa shared the closest genetic relationship with DYVV, clearly indicating that DYVV-sa was an isolate of DYVV. In addition, the majority of DYVV-sa virus-derived small interfering RNA (vsiRNA) were 21 nt and 22 nt, and those of 21 nt were more abundant. The first nucleotide at the 5′ termini of vsiRNAs derived from DYVV-sa preferred U and C. The proportion of vsiRNAs derived from the negative strand was higher than that from the positive strand. The distribution of vsiRNAs along the viral genome was generally even, with some hot spots formed in local regions. [Conclusion] This study found that DYVV can infect S. androgynus and successfully obtains the full-length genomic sequence of the DYVV-sa isolate. These findings expand the known natural host range of DYVV, provide crucial theoretical foundations for research on its genetic diversity and phylogenetic relationship, and offer clues for the prevention and control of viral diseases attacking S. androgynus.

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*E-mail: ZHU Lijuan,
CHEN Xing,
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守宫木具有较高的药用和食用价值，其生长过程受到多种病毒病害的危害，严重影响了守宫木的产量和质量。目前有关我国守宫木病毒病害研究的较少。 【目的】 分离鉴定我国守宫木病毒病原。 【方法】 分析本实验室前期守宫木叶片小RNA测序(small RNA sequencing, sRNA-seq)的数据；利用逆转录聚合酶链式反应(reverse transcription-polymerase chain reaction, RT-PCR)对10种不同品种的守宫木叶片样品进行检测；以阳性样品S4叶片的总RNA为模板，结合RT-PCR、cDNA末端快速扩增(rapid amplification of cDNA ends, RACE)和Sanger测序技术获得曼陀罗黄脉病毒(datura yellow vein virus, DYVV)守宫木分离物(DYVV-sa)全基因组序列。 【结果】 基于sRNA-seq的数据分析发现守宫木中存在DYVV，不同品种样本经RT-PCR检测显示S4和S12表现为DYVV阳性。以S4品种为模板，克隆获得DYVV-sa基因组全长序列，其大小为13 185 nt，可编码6个开放阅读框(open reading frames, ORFs)，与分离自黑叶苏珊的DYVV序列相似性高达95.8%-98.1%，同时系统发育分析显示DYVV-sa与DYVV亲缘关系最密切，因此确定DYVV-sa为DYVV的分离株。对DYVV-sa病毒来源的小干扰RNA (virus-derived small interfering RNA, vsiRNA)进行分析发现，DYVV-sa-vsiRNA大小以21 nt和22 nt为主，其中21 nt更为丰富；DYVV-sa-vsiRNA的5′端第一个核苷酸优先偏好U和C；来源于负链的vsiRNAs所占比例高于正链，并在整个病毒基因组中均有分布，局部区域形成热点。 【结论】 本研究发现DYVV可侵染守宫木植株并克隆获得DYVV-sa分离株基因组全长序列，研究结果拓展了DYVV的天然寄主范围，为DYVV的多样性研究和进化分析提供了基础，同时为守宫木病毒病害的防治提供了理论依据。

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作者贡献声明

刘珊羽：参与实验及初稿撰写；张添宏：实验实施与数据分析；池毓斌：实验设计与结果监管；徐钟天：sRNA-seq数据分析；谌星：提供守宫木病叶样本并参与文稿修改；朱丽娟：研究框架设计、论文撰写、投稿及全程修订。

