Diversity analysis of Tomato leaf curl New Delhi virus-[potato], causing apical leaf curl disease of potato in India

The complete coat protein (cp) gene sequence of eighty Tomato leaf curl New Delhi virus-[potato] (ToLCNDV-[potato]) isolates collected from eleven states were determined. Phylogenetic analysis based on cp gene grouped the isolates into two major clades (I & II) and they shared 95.9–100.0% identity. The DNA A and DNA B of eight representative isolates (six from clade I and two from clade II) were 2739–2740 and 2692–2694 nts long and shared 94.6–99.4% and 97.2–99.5% homology within the isolates, respectively. Among the eight isolates, the DNA A of two isolates (Clade II), GWA-5 and FAI-19 had 94.6–95.3% sequence identity to other six isolates and formed a sub-clade within the ToLCNDV-[potato] isolates. Similar grouping was also revealed with AC1 and AC4 genes of these eight isolates. The DNA A components shared more than 90.0% identity with the DNA A of ToLCNDV isolates from cucurbitaceous crops, tomato, bhendi, 89.0–90.0% with ToLCNDV-papaya isolates and 70.4–74.0% with other tomato leaf curl viruses. Hence, the begomovirus infecting potatoes are the ToLCNDV isolates, designated as ToLCNDV-[potato]. Whereas, the DNA B components shared 86.6–91.7% identity with ToLCNDV isolates from cucurbits, tomato and bhendi. Evidence for intra-species recombination was detected only in DNA A with a maximum of three events in GWA-5 and FAI-19 isolates. Analysis of cp gene, DNA A, iterons and recombination events clearly indicate that two groups of ToLCNDV-[potato] infects potato in India.     

Genetic diversity and recombination analysis based on capsid protein gene of <Emphasis Type="Italic">Chilli veinal mottle virus</Emphasis> isolates from Pakistan

Chilli veinal mottle virus (ChiVMV), is a Potyvirus that causes severe yield losses in capsicum worldwide including Pakistan. In the current study, genetic diversity and molecular evolution of ChiVMV were explored based on the CP gene sequences. In multiple sequence alignments of the CP gene of 29 ChiVMV isolates, Pakistani isolates shared 82–92% and 78–96% nucleotide and amino acid identities, respectively with other ChiVMV isolates. In nucleotide and amino acid based phylogenetic analysis of the CP gene, the Pakistani isolates clustered with Indian (JN692501 and JN624776) and Chinese (KC711055, KC711055, JX088636 and HQ218936) isolates in a separate clade. In all Pakistani isolates, conserved motifs (DAG, WCIEN, QMKAAL, and AFDF) were located at 6–8, 141–145, 222–225, and 242-248th amino acid positions, respectively. Eleven recombination events were detected in the isolates investigated. One Pakistani isolate KX236451 was suggested to be a recombinant between the Pakistani isolate (KT876050) and the Indian isolate (JN692501). Most of the codons were found under negative selection except for codons at 28, 34, and 38th positions that were found under positive selection by REL method. An infrequent gene flow was observed between the ChiVMV isolates from Pakistan and other countries of the world. To our knowledge, this is the first report on genetic diversity of Pakistani isolates of ChiVMV based on recombination and phylogenetic analysis. Findings of this study may be helpful in developing sustainable management strategies against ChiVMV not only in Pakistan but also in other countries, ultimately resulting in enhanced and good quality production of chilli crop.     

Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe

The genetic variation and evolutionary mechanisms shaping Cucumber vein yellowing virus (CVYV) populations were investigated by analysis of nucleotide sequences coding for P1b, P1b/P3 and coat proteins (CP) from isolates collected in different countries. The complete genome sequence of isolate ISM from Israel was also determined and compared to those of isolates Jor from Jordan and ALM32 from Spain. This isolate had overall nucleotide identities of 94·23 and 94·96% with ALM32 and Jor, respectively. Nucleotide variation among isolates was not homogeneously distributed, with the 5′ half of the genome being more variable than the 3′ half. A Bayesian phylogenetic tree of the CP showed that CVYV isolates clustered into two main clades: isolates from the Middle East region (Lebanon, Israel and Jordan) clustered in both clades whereas the isolate from Tunisia clustered in clade I and the European isolates clustered as a homogeneous phylogroup in Clade II. A similar topology was observed for P1b but with incongruences with respect to the CP, suggesting genetic exchange among virus isolates, which were confirmed with recombination algorithms. The low genetic diversity within the European phylogroup with respect to the other isolates, neutralist tests and genetic differentiation analyses suggest that the Middle East region is the cradle of CVYV and that a unique virus introduction event occurred in Europe, where the virus spread rapidly. Taken together, these findings indicate a risk of emergence of virulent CVYV isolates in Europe either through migration from the Middle East or by genetic changes of the European isolates.     

