Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt(Sharqia,Qalyubia and Garbia).In this study,RT-PCR,Single-Strand Conformation Polymorphism(SSCP)and nucleotide sequence analysis were used for four independent CTV genomic regions(p65,p18,p20,and p23)to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates.RTPCR products(650 bp)for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing.SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns.Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7%with T36 isolate from USA,Florida.Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate(T36 isolate group),suggesting that they may have originated from closely related ancestors.Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang,p18,p20 and p65,amplified from isolate A3,Sharqia governorate,revealed that the p18,p65,and p20 genes were related to the T3-KB isolate from South Africa with 99%–100%sequence homology.Phylogenetic relationship analysis for p65,p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group.The recombination analysis identified three of six isolates from Sharqia,and Garbia as potential recombinant for p23 gene.The isolates T36 and T3 were identified as major donors for recombination events in isolate A3.Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event.The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

Expressing p20 hairpin RNA of Citrus tristeza virus confers Citrus aurantium with tolerance/resistance against stem pitting and seedling yellow CTV strains

The Citrus tristeza virus (CTV) uses 3 silencing suppressor genes, p20, p23 and p25, to resist the attacks from its Citrus hosts. Inactivating these genes is therefore obviously a potential defensive option in addition to the current control strat-egies including aphid management and the use of mild strain cross protection. In this study, we cloned partial DNA frag-ments from the three genes, and used them to construct vectors for expressing hairpin RNAs (hpRNAs). To facilitate the formation of hpRNAs, the constructs were introduced in a loop structure. Fol owing transformation of sour orange (Citrus aurantium) with these constructs, 8 p20 hpRNA (hp20) and 1 p25 hpRNA (hp25) expressing lines were obtained. The 7 hp20 transgenic lines were further characterized. Their reactions to CTV were tested fol owing inoculation with CT14A and/or TR-L514, both of which are severe strains. Results showed that 3 lines (hp20-5, hp20-6 and hp20-8) were completely resistant to TR-L514 under greenhouse conditions for no detectable viral load was found in their leaves by PCR. However, they exhibited only partial suppression of TR-L514 under screen house conditions since the virus was detected in their leaves, though 2 months later compared to non-transgenic controls. Further tests showed that hp20-5 was tolerant also to CT14A under screen house conditions. The growth of hp20-5 was much better than others including the controls that were concurrently chal enged with CT14A. These results showed that expressing p20 hpRNA was sufifcient to confer sour orange with CTV resistance/tolerance.

Genetic Diversity and Global Distribution of Citrus tristeza virus (CTV) Strains

Citrus tristeza virus （CTV）, the most devastating viral pathogen in citrus, causes tremendous economic losses to citrus industry worldwide. The CTV isolates exhibit variable pathogenicities on their hosts indicating a mixed population of the CTV in nature. Several fragments within the CTV genome have been used for studying the genetic diversity of the CTV, however, the best region for rapid the CTV strain differentiation is still absent at present. In present study, a systemic analysis was carried out to evaluate the best region within the CTV genome for rapid CTV strain differentiation. Results of our study showed that the major coat protein （CP） coding region was the best region for this purpose. Using pair-wise distance frequency distribution plot, a reasonable genetic distance cut-off value was set for the CTV CP gene for the CTV strain differentiation. Using this criterion, eight CTV strains, including seven well characterized and a new strain, were successfully differentiated using 537 CTV isolates reported from 38 countries. The global strain distribution pattern was then determined and discussed. Our results also provided a new insight into the evolution and spreading of the virus, as well as the information for developing proper disease management strategy.