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Phytopathology, 2023, 113(4): 616-625., articleTitle=Transgene silencing, RNA interference, and the antiviral defense mechanism directed by small interfering RNAs, refAbstract=null)], funds=[Fund(id=1226964061288579137, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, awardId=2024J01908, language=EN, fundingSource=Fujian Provincial Natural Science Foundation(2024J01908), fundOrder=null, country=null), Fund(id=1226964061406019655, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, awardId=2024J01908, language=CN, fundingSource=福建省自然科学基金(2024J01908), fundOrder=null, country=null), Fund(id=1226964061519265867, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, awardId=JAT241135, language=EN, fundingSource=Fujian Provincial Education and Scientific Research Project for Young and Middle-aged Teachers(JAT241135), fundOrder=null, country=null), Fund(id=1226964061636706387, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, awardId=JAT241135, language=CN, fundingSource=福建省中青年教师教育科研项目(JAT241135), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1226964052753171106, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, xref=null, ext=[AuthorCompanyExt(id=1226964052757365411, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964052753171106, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 National Park Research Center, Sanming University, Sanming, Fujian, China), AuthorCompanyExt(id=1226964052765754020, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964052753171106, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 三明学院，国家公园研究中心，福建 三明)]), AuthorCompany(id=1226964052849640110, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, xref=null, ext=[AuthorCompanyExt(id=1226964052858028719, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964052849640110, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 Medical Plant Exploitation and Utilization Engineering Research Center, Sanming University, Sanming, Fujian, China), AuthorCompanyExt(id=1226964052908360369, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964052849640110, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 三明学院，药用植物开发利用工程研究中心，福建 三明)]), AuthorCompany(id=1226964053009023676, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, xref=null, ext=[AuthorCompanyExt(id=1226964053017412286, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964053009023676, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang, China), AuthorCompanyExt(id=1226964053025800895, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, companyId=1226964053009023676, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3 宁波大学，植物病毒学研究所，农产品质量安全危害因子与风险防控国家重点实验室，浙江 宁波)])], figs=[ArticleFig(id=1226964057333351337, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 1, caption=Detection of field Sauropus androgynus leaf samples by RT-PCR. M: DNA marker; 1-10: Representing different varieties of Sauropus androgynus samples collected from the field, designated as S1, S2, S3, S5, S4, S8, S10, S11, S13 and S12, respectively., figureFileSmall=/5SAjl2n/zAThct77dWOQA==, figureFileBig=b0O1IIW1ubBmELGzURoORA==, tableContent=null), ArticleFig(id=1226964057459180464, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图1, caption=田间守宫木叶片样品的RT-PCR检测及样品的病症。M：DNA marker；1-10：分别为田间采集的S1、S2、S3、S5、S4、S8、S10、S11、S13和S12不同品种守宫木样品。, figureFileSmall=/5SAjl2n/zAThct77dWOQA==, figureFileBig=b0O1IIW1ubBmELGzURoORA==, tableContent=null), ArticleFig(id=1226964057677284280, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 2, caption=Symptoms of DYVV-positive samples in S. androgynus leaves., figureFileSmall=VibTRu+h6jx20zUrMKc+KQ==, figureFileBig=1jMQKIYqZ1B2N786y4UkCw==, tableContent=null), ArticleFig(id=1226964057815696319, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图2, caption=田间守宫木DYVV阳性叶片的症状, figureFileSmall=VibTRu+h6jx20zUrMKc+KQ==, figureFileBig=1jMQKIYqZ1B2N786y4UkCw==, tableContent=null), ArticleFig(id=1226964057924748225, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 3, caption=Amplification of the full-length genome and its 5′ and 3′ terminal regions of DYVV-sa. Lane M: DNA marker; Lanes 1-9: Overlapping RT-PCR products; 5′ RACE: Amplification product of 5′ terminal; 3′ RACE: Amplification product of 3′ terminal., figureFileSmall=uCI+BGbuse/xCTC1Fo8iuA==, figureFileBig=SN6fRHprTaWgYWyiBO8zfQ==, tableContent=null), ArticleFig(id=1226964058054771658, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图3, caption=DYVV-sa基因组全长及5′和3′末端的扩增。泳道M：DNA marker；泳道1-9：分段扩增DYVV-sa的重叠PCR产物；5′ RACE：5′末端扩增的PCR产物；3′ RACE：3′末端扩增的PCR产物。, figureFileSmall=uCI+BGbuse/xCTC1Fo8iuA==, figureFileBig=SN6fRHprTaWgYWyiBO8zfQ==, tableContent=null), ArticleFig(id=1226964058151240655, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 4, caption=Confirmation of 5′ and 3′ terminal sequences of DYVV-sa. A: The sequencing results of 5′ RACE; B: The sequencing results of 3′ RACE., figureFileSmall=Se08LCdKBztFKfpHkxQ5wg==, figureFileBig=pIiCxZCaQzQQvqHXpwtWOA==, tableContent=null), ArticleFig(id=1226964058243515351, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图4, caption=DYVV-sa 5′和3′末端序列的确定。A：5′ RACE的测序结果；B：3′ RACE测序结果。, figureFileSmall=Se08LCdKBztFKfpHkxQ5wg==, figureFileBig=pIiCxZCaQzQQvqHXpwtWOA==, tableContent=null), ArticleFig(id=1226964059585692637, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 5, caption=Schematic representation of DYVV-sa genomes shown in reverse (positive-sense) polarity. 1-13 185 nt: Complete genome of DYVV-sa; 165-1 517 nt: Encoding N protein; 1 578-2 561 nt: Encoding P protein; 2 642-3 607 nt: Encoding putative cell-to-cell movement protein P3 is highlighted by blue; 3 730-4 584 nt: Encoding M protein; 4 626-6 554 nt: Encoding G protein; 6 716-13 036 nt: Encoding L protein., figureFileSmall=KpUDTwR24B5au9TPYQK+0g==, figureFileBig=EXk/nzwNNj2QBLfjPvBUFw==, tableContent=null), ArticleFig(id=1226964059682161632, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图5, caption=DYVV-sa基因组反向互补链(正链)的示意图。1-13 185 nt：指DYVV-sa基因组全长；165-1 517 nt：编码N蛋白；1 578-2 561 nt：编码P蛋白；2 642-3 607 nt：编码假定细胞间运动的蛋白P3 (蓝色填充)；3 730-4 584 nt：编码M蛋白；4 626-6 554 nt：编码G蛋白；6 716-13 036 nt：编码L蛋白。, figureFileSmall=KpUDTwR24B5au9TPYQK+0g==, figureFileBig=EXk/nzwNNj2QBLfjPvBUFw==, tableContent=null), ArticleFig(id=1226964059812185066, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 6, caption=Phylogenetic trees built on amino acid sequence of L protein of DYVV-sa and other members of genus Betanucleorhabdovirus. The trees were generated using MEGA X and the maximum-likelihood algorithms with 1 000 bootstrap replications based on the LG+G+I+F model, CYDV as the outgroup, the percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1 000 replicates) above 50% are shown next to the branches, virus isolates, abbreviations, genomic length and GenBank accession numbers are listed in Table 3., figureFileSmall=0/60PH+ub2UgS7w50bKIGg==, figureFileBig=UwPNuehM6aOFYoO1Usltqw==, tableContent=null), ArticleFig(id=1226964059925431281, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图6, caption=DYVV-sa L蛋白氨基酸序列与乙型细胞核弹状病毒属其他成员系统发育树。基于LG+G+I+F模型，以CYDV为外群，使用MEGA X软件中最大似然法构建发育树，百分比超过50%在分支旁边显示，病毒分离株、缩写、基因组长度和GenBank登录号列于表3。, figureFileSmall=0/60PH+ub2UgS7w50bKIGg==, figureFileBig=UwPNuehM6aOFYoO1Usltqw==, tableContent=null), ArticleFig(id=1226964060030288887, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Figure 7, caption=Profile of DYVV-sa derived small interfering RNAs (vsiRNAs). A: Length distribution of DYVV-sa vsiRNAs; B: 5′ terminal nucleotide preference of DYVV-sa vsiRNAs; C: Distribution of vsiRNAs alongside the viral genome of DYVV-sa; D: vsiRNAs polarity of DYVV-sa., figureFileSmall=8B5mKvJtC9lGWoJPhqIuTg==, figureFileBig=tb/6Zyl/UxX9tlkODBG5lA==, tableContent=null), ArticleFig(id=1226964060168700925, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=图7, caption=DYVV-sa来源的小干扰RNA的概述。A：DYVV-sa来源的小干扰RNA的长度分布；B：DYVV-sa来源的小干扰RNA 5′端核苷酸的偏好性；C：DYVV-sa来源的小干扰RNA沿病毒基因组的分布；D：DYVV-sa来源的小干扰RNA正负链比例。, figureFileSmall=8B5mKvJtC9lGWoJPhqIuTg==, figureFileBig=tb/6Zyl/UxX9tlkODBG5lA==, tableContent=null), ArticleFig(id=1226964060311306241, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Table 1, caption=