葡萄卷叶伴随病毒2号和3号辽宁分离物部分基因组的序列分析

 将采自辽宁兴城地区在生长期间具典型卷叶病症状的金星无核(Venus Seedless)葡萄品种休眠枝条,用RT-PCR检测4种葡萄卷叶伴随病毒(Grapevine leafroll-associated viruses,GLRaVs),扩增得到了葡萄卷叶伴随病毒2号(GLRaV-2)和葡萄卷叶伴随病毒3号(GLRaV-3)两种病毒的主要外壳蛋白(major coat protein,CP)基因的完整序列(GenBank登录号分别为FJ786017和FJ786016)。这表明该葡萄植株受到了GLRaV-2和GLRaV-3辽宁分离物(GLRaV-2-LN和GLRaV-3-LN)的复合侵染。根据检测结果,克隆了GLRaV-2-LN基因组3'端CPm (minor capsid protein)、p19(19-kDa protein)和p24(24-kDa protein)基因(GenBank登录号分别为FJ786018、FJ786019和FJ786018)。序列分析表明,GLRaV-3-LN的CP基因全长942 nt,与已报道的国内外其它分离物CP基因全序列相比,核苷酸序列同源性为89.8%~91.8%,由此推导的氨基酸序列同源性为94.9%~97.4%。GLRaV-2-LN的CP、CPm、p19和p24基因全长分别为597 nt、672 nt、486 nt和618 nt。与国外报道的几个分离物的相应蛋白基因全序列相比,核苷酸序列同源性分别为88.3%~100.0%、78.7%~99.9%、75.1%~99.4%和87.5%~99.5%;由此推导的氨基酸序列同源性分别为92.9%~100.0%、89.2%~100.0%、73.9%~99.4%和89.3%~99.0%。     

Characterization of Japanese <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG-2-1 isolates using rDNA-ITS sequences,culture morphology,and growth temperature

Rhizoctonia solani AG-2-1 is classified into three subsets (Subsets 1–3) based on the rDNA-ITS sequence. Few Japanese isolates, however, have been phylogenetically analyzed. To understand the distribution and diversification of AG-2-1 isolates in Japan, we examined 23 Japanese AG-2-1 isolates (15 from Hokkaido, the northernmost island, and eight from NARO Genebank) in terms of rDNA-ITS sequences, culture morphology, and temperature-dependent growth characteristics. Of these, 15 isolates were found to belong to Subset 1. One isolate, which formed a light brown colony with concentric rings and grew slowly at 25 °C, was classified into Subset 2. Six isolates had varied culture morphology and relatively faster growth than Subset 1 isolates at 30 °C. They formed a clade on the phylogenetic tree, designated clade HK, with cauliflower isolates from Belgium and the Netherlands, with a bootstrap value of 47%, and were separate from the three known subsets. Sequence similarity in the rDNA-ITS region for this clade ranged from 98.2 to 100%, whereas clade HK isolates had 96.7–98.6% similarity with the isolates in each subset. This result suggests that clade HK is likely an independent intragroup within AG-2-1, although the rDNA-ITS sequences in this clade were variable. One isolate was not assignable to any clade because it was intermediate between isolates in clade HK and Subset 2. This is the first report describing variation among rDNA-ITS sequences of Japanese AG-2-1 isolates.     

Virulence profiling of <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis> isolates,causing bacterial blight of rice in India