Characterization of Citrus tristeza virus Isolates by Indicators and Molecular Biology Methods

Citrus tristeza virus （CTV） exists in citrus as a large number of distinct strains differing in biological characters. The control strategies such as mild strains cross protection （MSCP） require a clear understanding of the characterization of CTV. For better understanding of the structure of CTV population and the relationship between molecular and biological characterization, 72 CTV samples collected from five provinces in China were studied, using biological indexing, p25/Hinf I restriction fragment length polymorphism （RFLP）, multiple molecular markers, and bidirectional RT-PCR assay. The mixture of severe stem pitting isolates was found to be dominant in the field. CTV isolates with p25/Hinf Ⅰ RFLP group 3 and p23/BD-PCR group Ⅰ, Ⅲ were the main cause of epidemics, and most CTV isolates were found to be the mixture of T30 and VT genotypes. More accurate identification of strain mixtures in the field and better understanding of the biological traits of the isolates may be achieved by applying the three molecular detection methods simultaneously.

Preliminary Studies on CPG/Hinf Ⅰ RFLP Groups of Citrus tristeza virus Infected Sweet Oranges in China

Citrus tristeza virus （CTV） causes economically important losses to the citrus industry worldwide. Mild strain cross protection （MSCP） against tristeza has hardly been practised due to mixed infection of different CTV-strains and little background of its molecular biology in China. For better cognition on CTV, 192 sweet orange samples collected from eight provinces （Chongqing, Sichuan, Fujian, Hunan, Guangxi, Yunnan, Guangdong and Jiangxi） were tested by direct tissue blot immuno-assay （DTBIA）, and 158 of them were tested positively, which therefore were subjected to coat protein gene （CPG）/Hinf Ⅰ restriction fragment length polymorphism （RFLP） analysis. Sample bulks were compared between Chongqing and Fujian by some statistical data, including ratios of single infection and mixed infection to local samples, proportions of CTV isolates with single RFLP groups, and rates of each RFLP group. The simplified analysis of samples from the other six provinces were then conducted. This study suggests that CTV isolates with CPG/Hinf Ⅰ RFLP groups Ⅲ and Ⅰ are the main epidemic ones in China, and mixed infection of CTV in fields are popular. Based on observation of severity of stem-pitting symptom in field trees, CTV isolates with CPG/Hinf Ⅰ RFLP groups Ⅲ and Ⅰ caused severe stem-pittings in sweet oranges in China.

Distribution and Research Advances of Citrus tristeza virus

Citrus tristeza virus （CTV） is one of the most important causal agents of citrus diseases and exists as numerous strains. CTV is replicated in phloem cells of plants within the family Rutaceae and is transmitted by a few of aphid species. CTV epidemics have caused death of millions of citrus trees in many regions all over the world, where the sour orange （Citrus aurantium） was used as rootstock. Also the production of grapefruit （C. paradisi） and sweet orange （C. sinensis） has been affected by CTV strains. CTV gives uplift to three prominent syndromes, namely quick-decline （tristeza）, stempitting and seedling-yellows. The disease is graft-transmissible in nature but not seed-transmitted. However, the tristeza disease in most citrus groves was a man-made problem created by the desire of horticulturists to introduce cultivars from other citrus growing areas. The utmost importance of the disease called for review articles in numbers of plant protection, epidemiology books, citriculture and proceedings. This review collects the information with respects to disease history, distribution host range, virus isolates association, identification and detection, transmission and management; especially on the current status of CTV prevailing and controlling in Pakistan. It provides valuable information for CTV disease and its controlling approaches.

Genetic Evolution Analysis on Wild Isolates of Citrus Tristeza Virus Originated in China Based on Coat Protein Genes Sequences

The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.

Phylogenetic Analysis of Citrus tristeza virus Isolates of Wild Type Citrus in China

The genetic variation and phylogenetic relationships of Citrus tristeza virus （CTV） isolates collected from Chinese wild type citrus were analyzed by comparing the sequences of nine genomic regions （p23, p20, p13, p18, p25, p27, POL, HEL and k17） with the CTV isolates of cultivated citrus from different countries. The results showed that the divergence pattern of genomic RNA of the CTV isolates from wild type citrus was similar to that of other isolates from cultivated citrus, the 3′ proximal region was relatively conserved, and the 5′ proximal region had greater variability. The nine genomic regions of CTV isolates analyzed were found to have been under purifying selection in the evolution process. Phylogenetic analysis showed that the eleven Chinese wild CTV isolates were located at different clades and did not relfect their geographical origins, suggesting genetic diversity among the Chinese wild CTV populations. These results will aid in the understanding of molecular evolution of the Chinese CTV populations.