Primers used in this study

, figureFileSmall=null, figureFileBig=null, tableContent=
Primers namePrimer sequences (5′→3′)Note
DYVV-3705FGATTTCTTCTGGATGCCCVirus detection for DYVV-sa
DYVV-4276RCTGCGACATAGTATCTTTAGCC
DYVV-6946FATTTCTTGACGGAGCGAGVirus detection for DYVV-sa
DYVV-7549RGCAGCATTTGAGAGGTTAGA
DYVV-R1ACGAACATGATTGTGGAGTC5′ RACE
DYVV-R2CTCTATGAATTGGAAATGCATGC
AAPGGCCACGCGT CGACTAGTAC GGGGGGGGGG GGGGGGGG
UAPCTACTACTACTAGGCCACGCGTCGACTAGTAC
DYVV-F1TTATGTTCAGTGCCACCTGCA3′ RACE
DYVV-F2CTCTTCATCATTCATAGTACTGATC
R1TACCGTCGTTCCACTAGTGATTTCACTATAGGTTTTTTTTTTTTTTT
R2TACCGTCGTTCCACTAGTGATTT
DYVV-001FTAGAGATAGAAACACACAATATACAATCTACGAmplication of full-genome
DYVV-1398RCAACGTGAGGGTCACATCAG
DYVV-1385FTGACCCTCACGTTGGACCATAmplication of full-genome
DYVV-2949RCCTTCACCCGATATCCAATG
DYVV-2934FGGATATCGGGTGAAGGTATGCAmplication of full-genome
DYVV-4378RGGAGATTGACAGCTGTCAGC
DYVV-4351FGAATACGGGCTGACAGCTAmplication of full-genome
DYVV-5817RGCAGGCTGTTCGAGTCAG
DYVV-5786FCATATGCTGGGGTCCTGACAmplication of full-genome
DYVV-7254RCATCAGCAGAAGCAGCTGA
DYVV-7233FATTTCAGCTGCTTCTGCTGAAmplication of full-genome
DYVV-8752RCGCAAAGAAAGTACTAAATGCACTGA
DYVV-8720FGCCAACCTCAGTGCATTTAGTACAmplication of full-genome
DYVV-10225RCGATAAGAGGACGGATATCAG
DYVV-10213FCGTCCTCTTATCGATATTACCGTAAmplication of full-genome
DYVV-11677RCCTTTCTAAGACATCTATCCTTCCTAG
DYVV-11678FAGGAGGAGGGAAGTTGACTGAmplication of full-genome
DYVV-13185RGAGATAGAAACACACAATATACTATCTGCTCA
), ArticleFig(id=1226964060483272716, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=表1, caption=

本研究所用引物

, figureFileSmall=null, figureFileBig=null, tableContent=
Primers namePrimer sequences (5′→3′)Note
DYVV-3705FGATTTCTTCTGGATGCCCVirus detection for DYVV-sa
DYVV-4276RCTGCGACATAGTATCTTTAGCC
DYVV-6946FATTTCTTGACGGAGCGAGVirus detection for DYVV-sa
DYVV-7549RGCAGCATTTGAGAGGTTAGA
DYVV-R1ACGAACATGATTGTGGAGTC5′ RACE
DYVV-R2CTCTATGAATTGGAAATGCATGC
AAPGGCCACGCGT CGACTAGTAC GGGGGGGGGG GGGGGGGG
UAPCTACTACTACTAGGCCACGCGTCGACTAGTAC
DYVV-F1TTATGTTCAGTGCCACCTGCA3′ RACE
DYVV-F2CTCTTCATCATTCATAGTACTGATC
R1TACCGTCGTTCCACTAGTGATTTCACTATAGGTTTTTTTTTTTTTTT
R2TACCGTCGTTCCACTAGTGATTT
DYVV-001FTAGAGATAGAAACACACAATATACAATCTACGAmplication of full-genome
DYVV-1398RCAACGTGAGGGTCACATCAG
DYVV-1385FTGACCCTCACGTTGGACCATAmplication of full-genome
DYVV-2949RCCTTCACCCGATATCCAATG
DYVV-2934FGGATATCGGGTGAAGGTATGCAmplication of full-genome
DYVV-4378RGGAGATTGACAGCTGTCAGC
DYVV-4351FGAATACGGGCTGACAGCTAmplication of full-genome
DYVV-5817RGCAGGCTGTTCGAGTCAG
DYVV-5786FCATATGCTGGGGTCCTGACAmplication of full-genome
DYVV-7254RCATCAGCAGAAGCAGCTGA
DYVV-7233FATTTCAGCTGCTTCTGCTGAAmplication of full-genome
DYVV-8752RCGCAAAGAAAGTACTAAATGCACTGA
DYVV-8720FGCCAACCTCAGTGCATTTAGTACAmplication of full-genome
DYVV-10225RCGATAAGAGGACGGATATCAG
DYVV-10213FCGTCCTCTTATCGATATTACCGTAAmplication of full-genome
DYVV-11677RCCTTTCTAAGACATCTATCCTTCCTAG
DYVV-11678FAGGAGGAGGGAAGTTGACTGAmplication of full-genome
DYVV-13185RGAGATAGAAACACACAATATACTATCTGCTCA
), ArticleFig(id=1226964060613296149, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Table 2, caption=

Pairwise comparisons of nucleotide (nt) and putative amino acid (aa) sequence identities between DYVV-sa and other betanucleorhabdoviruses

, figureFileSmall=null, figureFileBig=null, tableContent=
Virus

Nucleotide

sequence identity (%)

Amino acid sequence identity (%)
NPP3MGL
AaNV41.836.812.523.214.325.537.4
ApRVA44.045.717.120.017.228.339.2
AscSyV244.240.915.320.219.325.438.2
BCaRV49.649.125.726.632.239.849.1
BFTV39.69.611.08.410.69.450.2
BmV266.278.764.472.360.671.467.8
CdVCV50.257.46.533.528.539.147.1
CnV151.053.230.331.931.239.348.0
DYVV97.296.497.698.195.897.197.7
PBRV153.342.818.922.721.839.843.1
PleArV161.971.046.363.948.965.743.1
RhoDeV146.641.520.624.125.432.644.3
SYNV47.248.924.426.624.440.843.5
SYVV51.855.829.835.631.047.749.0
TarBRV148.952.524.624.329.440.345.6
TBRV153.759.232.841.110.29.150.0
TBRV253.659.728.841.737.351.467.8
ZPNRV31.868.236.447.737.649.149.0
), ArticleFig(id=1226964060722348061, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=表2, caption=

DYVV-sa与乙型细胞核弹状病毒属其余成员全基因组核苷酸和各ORFs氨基酸序列的两两比较

, figureFileSmall=null, figureFileBig=null, tableContent=
Virus

Nucleotide

sequence identity (%)

Amino acid sequence identity (%)
NPP3MGL
AaNV41.836.812.523.214.325.537.4
ApRVA44.045.717.120.017.228.339.2
AscSyV244.240.915.320.219.325.438.2
BCaRV49.649.125.726.632.239.849.1
BFTV39.69.611.08.410.69.450.2
BmV266.278.764.472.360.671.467.8
CdVCV50.257.46.533.528.539.147.1
CnV151.053.230.331.931.239.348.0
DYVV97.296.497.698.195.897.197.7
PBRV153.342.818.922.721.839.843.1
PleArV161.971.046.363.948.965.743.1
RhoDeV146.641.520.624.125.432.644.3
SYNV47.248.924.426.624.440.843.5
SYVV51.855.829.835.631.047.749.0
TarBRV148.952.524.624.329.440.345.6
TBRV153.759.232.841.110.29.150.0
TBRV253.659.728.841.737.351.467.8
ZPNRV31.868.236.447.737.649.149.0
), ArticleFig(id=1226964060848177190, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=EN, label=Table 3, caption=