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo), remains a major production constraint in rice cultivation especially in irrigated and rainfed lowland ecosystems in India. The pathogen is highly dynamic in nature and knowledge on pathotype composition among the Xoo population is imperative for designing a scientific resistance breeding program. In this study, four hundred isolates of Xoo collected from diverse rice growing regions of India were analyzed for their virulence and genetic composition. Virulence profiling was carried out on a set of differentials consisting of 22 near isogenic lines (NILs) of IR24 possessing different BB resistance genes and their combinations along with the checks. It was observed that different NILs possessing single BB resistance gene were susceptible to about 59–94% of the Xoo isolates except IRBB 13 (containing BB resistance gene xa13), which showed susceptibility to about 35% of the isolates. Based on the reaction of the Xoo isolates on the differentials, they were categorized into 22 pathotypes. Among the 22 pathotypes, IXoPt-1 and IXoPt-2 were least virulent and IXoPt # 18–22 were highly virulent. Pathotype IXoPt-19 which was virulent on all single BB resistance genes except xa13 constituted the major pathotype (22.5% isolates) and was widely distributed throughout India (16 states). This was followed by pathotype IXoPt-22 (17.25%) which was virulent on all the NILs possessing single BB resistance genes. Molecular analysis was carried out using two outwardly directed primers complementary to sequence of IS1112, a repetitive element of Xoo. A high level of genetic polymorphism was detected among these isolates and the isolates were grouped into 12 major clusters. The data indicated complex nature of evolution of the Xoo pathotypes and there was no strong correlation between pathotypes and genetic clusters as each genetic cluster was composed of Xoo isolates belonging to different pathotypes. The study indicated that none of the single BB resistance genes can provide broad spectrum resistance in India. However, two-gene combinations like xa5 + xa13 and different 3 or 4 genes combination like Xa4 + xa5 + xa13, Xa4 + xa13 + Xa21, xa5 + xa13 + Xa21 and Xa4 + xa5 + xa13 + Xa21 are broadly effective throughout India.     

百合斑驳病毒云南分离物 全基因组序列分析及CP结构预测

 对云南嵩明百合上发生的百合斑驳病毒(Lily mottle virus, LMoV)进行全基因组序列测定及分析,并对LMoV嵩明分离物(LMoV-SMi1、LMoV-SMi2)和玉溪分离物(LMoV-YXi1、LMoV-YXi2)外壳蛋白(coat protein,CP)基因进行序列比较,发现云南的LMoV分为2个类群,玉溪分离物属于种群I,嵩明分离物属于种群II。2个类群间的核苷酸和氨基酸同源性分别为86.7%~89.5%、90.1%~92.7%,玉溪分离物和嵩明分离物相比,cp基因发生了3个核苷酸的缺失。对国内外LMoV所有分离物的cp基因氨基酸序列进行系统进化分析,结果表明所有LMoV分离物可划分为2个种群,种群I分离物较种群II分离物几乎均存在1个苏氨酸缺失的差异。此外,对LMoV-SMi2的CP相关特性和空间结构进行了初步预测,认为该蛋白为球状,具有较强的表面可能性,不存在跨膜区域,大多数区域能够形成主要的抗原决定簇,主要集中在aa12-22、aa31-42、aa83-99、aa179-191、aa215-223、aa249-259区段,可作为制备抗血清选择抗原的参考。LMoV-SMi2和LMoV-YXi1在二级结构和三级结构上存在一定的差异,但总体空间结构差异不大。     

Characterization of <Emphasis Type="Italic">Bean common mosaic virus</Emphasis> and <Emphasis Type="Italic">Bean common mosaic necrosis virus</Emphasis> isolates in common bean growing areas in Turkey

Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are well-known legume-infecting potyviruses. The incidences of BCMV and BCMNV infections were determined by ELISA in 367 seed and leaf samples which were collected in 15 common bean-growing provinces of Turkey. Of the samples tested, 67 (18.2 %) occurred to be infected with BCMV, however only 5 (1.4 %) were infected with BCMNV. A total of 45 ELISA-positive samples were selected from single-virus infected ones to determine BCMV and BCMNV pathogenicity groups (PGs) by using a set of bean cultivars that contain different combinations of resistance genes. Some BCMV populations exhibiting unusual pathogenicity were identified. One of them, named TR-180, was found to overcome resistance conferred by bc-1, bc-1 ² , bc-2 and bc-2 ² recessive alleles in common bean and assigned to PG VII. This isolate shared high (99 %) sequence identity with previously identified BCMV RU-1 and RU-1-related strains (RU1-OR-B and RU1-OR-C) according to a BLAST analysis of the nucleotide sequences of RT-PCR amplified products comprising the complete coat protein and 3′ partial NIb regions. The isolates TR-203 and TR-256 produced a distinctive reaction pattern in the dominant I gene-bearing bean cultivars Amanda and Isabella at lower (<30 °C) temperatures and were classified into PG IVb. These isolates were found to be 99 % identical to US-1 strain based on 3′ terminal nucleotide sequences of the BCMV genome. A fourth isolate, TR-243, involved mixed BCMV populations, as confirmed by partial nucleotide sequence analysis; one was classified as belonging to PG VII being similar to TR-180, and another was assigned to PG IVb. In conclusion, on the basis of both the reactions of differential bean cultivars and ELISA results, most of BCMV isolates were assigned to pathogroup PG VII and BCMNV isolates to PG VIb. This study is the first to show that four recessive resistance alleles of common bean can be overcome by a single field isolate of BCMV, and that a wide range of BCMV pathogroups are present in Turkey.     

