基于相对密码子频率的芜菁花叶病毒基因组序列的进化分析

现有92株芜菁花叶病毒(TuMV)的全基因组序列已在GenBank报道,据分析报道其中58株不含重组序列。利用系统聚类法对92株TuMV的全基因组序列和58株TuMV全基因组序列的相对密码子频率RSCU值进行聚类分析。同时利用系统发育分析方法分析了这92株和58株TuMV全基因组序列。结果发现,92株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度很低;而不含重组序列的58株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度却非常高,且与寄生宿主类型基本对应。这表明在不存在重组的情况下,TuMV密码子频率的偏性可能是宿主内的一种选择压力,影响TuMV基因组的点突变进化方向,促使TuMV适应宿主内环境。     

A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan

The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal-BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal-BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.     

Genetic and molecular variability of a<Emphasis Type="Italic">Turnip mosaic virus</Emphasis> population from horseradish (<Emphasis Type="Italic">Cochlearia armoracia</Emphasis> L.)

Variability and genetic structure of a novel Turnip mosaic virus (TuMV) population from horseradish (Cochlearia armoracia L.) were examined. Over 60 horseradish plants were tested to identify a total of 28 TuMV isolates, constituting the Cochlearia ARmoracia (CAR) TuMV population. Two subgroups of the CAR TuMV isolates could be distinguished: subgroup N did not infect oilseed rape (Brassica napus var. oleifera) cv. Westar plants, while subgroup A infected these plants systemically. Two types of infection of oilseed rape plants were induced by inoculation with the CAR TuMV isolates: systemic mosaic infection and systemic necrotic lesions. The complete sequences of isolates CAR37 (subgroup N) and CAR37A (subgroup A) were determined and compared. The sequences of HC-Pro and CP genes of CAR37 and CAR37A and other isolates of TuMV from other countries were compared to provide some insight into their relatedness. CAR37A, initially regarded as a variant, proved to be very different from CAR37. Re-sequencing after repeated passages confirmed the genetic stability of both isolates.     

Characterization of Turnip mosaic virus from the Asian‐BR Population in Iran

Brassicaceae crops in eight provinces of the North‐west Iran were surveyed for Turnip mosaic virus (TuMV) infection during 2011 and 2012. Many symptomatic plants (38%; 226 of 598) were found to be infected with TuMV. The highest frequency was in turnip (61%), followed by radish (55%), oilseed rape (38%), and brassica weeds including annual bastard cabbage (42%), small tumbleweed‐mustard (50%) and wild radish (45%), but not Brassica oleracea and Lepidium sativum. Using biological assays, Iranian TuMV isolates grouped in three [B], [B(R)] and [BR] host‐infecting types. Phylogenetic analysis using complete coat protein (CP) gene nucleotide sequences showed that the Iranian isolates belonged to the Basal‐B and Asian‐BR populations. No evidence of recombination was found in these isolates using different recombination‐detecting programmes. To our knowledge, our study shows for the first time the occurrence of TuMV Asian‐BR subpopulation in the mid Eurasian region of Iran. The data suggest that the Asian‐BR subtype population is found across southern Eurasia and might be a continuous population in East Asia (mostly Japan and China) and Minor Asia (Turkey), the places considered to be one of the origins of TuMV populations.     

Variation between Turnip mosaic virus Isolates in Zhejiang Province,China and Evidence for Recombination

The 3′‐terminal sequences (c. 1700 nt) of the RNA genome of 10 Turnip mosaic virus (TuMV) isolates from different hosts in Zhejiang province, China, were determined. Phylogenetic analysis of the coat protein nucleotide sequences revealed that most TuMV sequences fell into two distinct clusters. The Chinese isolates B1‐B4 (from Brassica spp.) were similar and placed in the largest group (Group 1), while the isolates R1‐R6 (from Raphanus) were usually placed in a distinct but smaller group (Group 2). There were only approximately 90% identical nucleotides between the two groups. However, one isolate (R5) showed evidence of recombination in that the region between nucleotides 430 and 450, from the start of the coat protein gene and its 3′‐terminus, was a Group 1 type.     