Description of the viruses used for phylogenetic analyses in this article

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesVirus nameAcronymGenBank accession numberGenome length (nt)Genus
Betanucleorhabdovirus alphalycopersiciTomato Betanucleorhabdovirus 1TBRV1OL47211913 426Betanucleorhabdovirus
Betanucleorhabdovirus asclepiadisAsclepias syriaca virus 2AscSyV2BK01429912 940Betanucleorhabdovirus
Betanucleorhabdovirus bacopaeBacopa monnieri virus 2BmV2BK01448013 165Betanucleorhabdovirus
Betanucleorhabdovirus betalycopersici

Tomato

Betanucleorhabdovirus 2

TBRV2OL47211413 423Betanucleorhabdovirus
Betanucleorhabdovirus cardamomiCardamom vein clearing virusCdVCVMN27331113 392Betanucleorhabdovirus
Betanucleorhabdovirus cnidiiCnidium virus 1CnV1MZ98339014 002Betanucleorhabdovirus
Betanucleorhabdovirus daturaeDatura yellow vein virusDYVVKM82353113 188Betanucleorhabdovirus
Betanucleorhabdovirus lotiBirds-foot trefoil-associated virusBFTVBK01082613 626Betanucleorhabdovirus
Betanucleorhabdovirus maliApple rootstock virus AApRVAMH77854514 043Betanucleorhabdovirus
Betanucleorhabdovirus medicagonisAlfalfa-associated nucleorhabdovirusAaNVMG94856313 875Betanucleorhabdovirus
Betanucleorhabdovirus picridisPicris betanucleorhabdvirus 1PBRV1OL47211715 193Betanucleorhabdovirus
Betanucleorhabdovirus plectranthiPlectranthus aromaticus virus 1PleArV1BK01430012 994Betanucleorhabdovirus
Betanucleorhabdovirus retesonchiSonchus yellow net virusSYNVL3260313 720Betanucleorhabdovirus
Betanucleorhabdovirus rhododendriRhododendon delavayi virus 1RhoDeV1BK01430113 719Betanucleorhabdovirus
Betanucleorhabdovirus ribesBlack currant-associated rhabdovirusBCaRVMF54302214 432Betanucleorhabdovirus
Betanucleorhabdovirus taraxiTaraxacum betanucleorhabdvirus 1TarBRV1OL47211813 716Betanucleorhabdovirus
Betanucleorhabdovirus venasonchiSowthistle yellow vein virusSYVVMT18567513 721Betanucleorhabdovirus
), ArticleFig(id=1226964060990783535, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956552532308767, language=CN, label=表3, caption=

本研究用于系统发育分析的病毒的描述

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesVirus nameAcronymGenBank accession numberGenome length (nt)Genus
Betanucleorhabdovirus alphalycopersiciTomato Betanucleorhabdovirus 1TBRV1OL47211913 426Betanucleorhabdovirus
Betanucleorhabdovirus asclepiadisAsclepias syriaca virus 2AscSyV2BK01429912 940Betanucleorhabdovirus
Betanucleorhabdovirus bacopaeBacopa monnieri virus 2BmV2BK01448013 165Betanucleorhabdovirus
Betanucleorhabdovirus betalycopersici

Tomato

Betanucleorhabdovirus 2

TBRV2OL47211413 423Betanucleorhabdovirus
Betanucleorhabdovirus cardamomiCardamom vein clearing virusCdVCVMN27331113 392Betanucleorhabdovirus
Betanucleorhabdovirus cnidiiCnidium virus 1CnV1MZ98339014 002Betanucleorhabdovirus
Betanucleorhabdovirus daturaeDatura yellow vein virusDYVVKM82353113 188Betanucleorhabdovirus
Betanucleorhabdovirus lotiBirds-foot trefoil-associated virusBFTVBK01082613 626Betanucleorhabdovirus
Betanucleorhabdovirus maliApple rootstock virus AApRVAMH77854514 043Betanucleorhabdovirus
Betanucleorhabdovirus medicagonisAlfalfa-associated nucleorhabdovirusAaNVMG94856313 875Betanucleorhabdovirus
Betanucleorhabdovirus picridisPicris betanucleorhabdvirus 1PBRV1OL47211715 193Betanucleorhabdovirus
Betanucleorhabdovirus plectranthiPlectranthus aromaticus virus 1PleArV1BK01430012 994Betanucleorhabdovirus
Betanucleorhabdovirus retesonchiSonchus yellow net virusSYNVL3260313 720Betanucleorhabdovirus
Betanucleorhabdovirus rhododendriRhododendon delavayi virus 1RhoDeV1BK01430113 719Betanucleorhabdovirus
Betanucleorhabdovirus ribesBlack currant-associated rhabdovirusBCaRVMF54302214 432Betanucleorhabdovirus
Betanucleorhabdovirus taraxiTaraxacum betanucleorhabdvirus 1TarBRV1OL47211813 716Betanucleorhabdovirus
Betanucleorhabdovirus venasonchiSowthistle yellow vein virusSYVVMT18567513 721Betanucleorhabdovirus
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侵染守宫木的曼陀罗黄脉病毒的分离鉴定及其基因组序列分析
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刘珊羽 1 , 张添宏 1 , 池毓斌 2 , 徐钟天 3 , 谌星 1, 2 , 朱丽娟 1, 2
微生物学报 | 研究报告 2025,65(9): 4029-4041
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微生物学报 | 研究报告 2025, 65(9): 4029-4041
侵染守宫木的曼陀罗黄脉病毒的分离鉴定及其基因组序列分析
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刘珊羽1, 张添宏1, 池毓斌2, 徐钟天3, 谌星1, 2 , 朱丽娟1, 2
作者信息
  • 1 三明学院，国家公园研究中心，福建 三明
  • 2 三明学院，药用植物开发利用工程研究中心，福建 三明
  • 3 宁波大学，植物病毒学研究所，农产品质量安全危害因子与风险防控国家重点实验室，浙江 宁波
Isolation, identification, and genomic sequence analysis of datura yellow vein virus infecting Sauropus androgynus
Shanyu LIU1, Tianhong ZHANG1, Yubin CHI2, Zhongtian XU3, Xing CHEN1, 2 , Lijuan ZHU1, 2
Affiliations
  • 1 National Park Research Center, Sanming University, Sanming, Fujian, China
  • 2 Medical Plant Exploitation and Utilization Engineering Research Center, Sanming University, Sanming, Fujian, China
  • 3 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang, China
出版时间: 2025-09-04 doi: 10.13343/j.cnki.wsxb.20250135
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守宫木具有较高的药用和食用价值，其生长过程受到多种病毒病害的危害，严重影响了守宫木的产量和质量。目前有关我国守宫木病毒病害研究的较少。 【目的】 分离鉴定我国守宫木病毒病原。 【方法】 分析本实验室前期守宫木叶片小RNA测序(small RNA sequencing, sRNA-seq)的数据；利用逆转录聚合酶链式反应(reverse transcription-polymerase chain reaction, RT-PCR)对10种不同品种的守宫木叶片样品进行检测；以阳性样品S4叶片的总RNA为模板，结合RT-PCR、cDNA末端快速扩增(rapid amplification of cDNA ends, RACE)和Sanger测序技术获得曼陀罗黄脉病毒(datura yellow vein virus, DYVV)守宫木分离物(DYVV-sa)全基因组序列。 【结果】 基于sRNA-seq的数据分析发现守宫木中存在DYVV，不同品种样本经RT-PCR检测显示S4和S12表现为DYVV阳性。以S4品种为模板，克隆获得DYVV-sa基因组全长序列，其大小为13 185 nt，可编码6个开放阅读框(open reading frames, ORFs)，与分离自黑叶苏珊的DYVV序列相似性高达95.8%-98.1%，同时系统发育分析显示DYVV-sa与DYVV亲缘关系最密切，因此确定DYVV-sa为DYVV的分离株。对DYVV-sa病毒来源的小干扰RNA (virus-derived small interfering RNA, vsiRNA)进行分析发现，DYVV-sa-vsiRNA大小以21 nt和22 nt为主，其中21 nt更为丰富；DYVV-sa-vsiRNA的5′端第一个核苷酸优先偏好U和C；来源于负链的vsiRNAs所占比例高于正链，并在整个病毒基因组中均有分布，局部区域形成热点。 【结论】 本研究发现DYVV可侵染守宫木植株并克隆获得DYVV-sa分离株基因组全长序列，研究结果拓展了DYVV的天然寄主范围，为DYVV的多样性研究和进化分析提供了基础，同时为守宫木病毒病害的防治提供了理论依据。