Molecular and experimental evidence of multi-resistance of <Emphasis Type="Italic">Cercospora beticola</Emphasis> field populations to MBC,DMI and QoI fungicides

Binucleate Rhizoctonia (BNR) spp. isolates were collected from taro (Colocasia esculenta (L.) Schott) and ginger (Zingiber officinale (Willd.) Roscoe) (Yunnanxiaojiang cv.) in Yunnan province. These Yunnan (YN) isolates did not anastomose with any of the tester isolates of the known AGs of binucleate Rhizoctonia spp. The growth of YN cultures on PDA was appressed, mealy and matlike after 4 days of incubation, then turned white brown, producing brown to dark brown, irregularly shaped sclerotia were embedded in the PDA medium after 14 days. All attempts to induce basidiospore production were unsuccessful, but the length and sequence of the internal transcribed spacer (ITS1 + 5.8S rDNA + ITS2) regions of 5.8S rDNA from the YN isolates were identical in length and sequence to isolates of all the other AGs of binucleate Rhizoctonia /Ceratobasidium spp. The sequences of 5.8S rDNA-ITS from the YN isolates were unique among AGs of BNR. The YN isolates had sequence similarities of 94% with isolates of AG Fb and P, 93% with AG E, 91% with AG R, 79–94% with AG S, and 74–87% with AG A, Ba, Bb, Bo, C, DI, DII, DIII, Fa, G, H, I, K, L, O, and Q. Four isolates of AG YN caused minor virulence (lesions ≦1mm²⁾ to ginger or taro in growth chamber studies. It was concluded that the YN isolates belong to a new anastomosis group AG-V of the Ceratobasidium spp..     

Phylogeny of Egyptian isolates of <Emphasis Type="Italic">Cucumber mosaic virus</Emphasis> (CMV) and <Emphasis Type="Italic">Tomato mosaic virus</Emphasis> (ToMV) infecting <Emphasis Type="Italic">Solanum lycopersicum</Emphasis>

Four Cucumber mosaic virus (CMV) (CMV-HM 1–4) and nine Tomato mosaic virus (ToMV) (ToMV AH 1–9) isolates detected in tomato samples collected from different governorates in Egypt during 2014, were here characterized. According to the coat protein gene sequence and to the complete nucleotide sequence of total genomic RNA1, RNA2 and RNA3 of CMV-HM3 the new Egyptian isolates are related to members of the CMV subgroup IB. The nine ToMV Egyptian isolates were characterized by sequence analysis of the coat protein and the movement protein genes. All isolates were grouped within the same branch and showed high relatedness to all considered isolates (98–99%). Complete nucleotide sequence of total genomic RNA of ToMV AH4 isolate was obtained and its comparison showed a closer degree of relatedness to isolate 99–1 from the USA (99%). To our knowledge, this is the first report of CMV isolates from subgroup IB in Egypt and the first full length sequencing of an ToMV Egyptian isolate.     

来源于砂梨和桃的苹果褪绿叶斑病毒分离物部分CP基因和3′端非翻译区的序列分析

 苹果褪绿叶斑病毒（Apple chlorotic leaf spot virus, ACLSV）是引起果树病害的一种重要病毒。ACLSV寄主范围广、发生较普遍,可侵染苹果、梨等仁果类果树和桃、扁桃、李、樱桃、杏等核果类果树,据报道我国梨产区感染ACLSV达80%以上。ACLSV引起植物症状的类型与寄主种类、病毒株系有关。ACLSV为线形病毒科（Betaflexiviridae）、纤毛病毒属（Trichovirus）的代表成员^［1］。ACLSV的CP相对比较保守,研究表明不同的ACLSV分离物的CP基因具有序列多样性,存在分子变异^［2～5］,CP基因分子特性的研究可为ACLSV株系划分提供依据。来源于欧洲、亚洲和北美的桃、李等核果类果树,以及苹果寄主上的ACLSV分离物的分子变异报道较多^［2,3,5］,来源于梨寄主上的ACLSV分子变异研究较少^［4,5］。     

