南方番茄病毒在海南省的发生分布及全基因组序列分析

Distribution and Genome Sequence Analysis of Southern Tomato Virus in Hainan,China

病毒病是海南番茄生产中危害最严重的病害之一,在利用小RNA深度测序技术鉴定海南番茄病毒病病原时发现,南方番茄病毒(Southern tomato virus,STV)在海南省多个市(县)的样品中存在,而且发现1株STV单独侵染的样品。为了解STV在海南省的发生分布情况,利用RT-PCR技术,对2015—2021年采自海南省的987份疑似病毒侵染的番茄叶片样品进行检测,结果表明:在9个市(县)的142份样品中检测到STV,早在2015年STV就已经在海南番茄上存在,检出率从2015年(8.82%)到2021年(22.45%)呈逐年上升趋势。同时结合RACE和RT-PCR技术扩增到4个STV海南分离物的全长基因组,长度均为3446 nt,包含2个部分重叠的ORFs,ORF1(147~1280 nt)和ORF2(1048~3336 nt)分别编码p42蛋白(377 aa)和RdRp蛋白(762 aa),5′UTR和3′UTR的长度分别为146 nt和110 nt。序列一致性分析表明,4个STV海南分离物间基因组序列一致性为99.86%~100.00%,与目前GenBank公布的所有STV分离物基因组间序列一致性为98.45%~99.94%。基于全基因组序列构建的系统发育树显示,80个STV分离物被明显分为2个组(组Ⅰ和组Ⅱ),组Ⅰ包括亚洲、美洲、欧洲和非洲分离物;组Ⅱ中除1个亚洲分离物外,其他均为欧洲分离物;4个海南分离物被分在组Ⅰ,STV分离物的分组与地域呈一定的相关性,而与寄主无相关性。4个海南分离物与组Ⅰ分离物基因组序列变异度较高的区域位于881~1061 nt和1521~1721 nt,与组Ⅱ分离物基因组序列变异度较高的区域位于2041~2241 nt和2761~2921 nt。STV分离物基因组间未发现重组事件。这是在海南省首次报道发现STV。本研究结果有助于了解STV在海南省的分布、发生趋势及遗传多样性,为病害防控提供科学依据。

Virus disease is one of the most serious diseases in tomato production in Hainan,China.The small RNA deep sequencing data of tomato virome in Hainan revealed the presence of Southern tomato virus(STV)in samples from several regions,and a single STV infected sample was found.RT-PCR screening of 987 field samples with virus-like symptoms collected from 2015 to 2021,was carried out to determine the distribution of STV in Hainan province.Re-sults indicated that STV was detected in 142 samples from nine regions,STV had existed in Hainan tomatoes as early as 2015,STV detection rate increased from 8.82%in 2015 to 22.45%in 2021,showing an upward trend year by year.The complete genome length of four isolates amplified using RT-PCR and RACE was identical,each consisting of 3446 nt.Two partially overlapping open reading frames(ORFs)presented in the positive-sense RNA strand,the 5′-proximal ORF(position 147-1280 nt)encoded a 377 amino acid(aa)peptide representing a potential coat protein(p42),the second ORF(position 1048-3336 nt)contained typical motifs for an RNA-dependent RNA polymerase(762 aa).The length of 5′untranslated region(UTR)and 3′UTR was 146 nt and 110 nt respectively.Paired comparison showed that the nu-cleotide similarity among four STV isolates was 99.86%-100.00%,the nucleotide similarities with other STV isolates available in GenBank were 98.45%-99.94%.In phylogenetic trees based on the complete genome of STV,eighty STV isolates were obviously divided into two groups(GroupⅠand GroupⅡ).GroupⅠincluded Asian,American,European and African isolates.In groupⅡ,except for one Asian isolate,the others were European isolates,and four Hainan isolates were divided into groupⅠ.The grouping of STV isolates was related to geographical location,may not be related to the host.The regions with high genomic sequence variability between Hainan isolates and groupⅠisolates were 881-1061 nt and 1521-1721 nt,and the regions with high genomic sequence variability between Hainan isolate and groupⅡisolate were 2041-2241 nt and 2761-2921 nt.No recombination events were found between STV isolates.This is the first report of STV in Hainan Province.The findings of this study would provide an important basis for un-derstanding the distribution and occurrence trends of STV in Hainan province and for the development of effective sur-veillance and control measure.