守宫木  /  曼陀罗黄脉病毒分离株  /  病毒来源的小干扰RNA

Sauropus androgynus has high medicinal and edible values. However, its growth is threatened by various viral diseases, which severely affect both the yield and quality of S. androgynus. Since research is limited regarding the viral diseases affecting S. androgynus in China. [Objective] To isotation, identifying the viral pathogens of S. androgynus in China. [Methods] The small RNA sequencing (sRNA-seq) data of S. androgynus leaves from our previous study were analyzed. RT-PCR was employed to detect the datura yellow vein virus (DYVV) in leaf samples of 10 different varieties of S. androgynus. With the total RNA of positive S4 leaves as a template, reverse transcription-polymerase chain reaction (RT-PCR), rapid amplification of cDNA ends (RACE), and Sanger sequencing were employed to determine the full-length genome sequence of the DYVV isolate from S. androgynus (named DYVV-sa). [Results] The analysis of the sRNA-seq data revealed the presence of DYVV in S. androgynus. RT-PCR detection of different varieties showed that only S4 and S12 tested positive for DYVV, and the full-length sequence of DYVV-sa was cloned based on S4. The genome of DYVV-sa was 13 185 nt in length and contained six open reading frames (ORFs). The DYVV-sa showed the identity as high as 95.8%-98.1% with the DYVV sequences isolated from Thunbergia alata. Moreover, the phylogenetic tree also demonstrated that DYVV-sa shared the closest genetic relationship with DYVV, clearly indicating that DYVV-sa was an isolate of DYVV. In addition, the majority of DYVV-sa virus-derived small interfering RNA (vsiRNA) were 21 nt and 22 nt, and those of 21 nt were more abundant. The first nucleotide at the 5′ termini of vsiRNAs derived from DYVV-sa preferred U and C. The proportion of vsiRNAs derived from the negative strand was higher than that from the positive strand. The distribution of vsiRNAs along the viral genome was generally even, with some hot spots formed in local regions. [Conclusion] This study found that DYVV can infect S. androgynus and successfully obtains the full-length genomic sequence of the DYVV-sa isolate. These findings expand the known natural host range of DYVV, provide crucial theoretical foundations for research on its genetic diversity and phylogenetic relationship, and offer clues for the prevention and control of viral diseases attacking S. androgynus.