Biological, serological, and molecular differences among isolates of potato a potyvirus

ABSTRACT Sequences of the coat protein (CP) and 3'-end nontranslated region (3'NTR) of 13 isolates and the helper component proteinase (HC) of nine isolates of potato A potyvirus (PVA) were determined and compared with the eight previously determined PVA CP and 3'NTR sequences and one HC sequence. CP amino acid (aa), 3'NTR nucleotide, and HC aa sequence identities were 92.9, 93.4, and 94.8%, respectively. Sequence data, serological tests, and the necrotic local lesions induced in the leaves of the potato hybrid 'A6' confirmed that tamarillo mosaic virus is a strain of PVA. The aa substitutions A6T and G7S in the CP N-terminus were correlated with loss of aphid transmissibility. Development of necrotic lesions or nonnecrotic symptoms in the systemically infected leaves or lack of systemic spread in potato cv. King Edward were used to place the PVA isolates into four strain groups, but this grouping was not correlated with any differences in CP, HC, or 3'NTR. Recognition of CP by three monoclonal antibodies was used to place the PVA isolates into three groups different from the four groups above. The epitopes of two mono-clonal antibodies were mapped by site-directed mutagenesis to the same lysine residue at the CP aa 34.     

甘薯羽状斑驳病毒外壳蛋白基因的分子变异

应用单链构象多态性(single-strand conformation polymorphism,SSCP)技术结合核苷酸序列测定的方法,对我国甘薯主产区11个省份的甘薯羽状斑驳病毒(Sweet potato feathery mottle virus,SPFMV)外壳蛋白(CP)基因的分子变异情况进行了研究.结果表明,SPFMV CP基因的RT-PCR产物表现了较丰富的图谱类型,50个分离物共产生9种主要的SSCP带型;对显示不同带型的20个样品的CP基因进行了序列测定和进化树分析,CP基因核苷酸序列一致性为77.2％～99.9％.说明这些样品的SPFMV的CP基因存在较大的分子变异,可划分为EA、RC、O和C4个株系.     

Molecular variability of Apple chlorotic leaf spot virus in Shaanxi,China

Apple chlorotic leaf spot virus (ACLSV) is one of the latent viruses that occur in apple orchards worldwide but usually without visible symptoms. In 2010–2012, a total of 550 apple leaf samples from 12 different major apple-producing areas in Shaanxi, China, were tested by serological assay for ACLSV; the results revealed an infection level of 51.5 %. Because of the known variability in the putative amino acid sequences of the coat protein (CP), and thus the potential for non-detection by serological assay, the molecular variability of isolates of ACLSV collected in Shaanxi was analyzed using PCR and compared with isolates from the rest of the world. Sequences of 504 nt corresponding to 87 % of the CP gene of 12 isolates were acquired by RT-PCR and deposited in GenBank with the accession numbers KF134387–KF134298. Comparisons of the partial CP gene sequences of these 12 isolates as well as isolates previously reported in the world revealed the pairwise identities ranging from 68.9–99.8 % and 73.8–100 % at the nucleotide and amino acid level, respectively. Phylogenetic analysis based on these nucleotide sequences showed that the 72 isolates deposited in GenBank fell into three groups (P205, B6 and Ta Tao 5 Group). Our 12 ACLSV isolates were separated into the P205 and B6 groups, respectively. Multiple alignment analysis of the amino acid sequences of CP revealed that there was a combination of six amino acids at positions 40, 59, 75, 86, 130 and 184 in isolates from each group that could be used to distinguish among the three groups. Two recombination events were identified from all isolates by recombination analysis, and three ACLSV isolates collected in this study participated in these two events. Our results show that molecular variation was present in isolates of ACLSV collected in Shaanxi province and this may reflect introductions of the virus associated with different sources of germplasm.     