Overview of Strain Characterization in Relation to Serological and Molecular Detection of Citrus tristeza Closterovirus

Tristeza is a devastating viral disease in all the citrus growing countries throughout the world and has killed millions of citrus trees in severely affected orchards.The citrus species grafted on sour orange rootstock are affected by this disease.Predominantly,the sweet orange,grapefruit and lime trees grafted on sour orange exhibit severe symptoms like quick decline,vein clearing,pin holing,bark scaling and degeneration leading to variable symptoms.Symptomatic expression of Citrus tristeza virus(CTV)in different hosts has been attributed to virus isolates which are from severe to mild.Different serological and molecular assays have been deployed to differentiate the strains of CTV.Citrus tristeza virus is diversified towards its strains on the basis of biological,serological and molecular characterization.Phenotypic expression is due to genetic alteration and different molecular basis have now been adopted for strain differentiation.This review will give a brief idea about the different CTV isolates,their characterization based on nucleic acid and serological assays.Different methods along with salient features for strain characterization has also been reviewed.This review will also open the new aspects towards formulation of management strategies through different detection techniques.

Genetic Characteristics of <i>Citrus Tristeza Virus</i>Isolates from Cultivated Citrus in China Based on Coat Protein Gene

Citrus tristeza virus (CTV) is an important citrus pathogen causing considerable economic loss to citrus production. Knowledge on genetic evolutionary of the CTV population in China remains limited. In this study, 1439 samples were collected from nine citrus-producing areas of China. The coat protein (CP) genes of CTV were amplified by RT-PCR, and sequenced to analyze the genetic evolution. Analysis of the base composition showed an AU preference pattern, with the GC content was lower than AU content. Nine CTV populations were clustered into one clade in neighbor-joining (NJ) tree, indicative of a close phylogenetic relationship among the populations in China. Analysis of molecular variation (AMOVA) revealed that 77.72% genetic variations of CTV populations were observed among populations, with an FST value of 0.223. The values of dN/dS and neutrality test of CP gene were ranged from 0.016 to 0.082 and -1.377 to 1.456, respectively, the results suggesting that all of nine CTV populations were relatively constantly maintained under purifying selection. Our study demonstrated the genetic characteristics and molecular evolution relationship of CTV populations in China, and provided a theoretical basis for scientific control of CTV.

感染CTV甜橙中挥发性成分的分析及萜类合成相关基因的表达变化

为明确柑橘衰退病毒(Citrus tristeza virus,CTV)对柑橘挥发性物质的影响,本研究采用顶空固相微萃取法(Headspace Solid-phase Micro-Extractions,HS-SPEM)结合气相色谱-质谱联用(Gas Chromatography-Mass Spectrometry,GC-MS)技术分析了感染CTV的甜橙和健康甜橙挥发性成分.结果表明,CTV侵染使甜橙挥发性成分总量显著降低,仅为健康甜橙的71.00%,与健康甜橙中检测出的59种挥发性成分相比,感病甜橙中检测出55种,两者共有物质51种,其中33种的质量分数显著降低;此外,还有8种仅在健康甜橙中被检出,4种仅在CTV侵染甜橙中被特异检出,分别为百里香酚、香叶酸甲酯、石竹素和2-亚甲基-莰烷;检出的挥发性物质以萜类居多,为44种.采用实时荧光定量PCR(RT-qPCR)技术进一步分析了4个萜类合成关键基因(香叶基香叶基二磷酸合酶、法呢基焦磷酸合酶、γ-萜品烯合酶和柠檬烯合酶)表达量,结果表明,感染CTV甜橙中4个基因表达显著下降,与感染CTV甜橙中γ-萜品烯和柠檬烯质量分数显著减少趋势一致,暗示了CTV侵染甜橙影响了寄主萜类合成途径进而影响了挥发性物质的释放.