Sauropus androgynus  /  datura yellow vein virus isolate  /  virus-derived small interfering RNA
刘珊羽, 张添宏, 池毓斌, 徐钟天, 谌星, 朱丽娟. 侵染守宫木的曼陀罗黄脉病毒的分离鉴定及其基因组序列分析. 微生物学报, 2025 , 65 (9) : 4029 -4041 . DOI: 10.13343/j.cnki.wsxb.20250135
Shanyu LIU, Tianhong ZHANG, Yubin CHI, Zhongtian XU, Xing CHEN, Lijuan ZHU. Isolation, identification, and genomic sequence analysis of datura yellow vein virus infecting Sauropus androgynus[J]. Acta Microbiologica Sinica, 2025 , 65 (9) : 4029 -4041 . DOI: 10.13343/j.cnki.wsxb.20250135
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守宫木[Sauropus androgynus (L.) Meer]又名五指山野菜、天绿香、树仔菜、越南菜、泰国枸杞、甜菜等，属大戟科守宫木属的多年生常绿灌木。广泛分布于印度、马来西亚、中国等地区，在我国普遍种植于海南、广东、广西、云南和福建。守宫木具有较高的食用和药用价值，其嫩梢和嫩叶均可食用，且与其他蔬菜相比维生素含量更高，特别是维生素A和C；其根、叶和种子均可药用，从中提取的植物化学和生物成分被报道可用于治疗各种疾病，包括喉炎、咳嗽、肝炎、便秘、糖尿病、关节炎、癌症和衰老等[1-4]。植物的生长及其活性化合物的代谢在非生物和生物胁迫下均会发生改变[5]，病毒侵染是多年生植物常见的生物胁迫。因此对守宫木病毒的研究将有助于深入了解其所面临的生物胁迫。
守宫木在生长过程中易受到多种病毒的感染，目前在泰国守宫木上发现了4种病毒，分别为胜红蓟黄脉病毒(Ageratum yellow vein virus, AYVV)、新德里番茄曲叶病毒(tomato leaf curl New Delhi virus, ToLCNDV)、守宫木卷叶病毒(Sauropus leaf curl virus, SaLCV)[6]和守宫木黄化病毒(Sauropus yellowing virus, SaYV)[7]。2024年，本实验室通过宏转录组测序(metatranscriptome, RNA-seq)，在我国守宫木上发现并克隆了一个属于Allexivirus的新病毒——守宫木病毒(Sauropus androgynus virus, SaV)[8]。然而，目前有关我国守宫木病毒病害的研究报道甚少，导致其病害预防缺少理论依据。因此深入鉴定和研究我国守宫木病毒病原对于病害防治具有重要意义。
曼陀罗黄脉病毒(Datura yellow vein nucleorhabdovirus, DYVV)属于弹状病毒科(Rhabdoviridae)、乙型弹状病毒亚科(Betarhabdovirinae)中的乙型细胞核弹状病毒属(Betanucleorhabdovirus)[9-11]。Thomas等[9]于20世纪80年代在澳大利亚叶脉黄化病症的曼陀罗中首次分离获得该病毒。通过嫁接实验发现，该病毒可感染几种番茄(Grosse Lisse、Floradade、Rutgers、Strobelee和Scorpio)、茄子(Solanum melongena)、心叶烟(Nicotiana glutinosa)和普通烟(N. tabacum)，但不感染矮牵牛(Petunia×hybrida)、黄花烟草(N. rustica)、假酸浆(Nicandra physalodes)、辣椒(Capsicum annuum)、龙葵(Solanum nigrum)和马铃薯(Solanumtuberosum)[9]。此外，该病毒无法通过机械接种或种子传播[9]。在介体昆虫研究中发现，DYVV在银叶蝉(Omiya argentata)和阿朱尔叶蝉(Aljulia aljuljae)体内的潜伏期分别为至少24 d和14 d；在叶蝉(leafhoppers)与飞虱(planthoppers)混合种群中的潜伏期为8-18 d；而在蚜虫(aphids)和甲虫幼虫(beetle larvae)中未观察到明显潜伏期，且这些介体昆虫均不具备传播该病毒的能力[9]。随后，Dietzgen等[12]从观赏植物黑叶苏珊(Thunbergia alata)中分离获得DYVV，利用简并引物获得了DYVV聚合酶基因的短片段，证实了该分离物与Thomas等[9]报道的DYVV序列高度相似，且与莴苣黄网弹状病毒(Sonchus yellow net nucleorhabdovirus, SYNV)具有最密切的系统发育关系[13]。2015年，Dietzgen等[14]进一步分析了黑叶苏珊中DYVV全基因组序列，发现该病毒为负单链RNA病毒，全长13 188 nt，含互补的3′先导序列和5′尾序，可编码由高度保守的基因间区隔开的6个开放阅读框(open reading frames, ORFs)，分别为核衣壳蛋白(nucleocapsid protein, N)、磷酸蛋白(phospoprotein, P)、运动蛋白(movement protein, P3)、基质蛋白(matrix protein, M)、糖蛋白(glycoprotein, G)和RNA依赖的RNA聚合酶(RNA dependent RNA polymerase, L)。利用瞬时表达系统观察发现，在本生烟(Nicotianabenthamiana)中除G外，其余蛋白均定位于细胞核，其中N和P共表达时相互作用明显且N蛋白的存在可增加P核定位[14]。除上述自然感染的2个寄主外，尚未见DYVV自然侵染其他寄主的报道。因此进一步鉴定DYVV自然界中潜在的寄主，可为其防控提供依据。
本研究从福建省福州市疑似感染病毒的守宫木植株中检测并克隆了DYVV分离物的基因组全长，暂命名为DYVV-sa，并对其全基因组序列和vsiRNA进行了分析，以期为DYVV的多样性、进化和宿主拓展提供新的见解，并为守宫木上该病毒的防治提供理论依据。
1 材料与方法
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1.1 植物样品
2023年9月，于福建省福州市福建农林大学田间种植区分别采集10种不同品种守宫木疑似病叶样品2-3片，依次编号为S1、S2、S3、S5、S4、S8、S10、S11、S13、S12。样品采集后立即装入纸带，并迅速投入液氮中进行冷冻处理以确保RNA完整性，随后转移至-80 ℃冰箱保存备用。
1.2 载体和菌株
载体pMDTM 19-T购自TaKaRa公司，大肠杆菌(Escherichia coli) JM109由本实验室保存。
1.3 主要试剂和引物
水饱和酚pH 4.7-5.5，北京索莱宝科技有限公司；M-MLV Reverse Transcriptase Kit，Promega公司；2×Taq Master Mix，南京诺唯赞生物科技股份有限公司；StarMarker D2000 Plus，北京康润诚业生物科技有限公司；5′ RACE试剂盒，Invitrogen公司；E. coli poly(A) polymerase，NEB公司；多功能DNA纯化回收试剂盒，北京博迈德基因技术有限公司；质粒提取试剂盒，Omega公司；其余常用化学药品，Sigma-Aldrich公司或国药集团化学试剂有限公司。本研究所用的引物由北京擎科生物科技股份有限公司合成，具体见表1。
1.4 RNA提取
取适量的守宫木叶片于灭菌的研钵中，加入液氮并充分研磨成粉末后，立即装入经液氮冻过的2.0 mL离心管中，至1/3体积；迅速加入500 μL 80 ℃预热的水饱和酚与等体积的RNA提取缓冲液(0.1 mol/L LiCl、pH 8.0 10 mmol/L Tris-HCl、10 mmol/L EDTA和10% SDS)，振荡混匀30 s，静置3-5 min；再加入等体积的CHCl3，与上述同样振荡和静置后；常温13 523×g离心10 min；取450-500 μL上清于新的1.5 mL离心管中并加入等体积的4 mol/L LiCl溶液；混匀并于-20 ℃静置≥4 h；4 ℃、13 523×g离心15 min，取出RNA沉淀并用75%乙醇洗涤2次，用适量的DEPC H2O溶解，-20 ℃保存。