Homologous recombination between different genotypes of hepatitis B virus

Phylogenetic analysis was used to examine the evolutionary relationships among 99 complete HBV sequences. Analysis revealed nine viral genomes clustered with different genotypes depending on genome region analyzed. This discordance indicated that recombination events occurred during HBV history. The putative breakpoints between genomes of different genotypes have been mapped. Six mosaic genomes representing B/C hybrids were isolated in East Asia and three A/D hybrids in Italy. At least some recombinant strains appear to be fully viable and possess high evolutionary potential. As a result, B/C recombinants overspread through the East Asia region. They were found among the isolates from Japan, China and Indonesia. Our results suggest that recombination is a significant and relatively frequent event in the evolution of HBV genome. A possible mechanism and the implications of recombination for the natural history of HBV, clinically important properties, and phylogenetic reconstruction are discussed.     

全基因组序列的系统发育与重组分析鉴定我国马铃薯Y病毒株系

为明确我国马铃薯Y病毒(Potato virus Y,PVY)株系组成及其在不同寄主上的分布特征,文章对31条PVY中国分离物的基因组编码区进行了系统发育及重组分析。系统发育分析结果显示,最大似然法(maximum likelihood,ML)和邻接法(neighbor-joining,NJ)重建的系统发育拓扑结构基本一致,GF_YL20、FZ10、DF、SD1、1116和9703-3等6个分离物均未与已知株系相聚,其他株系来源相同的分离物以较高的自展值相聚成簇,显示出较强的株系特异性。重组分析显示,31个PVY分离物中,共有28个PVY分离物均检测到具有显著的重组信号,这些分离物主要包括PVY~(N-Wi)、PVY~(NTN)和PVY~(NTN-NW)三种株系。进一步分析显示,分离物1104、DF、SD1、1116和9703-3为未报道过的PVY新重组分离物。株系统计结果显示PVY重组株系已上升为优势株系,生产上需要密切注意这些株系,尤其新重组分离物的发展动态。以上结果表明,综合应用PVY全基因组序列的系统发育和重组分析,可以实现PVY株系的准确鉴定。     

Characterisation of resistance to turnip mosaic virus in oilseed rape (Brassica napus) and genetic mapping of TuRB01

Turnip mosaic virus (TuMV) is the major virus infecting Brassica crops. A dominant gene, TuRB01, that confers extreme resistance to some isolates of TuMV on Brassica napus (oilseed rape), has been mapped genetically. The mapping employed a set of doubled-haploid lines extracted from a population used previously to develop a reference RFLP map of the B. napus genome. The positioning of TuRB01 on linkage group N6 of the B. napus A–genome indicated that the gene probably originated from Brassica rapa. Resistance phenotypes were confirmed by indirect plate-trapped antigen ELISA using a monoclonal antibody raised against TuMV. The specificity of TuRB01 was determined using a wide range of TuMV isolates, including representatives of the European and American/Taiwanese pathotyping systems. Some isolates of TuMV that did not normally infect B. napus plants possessing TuRB01 produced mutant viruses able to overcome the action of the resistance gene. TuRB01 is the first gene for host resistance to TuMV to be mapped in a Brassica crop. A second locus, TuRB02, that appeared to control the degree of susceptibility to the TuMV isolate CHN 1 in a quantitative manner, was identified on the C-genome linkage group N14. The mapping of other complementary genes and the selective combining of such genes, using marker-assisted breeding, will make durable resistance to TuMV a realisable breeding objective. Received: 14 December 1998 / Accepted: 10 April 1999     

Novel intertypic recombinants of epstein-barr virus in the chinese population

Among 34 Epstein-Barr virus isolates from nonimmunocompromised Chinese donors, we identified three intertypic recombinants with type 1 sequences at the EBNA2 locus and type 2 sequences at some or all of the EBNA3A, -3B, and -3C loci. These appear to have arisen from independent, evolutionarily recent recombination events; such events may be commoner in nonimmunocompromised populations than hitherto imagined.     