柑桔衰退病毒相关研究进展

柑桔衰退病毒引起的柑桔衰退病是一种广泛分布于世界各柑桔主产区的重要柑桔病毒病害,对柑桔产业的危害极大。随着我国柑桔产业的快速发展,近年来柑桔衰退病在我国多个柑桔产区暴发,造成了严重的经济损失。为了给深入开展柑桔衰退病毒研究和有效防控柑桔衰退病提供参考,根据已有研究文献报道,就柑桔衰退病毒的起源、类型、传播方式、蛋白功能、病毒与寄主的互作关系、茎陷点症状形成、蚜传机理,以及防治方法进行了综述。

柑橘3种病毒类病原多重RT-PCR检测技术的建立及应用

【目的】建立柑橘黄化脉明病毒(citrus yellow vein clearing virus,CYVCV)、柑橘衰退病毒(citrus tristeza virus,CTV)和啤酒花矮化类病毒(hop stunt viroid,HSVd)的多重RT-PCR检测体系。【方法】设计多重RT-PCR引物,分析其特异性,确定其最佳浓度比、最适退火温度及灵敏度,在此基础上对福建地区的柑橘样品进行检测。【结果】确定了CYVCV-F/R、CTV-F/R和HSVd-F/R等3对引物的最佳浓度比例为1∶1∶2,最适退火温度为52.9℃,灵敏度结果显示该体系可检测模板稀释到10^(-2)的阳性样品。应用该体系对采自福建部分地区的157份柑橘样品进行检测,结果发现,CYVCV、CTV和HSVd的检出率分别为47.1%、56.7%和22.9%。【结论】成功建立了柑橘CYVCV、CTV和HSVd病原的多重RT-PCR检测方法,为该类病害的检测提供准确、快速的检测方法。

柑桔衰退病毒RB和VT基因型实时定量PCR检测方法建立和应用

为定量检测样品中柑桔衰退病毒(citrus tristeza virus,CTV)RB和VT基因型含量,以RB基因型的p33基因、VT基因型的ORF1a基因为靶标,建立了RB和VT基因型的特异性实时定量PCR方法。该方法检测RB和VT基因型质粒浓度下限均为2×10^(1) copies/μL,灵敏度为普通PCR的1000倍;对RB和VT基因型进行检测,质粒拷贝数对数(x)与Ct值(y)的标准曲线方程分别为y=-3.3255 x+37.8453和y=-3.2737 x+36.2839,R^(2)分别为0.9991和0.9954,扩增效率分别为99.85%和102.05%;方法的重复性良好,组内和组间Ct值变异系数均小于2.07%。对田间样品检测发现,不同样品之间RB基因型含量差异和VT基因型含量差异均较大。该方法特异性强,灵敏度高,适用于田间样品检测。

褐色橘蚜在健康与CTV植株上的EPG比较

利用刺探电位图谱(EPG)技术对褐色橘蚜Toxopter acitricida(Kirkaldy)在健康与感染CTV的植株上的取食行为进行了比较研究。结果显示,褐色橘蚜在二者上均产生8种取食波形,分别为非刺探波(np波)、路径波(A波、B波、C波)、Pd波、韧皮部分泌唾液波(El波)、韧皮部被动吸食波(E2波)以及木质部主动吸食波(G波)。刺探过程中,二者非刺探总时间(np波)存在差异;褐色橘蚜在健康植株上的刺探次数最多且C波的总持续时间最长,与感病植株差异显著。感病植株上,E1波的次数和持续时间均显著多于健康植株。褐色橘蚜在感病植株上E2波的总持续时间为(241.33±24.12 min),显著长于在健康植株上(160.30±24.63 min)的持续时间。由此可初步推断,感染CTV的植株在一定程度上会增加褐色橘蚜获毒与传毒的几率。