1.5 逆转录聚合酶链式反应(reverse transcription-polymerase chain reaction, RT-PCR)
以总RNA为模板，将其逆转录为互补DNA (complementary DNA, cDNA)。逆转录反应体系(10 μL)：将1 μg RNA与0.5 μL 3′端下游引物(10 μmol/L)混匀并用ddH2O补足至5.5 μL，65 ℃孵育5 min后冰浴2 min，依次加入2 μL 5×M-MLV buffer，2 μL 2.5 mmol/L dNTPs和0.5 μL M-MLV RT酶(200 U/μL)，混匀后于42 ℃孵育30 min，最后于85 ℃加热5 s失活。以逆转录获得的cDNA为模板，经PCR扩增获得目的片段。PCR反应体系：cDNA 1 μL，上、下游引物(10 μmol/L)各0.5 μL，2×Taq mix 10 μL，ddH2O 8 μL。PCR反应条件：95 ℃预变性3 min；95 ℃变性30 s，55 ℃退火30 s，72 ℃延伸(1 kb/min)，共30个循环。
1.6 cDNA末端快速扩增(rapid amplification of cDNA ends, RACE)技术
1.6.1 5′ RACE
取病毒阳性的S4样品总RNA 5 μg，加0.25 μL引物R1 (10 μmol/L)，补水至15.5 μL，混匀后70 ℃孵育10 min，冰浴1 min；依次加入2.5 μL 10×PCR buffer，1 μL 25 mmol/L MgCl2，2.5 μL 10 mmol/L dNTPs，2.5 μL 0.1 mol/L DTT，混匀后42 ℃孵育1 min后加入1 μL SuperScriptTM II RT酶，42 ℃孵育50 min，70 ℃反应15 min，37 ℃反应1 min。向反应液加入1 μL RNase mix，37 ℃反应30 min，并按照5′ RACE System for Rapid Amplification of cDNA Ends试剂盒的说明书纯化获得cDNA。接着取10 μL cDNA，5 μL 5×Tailing buffer，2.5 μL 2 mmol/L dCTP或dATP，6.5 μL ddH2O进行cDNA的3′末端加尾反应，先94 ℃加热2-3 min，冰浴1 min，后加入1 μL 15 U/μL的TdT酶，37 ℃孵育10 min，65 ℃加热10 min。最后以加尾的cDNA为模板，按照1.5节中的PCR方法进行第1轮扩增(引物AAP/R1)，以稀释50-100倍的第1轮PCR产物为模板，进行第2轮扩增(引物UAP/R2)。
1.6.2 3′ RACE
将S4样品提取的总RNA加上poly(A)尾，具体为：10 μg RNA，5 μL 10×buffer，5 μL ATP (10 mmol/L)，1 μL E. coli Poly(A) polymerase，ddH2O补足至50 μL，37 ℃反应10 min。随后根据TRIzol试剂的说明书纯化RNA，最后利用与5′ RACE相似策略PCR扩增目的片段。
1.7 PCR产物测序
目的条带经DNA纯化试剂盒回收纯化后，克隆至pMDTM 19-T载体，并转入大肠杆菌JM109感受态细胞。经菌落PCR筛选获得阳性克隆，提质粒送至生工生物工程(上海)股份有限公司测序，至少对3个阳性克隆进行了测序。
1.8 序列分析
利用DNAMAN v10.0和SnapGene v4.4.2拼接组装基因组全长序列、并对核苷酸和氨基酸序列进行分析比对。基于MEGA X中的最大似然法(maximum likelihood method)构建系统发育树[15]，bootstrap设置为1 000次重复，频率<50%被隐藏。
1.9 小RNA测序(small RNA sequencing, sRNA-seq)数据分析
采用FastQC对原始sRNA-seq数据进行质量评估，然后使用Cutadapt工具(v1.16)[16]进行处理以去除接头区域和低质量测序读段(reads)，只保留长度在18-30个核苷酸范围内且不含模糊碱基(N)的干净读段用于后续分析。使用VirusDetect软件鉴定的小RNA病毒组(默认参数设置)[17]，首先将小RNA序列组装为重叠群(contigs)，所得重叠群通过BLASTx/BLASTn算法与已知的病毒序列数据库进行比对。为了深入解析病毒来源的小干扰RNA的分子特征，使用Bowtie软件将干净的小RNA读段与DYVV-sa病毒参考基因组进行比对[18]，最多允许一次错配。分析来源于DYVV-sa病毒基因组的vsiRNAs，研究其vsiRNA大小分布、5′端碱基偏好性、基因组分布以及链特异性等特征。
2 结果与分析
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2.1 守宫木中DYVV病毒检测
本实验前期对疑似病毒病症守宫木叶片进行sRNA-seq，并将获得的数据经序列组装、拼接及比对发现，除了存在本实验前期报道的SaV[8]外，还存有DYVV。因田间种植的守宫木品种不同，为了明确DYVV在不同品种守宫木中的感染情况，本研究基于实验前期拼接获得的守宫木中DYVV参考序列，设计2对引物(DYVV-3705F/4276R和DYVV-6946F/7549R)对10个不同品种样品进行RT-PCR检测。结果发现其中2种样品(S4和S12)可扩增到大小约600 bp的特异性目的条带(图1)，经测序确定为病毒序列，结果表明守宫木确实存在DYVV感染，但感染率较低。
观察发现S4和S12守宫木叶片呈现卷叶和皱缩的病症(图2)，但经检测发现两者均含有SaV (数据未显示)，因此目前无法确定DYVV单独感染而引发的病症。
2.2 DYVV守宫木分离物5′和3′末端序列的确定
为了明确守宫木中DYVV的5′和3′末端序列，基于拼接的参考序列设计相关引物，以提取S4样品的总RNA为模板，利用5′和3′ RACE技术获得该病毒的末端片段(图3)。获得的片段经纯化克隆至pMD19-T载体，均筛选10个阳性克隆进行测序，测序结果经比对发现5′和3′末端所有克隆的序列几乎一致(图4)，因此可确定5′和3′末端的序列。
2.3 DYVV守宫木分离物基因组全长的扩增
基于上述确定的5′和3′末端序列及拼接获得的参考序列，设计9对覆盖全基因组的引物(表1)，同样以S4的总RNA为模板，分别进行RT-PCR。每对引物可扩增获得与预期大小一致的特异性目的片段，约为1 500 bp (图3)。经纯化后与pMDTM 19-T载体连接，并转化感受态细胞，至少筛选3个阳性克隆进行双向测序。最后，将所有测序结果以及上述确定的5′和3′末端序列拼接获得DYVV守宫木分离物基因组全序列信息，暂命名为DYVV-sa，并提交至NCBI数据库，登录号为PQ816761。
2.4 DYVV守宫木分离物全基因组结构分析
DYVV-sa全基因组由13 185 nt组成，比黑叶苏珊中获得的DYVV分离物(NC_028231)少3个核苷酸，G+C含量为53.2%。经预测反向互补链RNA (complementary RNA, cRNA)可编码6个ORFs，其基因组结构如图5所示。DYVV 5′ UTR和3′ UTR长度分别为164 nt和149 nt。ORF1 (165-1 517 nt)编码50.59 kDa N蛋白，是病毒核衣壳的主要组成成分，可调节基因组的转录和复制，还可诱导细胞介导的免疫应答反应[11]；ORF2 (1 578-2 561 nt)和ORF3 (2 642-3 607 nt)分别编码36.86 kDa的P蛋白和36.30 kDa的P3蛋白，被认为是病毒聚合酶的辅助因子，主要介导L蛋白在N-RNA模板上正确定位与连接[11]；ORF4 (3 730-4 584 nt)编码31.53 kDa M蛋白，该蛋白被认为可调节基因组RNA转录、促进植物弹状病毒的芽生过程以及参与核质间的运输和基因的表达，是病毒粒体的内部组分[11]；ORF5 (4 626-6 554 nt)编码70.73 kDa的G糖蛋白，主要负责与宿主细胞受体的结合，并引发细胞介导的免疫反应[11]；ORF6 (6 716-13 036 nt)编码240.05 kDa的L聚合酶，主要参与病毒的转录与复制[11]。