Molecular Characterization of the 3'-Terminal Region of Turnip mosaic virus Isolates from Eastern China

Turnip mosaic virus (TuMV; genus Potyvirus, family Potyviridae) causes great losses to cruciferous crop production worldwide. The 3′‐terminal genomic sequences of eight TuMV isolates from eastern China were compared with those of 74 other Chinese TuMV isolates of known host origin in the GenBank and isolated during the past 25 years. The reported sequences of the eight TuMV isolates are 1125 or 1126‐nucleotides (nt) long excluding the poly(A) tail. They all contain one partial open reading frame of 912 nt, encoding 304 amino acids, followed by a stop codon and a non‐translated region of 209–210 nt. Results of phylogenetic analyses showed that Chinese TuMV isolates clustered into three groups: basal‐BR, Asian‐BR and world‐B. The ratios of non‐synonymous and synonymous substitutions and results of amino acid alignment provided evidence for purifying or negative selection in TuMV populations of China.     

Genetic control of immunity to turnip mosaic virus in winter oilseed rape (Brassica napus ssp. oleifera) and the effect of foreign isolates of the virus

Immunity to a UK isolate (UK 1) of turnip mosaic virus (TuMV) was studied in eight lines of oilseed rape selected from cv Rafal. Six of these lines were uniformly immune and two segregated. Segregation ratios in the F₂ generation of reciprocal crosses between two uniformly immune lines and two uniformly susceptible cultivars (Mikado and Yeoman) showed that immunity was controlled by a dominant nuclear allele. The immunity was confirmed by the inability to detect virus particles in mechanically inoculated plants by back inoculations, ELISA and ISEM tests. Plants were immune to repeated inoculations and aphid transmissions. The immunity was effective against one other UK isolate and two German isolates of TuMV. Another UK isolate (UK 3) and a Greek isolate partially overcame the immunity causing local infection and a Canadian and a Danish isolate overcame it completely causing systemic mosaic-type symptoms. When these immunity-breaking strains were tested against swede line 165 which is also immune to UK 1 TuMV, the Canadian isolate overcame the immunity whereas the Danish isolate did not. Using this swede line, one susceptible and one immune line of oilseed rape as differentials, four distinct groups of TuMV isolates could be identified. Selections of oilseed rape immune to UK TuMV isolates were more severely affected by the Canadian TuMV than UK TuMV susceptible selections. The gene determining immunity to TuMV had no pleiotropic effect on susceptibility to cauliflower mosaic virus. The implications on these findings in relation to breeding for virus resistance are discussed.     

The reactions of swede (Brassica napus) to infection by turnip mosaic virus

Turnip mosiac virus (TuMV) and cucumber mosaic virus (CMV) were the only viruses commonly isolated from naturally diseased swedes (Brassica napus) showing leaf mosaic and leaf and root necrosis. Only TuMV caused these symptoms when re-inoculated to swede. TuMV-infected plants showed a severe loss in leaf (55%) and root (63%) fresh weight after 140 days. Systemic leaf symptoms in infected swede plants varied greatly, but were predominantly necrotic (N) or mosaic (M). Plants were classified into one of seven reaction classes ranging from slight or severe necrosis, and mosaics with and without slight veinal necrosis. Swede cultivars differed markedly in their reaction to TuMV and contained different proportions of N- or M-reacting plants. The reactions of progeny of four resistant cv. Bangholm plants were separately inherited; progeny of two plants reacting either symptomlessly or necrotically and those of the other two plants developing mosaic symptoms only. Five isolates of TuMV from swede crops in different regions caused similar reactions but differed in virulence in the progeny of a self-pollinated resistant swede plant.     

Detection and Molecular Variability of Turnip mosaic virus (TuMV) in Shaanxi,China

Turnip mosaic virus (TuMV) is one of the most devastating threats to oilseed rape by causing serious crop losses. A total of 86 leaf samples of oilseed rape from eight different locations in Shaanxi, China, were tested by RT‐PCR for TuMV; the results revealed an infection level of 43% by TuMV. The complete coat protein (CP) gene of 32 TuMV isolates was cloned and sequenced. Analysis of the CP gene with sequences from the database allowed the genetic classification of 170 TuMV isolates or sequences. Four genetic clusters were obtained: MB (mostly Brassica isolates), MR (mostly Radish isolates), IBR (mostly Intermediate between Brassica and Radish clusters) and OBR (mostly outside Brassica and Radish clusters). All subgroups were slightly related to the hosts, but unrelated to geographical origins. Most of Shaanxi TuMV isolates were on separate branches, compared with the 138 known isolates originating from other parts of the world. Our results help provide a better understanding of the genetic diversity of TuMV isolates infecting oilseed rape in Shaanxi, China.     