Biological, serological, and molecular variabilities of clover yellow vein virus

ABSTRACT A comparative study was made on the host reactions, serological properties, and nucleotide sequences of the coat protein (CP) gene of 10 clover yellow vein virus (C1YVV) isolates and one bean yellow mosaic virus (BYMV) isolate collected from different host plant species and locations in Japan. Two strains of C1YVV isolates, grouped on the basis of host reactions on Chenopodium amaranticolor, C. quinoa, Nicotianaclevelandii, N. benthamiana, Vicia faba, and Trifolium repens, corresponded to two serotypes determined by double-antibody sandwich- and triple-antibody sandwich-enzyme-linked immunosorbent assay using three polyclonal and nine monoclonal antibodies. These results were also confirmed by nucleotide sequence analysis of the CP gene. The CP gene of C1YVV isolates of strain 1, including the Australian isolate C1YVV-B, had 93 to 98% nucleotide identities and 97 to 99.6% amino acid identities. The CP of C1YVV isolates of strain 2, including the New Zealand isolate C1YVV-NZ, had 92 to 98% nucleotide identities and 95 to 98% amino acid identities. The nucleotide identities and the amino acid identities between the two C1YVV strains were 82 to 84%, and 90 to 94%, respectively. When compared with the CP sequences of 12 C1YVV isolates, the CP sequence of the BYMV isolate had 71 to 73% nucleotide identity and 73 to 77% amino acid identity. Amino acid sequence differences among C1YVV isolates from strains 1 and 2 were located mostly at the N-terminal regions of the CP. Our results indicated that the C1YVV isolates studied could be separated into two strains on the basis of host reactions, serology, and the nucleotide sequence of the CP gene.     

Efficacy of some rhizospheric and endophytic bacteria <Emphasis Type="Italic">in vitro</Emphasis> and as seed coating for the control of <Emphasis Type="Italic">Fusarium culmorum</Emphasis> infecting durum wheat in Tunisia

Sixty two rhizospheric and endophytic bacterial strains were evaluated for their biocontrol effect on two aggressive Fusarium culmorum isolates (Fc2 and Fc3). We observed that 35 % and 23 % of the tested strains inhibited the in vitro growth of Fc2 and Fc3 respectively. The observed antagonism was due to inhibition by contact (13–19 % of the strains) or at distance (10–16 % of the strains) for both fungal isolates. Some of the antagonistic bacteria showed the ability to produce diffuse and/or volatile compounds that inhibit the growth, the sporulation and macroconidia germination of F. culmorum. None of the tested antagonistic bacteria showed chitinase activity on synthetic medium. The sequencing of the 16S rDNA genes of some antagonistic bacteria showed that they belong to the genera Bacillus, Pseudomonas and Microbacterium. The double inoculation of durum wheat seeds by the antagonistic bacterial strains (B13, B18, BSE1, BSE3 and B16E) and the two F. culmorum isolates showed that germination and seedling vigor were generally improved in vitro. The percentage of infected seeds was also reduced. In greenhouse trials, the biocontrol effectiveness of F. culmorum was dependant from the virulence of the fungal strain and the specificity of the antagonistic interaction between bacterial and fungal strains. The bacterial strains B18 and B16E reduced F. culmorum infection on durum wheat plants probably due to their antagonistic and plant growth promoting activities and they may be used in a mixture as seed biopriming inoculum for plant growth bio-promoting and Fusarium wheat diseases biocontrol.     

一个马铃薯X病毒分离物的外壳蛋白基因序列分析与株系鉴定

对山东省侵染马铃薯的一个马铃薯X病毒(PVX)分离物PVX—SD1的外壳蛋白(CP)基因进行了克隆和序列分析。以提纯的病毒RNA为模板，应用RT-PCR扩增目的基因，通过常规的基因克隆法将扩增的CP基因导入pUC19载体，测序。结果表明，PVX—SD1的CP基因长719bp，可编码248个氨基酸；与Gen—Bank中报道的15个有代表性的株系或分离物相比较，核苷酸同源性在80．1％-99．7％，氨基酸同源性在89．8％-100％；与欧洲株系UK3仅1个核苷酸不同，同源性为99．7％，氨基酸同源性达100％，表明它们可能为同一株系，属于X^3组．     

韭葱黄条病毒厦门分离物外壳蛋白基因序列分析及其分组

 本文在测定了侵染厦门古宅大蒜的病毒分离物（LYSV XM）CP基因序列的基础上,进一步从GenBank登录的58个分离物中选取具有代表性的29个分离物建立CP基因核苷酸序列系统进化树。利用该系统进化树明确了LYSV XM与其他分离物间的进化关系,并在前人研究基础上提出一种基于CP基因核苷酸序列的类群分组方法。