柑橘抗CTV转基因与分子标记研究进展

综述了柑橘抗衰退病基因工程中两方面的研究进展。介绍多种来源于柑橘衰退病毒(Citrustriztezavirus,CTV)核酸序列的转基因柑橘和抗性种质资源中抗性基因的分子标记,以及所涉及的方法和遇到的问题。目前研究表明,虽然已成功实现对病毒衣壳蛋白(CP)等基因的转化和Ctv等抗性基因的标记,但尚未获得对CTV有高度抗性的转基因柑橘,而抗性基因亦不能实现定点克隆和转化。因此上述两方面研究还有待深入。

电融合获得用于选择抗CTV砧木的酸橙与甜橙体细胞杂种植株(英文)

在已知参数条件下 ,通过电场诱导酸橙 (Cit rusaurantiumL .)叶肉原生质体和沙漠蒂甜橙(C .sinensisOsbeckcv .Shamouti)的胚性愈伤组织原生质体融合 ,融合产物经培养再生出 40棵植株。染色体检查表明所得到的植株具有 3 6条染色体 ,为四倍体植株。再生植株具有翼叶 ,叶片厚 ,表现出多倍体的特征。采用 2个 1 0 碱基随机引物鉴别再生植株的杂种特性。在 2个引物的扩增带型中 ,再生植株的随机扩增带图里出现了融合亲本的特征带。对再生植株染色体计数和RAPD分析的结果表明它们是酸橙和甜橙种间异源四倍体体细胞杂种植株。这些体细胞杂种植株的获得为选择具有酸橙优良性状。

甜橙和柚中CTV强弱毒株系p20的遗传变异

【目的】对7个柑橘衰退病毒(CTV)株系进行遗传变异研究,明确寄主甜橙和柚中CTV强弱毒株系p20的变异水平。【方法】运用RT-PCR、克隆及测序等技术建立CTV p20种群,并借助MEGA6构建单倍型系统发育树,运用软件DNAStar对两种寄主中CTV强弱毒种群的遗传结构、变异水平进行分析,运用DnaSP软件对各种群进行单倍型多样性、核苷酸多样性分析和中性检验分析。【结果】构建了7个CTV p20种群,由162条序列构成,包含11个单倍型,单个种群有1个或更多单倍型出现。序列分析发现,来自不同种群的单倍型对应的原始核苷酸序列一致性为88.2%—100.0%,对应的氨基酸序列的一致性为92.3%—100.0%,最低的氨基酸序列一致性发生在CT23-1和CT9-2之间;其中单倍型PeraIAC-4、CT22和CT9-1共有50条序列,对应的原始核苷酸序列一致性为100.0%,属优势单倍型,与标准株系T36亲缘关系较近;单倍型多样性最丰富的是甜橙种群PeraIAC,单倍型多样性为0.800,而单倍型多样性最低的是柚种群CT22,单倍型多样性为0.170;相比柚种群的单倍型多样性(0.170—0.552)和核苷酸多样性(0.00032—0.05919),甜橙种群具有更为丰富的单倍型多样性(0.513—0.800)和核苷酸多样性(0.04208—0.05677)。系统发育树分析表明,来自甜橙的分离株种群结构复杂,甜橙种群中检测到的单倍型与标准株系T30、T36、VT和T3均有相关性;与标准株系T3相距很近的CT31-2与优势单倍型在系统发育树上距离最远,对应的原始核苷酸序列一致性仅为88.3%。中性检验结果表明,CTV甜橙种群趋于平衡或收缩状态,而CTV柚种群除CT23外则趋于扩张状态;其中TR-514Y、CT31和CT23种群的Tajima’s D值、Fu和Li’s D*值以及Fu和Li’s F*值均为正值且达到显著水平,而CT9种群的Tajima’s D值、Fu和Li’s D*值以及Fu和Li’s F*值均为负值且达到显著水平。运用DnaSP软件对各种群进行重组分析表明,在各种群中均未检测到重组事件发生。种群变异分析发现,各种群突变克隆百分比在0—30.8%,碱基突变频率在0—7.706×10^(-4),其中CTV甜橙强毒种群有最高的突变克隆百分比(30.8%),最高的碱基突变频率(7.706×10^(-4)),最多的碱基突变数量(11个)和最多的突变位点(7个);CTV甜橙弱毒种群的突变克隆百分比和碱基突变频率均明显低于甜橙强毒种群,CTV柚弱毒种群的突变克隆百分比和碱基突变频率略低于柚强毒种群。碱基突变类型分析发现碱基突变以碱基替代为主,其中A→G突变为优势类型,仅在柚强毒种群CT3的156和157位点间检测到一个碱基插入突变类型,为碱基A插入,未检测到碱基缺失突变类型。【结论】在寄主甜橙和柚中CTV强弱毒p20种群结构及变异存在差异,CTV甜橙种群有着更复杂的种群结构和更高的种群变异水平,且CTV强毒种群变异更大。