我国十省(市)十字花科蔬菜芜菁花叶病毒(TuMV)株系分化研究 Ⅰ.用Green氏方法划分株系

Provvidenti,R.(1980)和Green,S.K.(1985)先后用同一套鉴别寄主谱,研究了美国和我国台湾省的TuMV株系分化情况。本文用Green的方法,对由十省(市)7,982份病样中筛选出的19个TuMV主流分离物,在同一条件下进行了鉴定。结果表明,属于C_1株系的有黑_3分离物;属于C_4株系的有京_2、京_3、冀_2、宁_1(南京)、粤_1和川_1共6个分离物;属于C_5株系的有黑_1、辽_1、京_1、冀_1、沪_1、鲁_1、鲁_2共7个分离物。未检出C_2和C_3株系。黑_2、沪_2、宁_2和秦_1(陕西)共4个性状相近的分离物和冀_3分离物尚不能按Green的标准归类,暂分别定为C_(3-2)和C_6株系。此外,对Green氏方法应用于我国十字花科蔬菜TuMV株系分化研究中存在的问题作了讨论。     

Genetic mapping of the novel <Emphasis Type="Italic">Turnip mosaic virus</Emphasis> resistance gene <Emphasis Type="Italic">TuRB03</Emphasis> in <Emphasis Type="Italic">Brassica napus</Emphasis>

A new source of resistance to the pathotype 4 isolate of Turnip mosaic virus (TuMV) CDN 1 has been identified in Brassica napus (oilseed rape). Analysis of segregation of resistance to TuMV isolate CDN 1 in a backcross generation following a cross between a resistant and a susceptible B. napus line showed that the resistance was dominant and monogenic. Molecular markers linked to this dominant resistance were identified using amplified fragment length polymorphism (AFLP) and microsatellite bulk segregant analysis. Bulks consisted of individuals from a BC₁ population with the resistant or the susceptible phenotype following challenge with CDN 1. One AFLP and six microsatellite markers were associated with the resistance locus, named TuRB03, and these mapped to the same region on chromosome N6 as a previously mapped TuMV resistance gene TuRB01. Further testing of TuRB03 with other TuMV isolates showed that it was not effective against all pathotype 4 isolates. It was effective against some, but not all pathotype 3 isolates tested. It provided further resolution of TuMV pathotypes by sub-dividing pathotypes 3 and 4. TuRB03 also provides a new source of resistance for combining with other resistances in our attempts to generate durable resistance to this virus.     

The AU-rich RNA recombination hot spot sequence of Brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination

RNA recombination can be facilitated by recombination signals present in viral RNAs. Among such signals are short sequences with high AU contents that constitute recombination hot spots in Brome mosaic virus (BMV) and retroviruses. In this paper, we demonstrate that a defective interfering (DI) RNA, a model template associated with Tomato bushy stunt virus (TBSV), a tombusvirus, undergoes frequent recombination in plants and protoplast cells when it carries the AU-rich hot spot sequence from BMV. Similar to the situation with BMV, most of the recombination junction sites in the DI RNA recombinants were found within the AU-rich region. However, unlike BMV or retroviruses, where recombination usually occurred with precision between duplicated AU-rich sequences, the majority of TBSV DI RNA recombinants were imprecise. In addition, only one copy of the AU-rich sequence was essential to promote recombination in the DI RNA. The selection of junction sites was also influenced by a putative cis-acting element present in the DI RNA. We found that this RNA sequence bound to the TBSV replicase proteins more efficiently than did control nonviral sequences, suggesting that it might be involved in replicase "landing" during the template switching events. In summary, evidence is presented that a tombusvirus can use the recombination signal of BMV. This supports the idea that common AU-rich recombination signals might promote interviral recombination between unrelated viruses.     