2.5 DYVV守宫木分离物全基因组相似性比对
进一步将DYVV-sa与乙型细胞核弹状病毒属的其他成员进行多序列比对，结果发现与DYVV最为相似，基因组核苷酸一致性为97.2%，各ORFs氨基酸一致性为95.8%-98.1% (表2)，远高于该属成立新种的标准——全基因组的核苷酸序列一致性小于75%，因此明确DYVV-sa是DYVV在守宫木上的一个分离株。
2.6 DYVV守宫木分离物的亲缘关系
根据ICTV分类标准，本研究采用弹状病毒科常用的L蛋白构建系统发育树[11]，以明确DYVV-sa在乙型细胞核弹状病毒属中的进化地位。基于MEGA X软件，选用LG+G+I+F模型，通过极大似然算法构建了DYVV-sa的L蛋白与该属其他病毒的系统发育树。结果显示DYVV-sa与DYVV (NC_028231)具有高度相关性，聚集在一支(图6)，进一步证实了本研究鉴定的病毒为DYVV分离株。
2.7 DYVV-sa病毒来源的小干扰RNA分子特征分析
RNA沉默是通过产生21-24 nt病毒来源的小干扰RNA (virus-derived small interfering RNA, vsiRNA)介导抗病毒感染的有效防御机制。深入解析vsiRNAs的分子特征有助于增强对病毒-宿主相互作用的理解。本研究从守宫木样品中共测得23 085 103条原始数据，经严格的质量控制后，17 610 053条序列被保留用于下游分析，其中有3 207条vsiRNAs被比对到DYVV-sa基因组，基于比对结果发现绝大多数DYVV-sa vsiRNAs呈现出两极性特征，其大小以21 nt和22 nt为主，且在21 nt处有一个主峰值(图7A)。已有研究表明，AGO蛋白(argonaute)对sRNAs 5′端核苷酸偏好性具有调控作用[19]。因此，本研究分析鉴定了DYVV-sa vsiRNAs 5′端核苷酸的分布，结果发现其5′端核苷酸偏好性存在极为显著的差异，其中以尿嘧啶[uridine (U)，占比57%]和胞嘧啶[cytosine (C)，占比33.74%]最为丰富(图7B)。对vsiRNAs基因区域偏好性分析发现，DYVV-sa vsiRNAs在整个病毒基因组中均有分布，且在基因组前半部分呈现出相对热点区域，同时21 nt和22 nt vsiRNAs是其主要类型(图7C)。对DYVV-sa vsiRNAs的极性分析结果显示，来源于负链的vsiRNAs所占比例相较于正链更高，分别为58.09%和41.91% (图7D)。
3 讨论与结论
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DYVV最早是于曼陀罗中分离发现的一种乙型细胞核弹状病毒属病毒，后于黑叶苏珊中获得其基因组全长序列，通过嫁接实验可侵染几种番茄品种、茄子、烟草等植株[9,12-14]，目前GenBank数据库中仅有一条DYVV序列(NC_028231)。
本研究通过对采自福建农林大学田间疑似感染病害的守宫木的sRNA-seq数据进行分析，发现除了存在本实验前期报道的SaV外[8]，还存在DYVV。随后，通过RT-PCR检测发现仅S4和S12两个品种样品表现为DYVV阳性。推测感染率低的原因可能是：不同品种守宫木的种植区相互间隔一定距离，并设有物理隔离，有效阻断了病毒传播；其他守宫木品种抗病性较强；本次采样处于病害流行初期，病毒载量未达到检测阈值。同时，还将S4和S12守宫木样品委托云南省农业科学院生物技术与种质资源研究所分别采用病叶汁液负染和病叶组织超薄切片2种方法进行电镜观察，但在2种处理方式下均未观察到典型的病毒粒子结构，目前猜测可能是由于病毒滴度低而导致的。以S4的总RNA为模板，采用RT-PCR、RACE和Sanger测序相结合的方法成功获得守宫木中DYVV分离物的全基因序列，暂命名为DYVV-sa，提交至NCBI数据库，序列登录号为PQ816761。DYVV-sa的基因组全长为13 185 nt，可编码6个ORFs，依次为N、P、P3、M、G和L蛋白。目前，研究表明N、P和L蛋白主要参与病毒的转录与复制，N、G蛋白与昆虫介体的传毒有关[11]。经多序列比对发现，DYVV-sa与DYVV (NC_028231)最为相似，一致性高达95.8%-98.1%，远高于该属成立新种的标准——全基因组的核苷酸序列一致性小于75%，因此明确DYVV-sa是DYVV在守宫木上的一个分离物，且不同寄主DYVV进化变异程度低。系统发育树分析结果显示，DYVV-sa与DYVV分离物(NC_028231)亲缘关系最近，聚集在一支，该结果进一步说明了DYVV-sa是DYVV的分离株。
进一步分析DYVV-sa的vsiRNAs的分子特征，发现DYVV感染能引发守宫木RNA沉默介导的抗病毒免疫，来自DYVV-sa的vsiRNAs主要为21 nt和22 nt，其中21 nt最为丰富。各种Dicers/DCLs参与不同大小vsiRNAs的加工过程，DCL4主要负责产生21 nt vsiRNAs，而DCL2则负责产生22 nt vsiRNAs，后者在DCL4的活性受到抑制或受损时在对抗RNA病毒方面发挥着关键作用[20-21]。碱基偏好性发现DYVV-sa的vsiRNAs 5′端偏好U和C，已知sRNA的5′端初始核苷酸通常可调节其进入植物中特定AGO复合物的类型，该结果表明AGO1或AGO5参与了DYVV-sa来源的siRNAs招募和分类[19]。本研究结果拓展了DYVV潜在的天然寄主，丰富了守宫木病毒病害的病原类型，为DYVV分离株的遗传多样性研究和进化分析提供了基础，更为守宫木病毒病害的防治提供了理论依据。
基金
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  • 福建省自然科学基金(2024J01908)
  • 福建省中青年教师教育科研项目(JAT241135)
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2025年第65卷第9期
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doi: 10.13343/j.cnki.wsxb.20250135
  • 接收时间：2025-02-24
  • 首发时间：2026-02-07
  • 出版时间：2025-09-04
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  • 收稿日期：2025-02-24
  • 录用日期：2025-04-02
基金
Fujian Provincial Natural Science Foundation(2024J01908)
福建省自然科学基金(2024J01908)
Fujian Provincial Education and Scientific Research Project for Young and Middle-aged Teachers(JAT241135)
福建省中青年教师教育科研项目(JAT241135)
作者信息
    1 三明学院，国家公园研究中心，福建 三明
    2 三明学院，药用植物开发利用工程研究中心，福建 三明
    3 宁波大学，植物病毒学研究所，农产品质量安全危害因子与风险防控国家重点实验室，浙江 宁波
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https://castjournals.cast.org.cn/joweb/wswxb/CN/10.13343/j.cnki.wsxb.20250135
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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