CTV侵染对锦橙叶片营养元素含量的影响研究

锦橙是我国南方重要的柑桔栽培品种,栽培面积广,但易被柑橘衰退病病毒(Citrus tristeza virus,CTV)侵染。选用两年生实生锦橙为材料,一组嫁接感染CTV强毒株TRL514的枝条的皮和芽,另一组嫁接正常枝条作为对照,接种后用DTBIA法和RT-PCR法检测CTV侵染情况。接种了CTV的锦橙呈现顶梢枯死、叶片变黄、茎陷点等症状,通过测定春梢叶片氮、磷、钾、硫、钙、镁、铁、锰、铜、硼和锌等11种元素的含量发现:接种了CTV的锦橙氮、钾和铜的含量高于对照;而磷、钙、硫、硼、铁、锰和锌的含量较低;镁的含量差异不大。两组材料间营养元素含量的差异在一定程度上可以解释CTV侵染产生的木质部凹陷对植株的影响,并为今后柑橘衰退病的预防和诊断提供一定的依据。

广西柑橘衰退病和黄脉病调查及其病原病毒的遗传多样性分析

为明确柑橘衰退病毒(citrus tristeza virus,CTV)和柑橘黄脉病毒(citrus yellow vein clearing virus,CYVCV)在广西柑橘上的发生、分布及其遗传变异情况,于2020年至2021年对百色、北海、崇左、贵港、桂林、河池、贺州、来宾、柳州、南宁、梧州和玉林等12个柑橘产区进行了病毒病调查。采用RT-PCR对采集样品进行了病毒检测,并基于病毒分离物外壳蛋白(coat protein,CP)基因的核苷酸序列进行比对分析,构建系统发育树。结果表明:采集的737份柑橘样品中,CTV的检出率为20.62%,CYVCV检出率为18.32%,CTV的检出率略高于CYVCV。病毒复合侵染的现象在采集的柑橘样品中普遍存在,CTV和CYVCV复合侵染率高达34.50%。对RT-PCR产物测序共获得12个CTV分离物和6个CYVCV分离物的CP基因序列。遗传多样性分析发现,CTV和CYVCV的CP基因序列都较保守,CTV分离物的遗传进化与地理来源、寄主来源均没有明显相关性,但CYVCV分离物的遗传进化与地理位置具有相关性,而与寄主来源无明显相关性。上述研究结果可为深入了解CTV和CYVCV在广西的流行情况以及柑橘病毒病的检疫和防控提供参考。