Viruses infecting winter oilseed rape (Brassica napus ssp. oleifera)

Turnip mosaic virus (TuMV) and cauliflower mosaic virus (CaMV) have been found infecting field crops of winter oilseed rape (Brassica napus ssp. oleifera) in South Warwickshire. Other viruses found include broccoli necrotic yellows virus (BNYV) and a member of the beet western yellows virus group. Systemic leaf symptoms caused by TuMV varied within and between cultivars; the three predominant reaction types were classified as necrotic, mosaic and immune. Some recently introduced cultivars of oilseed rape were more severely affected by TuMV infection than older cultivars. Reactions to CaMV were less varied and immunity was not found. The seed yield from TuMV and CaMV-infected plants was less than that of healthy control plants. This effect was due to infected plants producing either fewer seeds, smaller seeds or both. Germination of seeds from infected plants was unaffected if sown soon after harvest. After storage for one year the germination of seed from a virus infected plant was significantly less than that of seed from a virus-free plant. All commercial cultivars tested were experimentally susceptible to turnip yellow mosaic virus (TYMV) and some American strains of cucumber mosaic virus (CMV).     

The Natural Occurrence of Turnip Mosaic Potyvirus in Allium ampeloprasum

An isolate of turnip mosaic potyvirus (TuMV) was obtained from Allium ampeloprasum grown in commercial greenhouses in Israel. Symptoms on infected plants include systemic chlorosis and yellow stripes, accompanied by growth reduction. Leaves were distorted, often showing necrotic flecking. The virus was readily transmitted mechanically, and in a non-persistent manner by aphids, among Allium, Chenopodium. Gomphrena and some Nicotiana spp. Purified preparations contained numerous filamentous particles similar to those observed in crude extracts of infected leaves. Particles from crude plant extracts had a normal length of 806 nm. Cells of infected plants contained cylindrical cytoplasmic inclusions with pinwheel, scrolls and laminated aggregates which indicated the presence of a potyvirus of Edwardson's subgroup III. and which resemble those of turnip mosaic virus (TuMV), The virus reacted strongly with antiserum to typical isolates of TuMV in immunoelectron microscopy and western blotting but not with antisera to several other potyviruses. Based on serological reactivity, electron microscopy, aphid transmission and cytopathology, the virus was identified as an isolate of TuMV.     

Frequent intrapatient recombination between human immunodeficiency virus type 1 R5 and X4 envelopes: implications for coreceptor switch

Emergence of human immunodeficiency virus type 1 (HIV-1) populations that switch or broaden coreceptor usage from CCR5 to CXCR4 is intimately coupled to CD4+ cell depletion and disease progression toward AIDS. To better understand the molecular mechanisms involved in the coreceptor switch, we determined the nucleotide sequences of 253 V1 to V3 env clones from 27 sequential HIV-1 subtype B isolates from four patients with virus populations that switch coreceptor usage. Coreceptor usage of clones from dualtropic R5X4 isolates was characterized experimentally. Sequence analysis revealed that 9% of the clones from CXCR4-using isolates had originated by recombination events between R5 and X4 viruses. The majority (73%) of the recombinants used CXCR4. Furthermore, coreceptor usage of the recombinants was determined by a small region of the envelope, including V3. This is the first report demonstrating that intrapatient recombination between viruses with distinct coreceptor usage occurs frequently. It has been proposed that X4 viruses are more easily suppressed by the immune system than R5 viruses. We hypothesize that recombination between circulating R5 viruses and X4 viruses can result in chimeric viruses with the potential to both evade the immune system and infect CXCR4-expressing cells. The broadening in cell tropism of the viral population to include CXCR4-expressing cells would gradually impair the immune system and eventually allow the X4 population to expand. In conclusion, intrapatient recombination between viruses with distinct coreceptor usage may contribute to the emergence of X4 viruses in later stages of infection.     

矮牵牛病毒病的初步研究

矮牵牛是一种草本花卉,主要用来布置花坛,但病毒侵染却严重地影响其观赏价值。国内外有关危害矮牵牛的病毒报道较多［１,２］,但较系统研究矮牵牛病毒病的报道较少,本文从矮牵牛病毒鉴定、优势病毒种类确定及防治矮牵牛病毒病进行了初步研究,现报道如下：材料与方法...