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1.
Arabis mosaic virus (ArMV) is an important pathogen infecting a wide range of plant species worldwide. In the present study, we carried out exhaustive phylogenetic analyses based on the coat protein (CP) sequence of ArMV isolates originating from different host plants and geographic regions. Maximum-likelihood reconstruction revealed the presence of three distinct, well-supported phylogroups. BaTS analyses indicated that the diversity of ArMV isolates may be correlated with both host plant and geographic origin. Moreover, population genetic analyses showed significant differences in the level of genetic diversity among variants within ArMV that originated from rhubarb plants, as expected by quasispecies. Further analysis revealed that both selection and recombination are shaping the population structure of ArMV. In total 14 groups of residues were detected as coevolving for different amino acid properties.  相似文献   

2.
Tomato black ring virus (TBRV), a member of the Nepovirus genus, is a serious plant pathogen distributed worldwide. It causes significant damage to several economically important crops, such as artichoke or strawberry. The TBRV bipartite genome consists of two polyadenylated single-stranded positive-sense RNA molecules, which may be accompanied by subviral particles such as defective interfering RNAs (DI RNAs) and satellite RNAs (satRNAs). In this study, we obtained the complete genome sequence of six TBRV isolates originating from different hosts and determined the presence of eight TBRV satRNAs. Subsequently, genetic variability, recombination, phylogenetic and selection pressure analyses were performed. The results revealed that the TBRV population is genetically diverse. The occurrence of potential recombination events, evidence of positive selection pressure acting on particular codons and the diversification of satRNAs within the TBRV population indicated that the virus mutates and can rapidly adapt to new environmental conditions or hosts. The presented data shed some light on TBRV evolutionary dynamics and epidemiology.  相似文献   

3.
Tomato black ring virus (TBRV) and beet ringspot virus (BRSV) are closely related but distinct members of subgroup B of the genus Nepovirus. Both viruses have broad host ranges and are transmitted by seed, pollen, and ectoparasitic nematodes. Although 13 TBRV and 3 BRSV genome sequences were already available, no attempt has been made to link sequence data from these recent sequences with those of historical isolates studied in the pre-sequencing era. High-throughput sequencing was used to generate eight new TBRV and BRSV genome sequences from three historical >60-year-old and two >30-year-old isolates, and three more recent isolates. These eight isolates were from the Czech Republic, Germany, and the UK. We compared these with all genomes sequenced previously. Intraspecies recombination (three of four TBRV and two of four BRSV isolates) was frequent amongst the eight new genomes. Interspecies recombination was also present within the RNA1 of TBRV isolates BRSV-3393 SG GB and BRSV-9888 ST GB. No satellite RNAs were associated with the eight new genomes. Two commercial enzyme-linked immunosorbent assay (ELISA) kits used to detect TBRV during routine testing differed in that one detected only TBRV and the other only BRSV, so they are likely to provide incorrect but potentially complementary virus occurrence information. We suggest both ELISA kits, or appropriate molecular tests, be used by biosecurity authorities to avoid this problem. This study illustrates the value of sequencing historical isolates preserved from the pre-sequencing era.  相似文献   

4.
Tomato black ring virus (TBRV) is a worldwide-distributed RNA virus infecting a wide range of different host plants, including crop species, trees, shrubs, and weeds. Here, we investigated the molecular evolution of TBRV and its adaptability to different plant species. The TBRV-Pi isolate was used to generate five independent evolution lineages serially passaged in either quinoa, tobacco, or tomato plants. After 15 passages, the genetic variability present in all the lineages was characterized for the movement (MP) and coat (CP) coding cistrons. We addressed two main questions: to what extent does the amount of genetic variability in the TBRV genome depend on the host species, and are there host species-specific adaptive mutations? Overall, 201 different nucleotide substitutions emerged during the evolution experiment, with some of them appearing multiple times in different lineages; two of them (one in CP and one in MP) were unique for a particular host plant. We have shown that the degree of genetic differentiation depends on the host species in which the virus evolved, and that positive selection is operating upon certain residues, particularly in CP. Moreover, we have characterized new types of defective RNAs that arose during the TBRV-Pi evolution in tobacco. Furthermore, this is the first report of a defective RNA from the RNA2 of TBRV.  相似文献   

5.
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6.
Fusarium poae is one of the Fusarium species isolated from cereal grains infected by Fusarium head blight (FHB), and in recent years it has been identified as a major FHB component. In this study, 97 F. poae isolates from Argentina (n = 62) and England (n = 35) were analysed by inter-simple sequence repeats (ISSR) to examine the genetic diversity and to determine whether intraspecific variation could be correlated with geographic and/or host origin. The molecular analysis showed high intraspecific variability within F. poae isolates, but did not reveal a clear relationship between variability and the host/geographic origin. Fusarium poae isolates from the same geographic region or host appeared in different subclusters. Conversely, isolates with the same haplotype were also collected from different geographic regions. However, we did observe subclusters consisting of isolates from Argentina only or from England only. Furthermore, a single seed sample was found to host different haplotypes. Analysis of molecular variance (AMOVA) indicated a high genetic variability in F. poae, with most of the genetic variability explained by differences within, rather than between Argentinean and English populations. This is the first report on genetic diversity of F. poae using ISSR markers. Moreover, ISSR fingerprinting generates highly polymorphic markers for F. poae and proved to be a useful and reliable assay for genetic variability studies.  相似文献   

7.
番茄黑环病毒分子生物学检测方法及分离物序列分析   总被引：1，自引：1，他引：1  
根据TBRV运动蛋白基因的保守序列设计引物，RT-PCR和IC-RT-PCR能从6个TBRV的分离物中分别扩增到与预期大小相同的DNA条带，序列测定和分析表明所测定的序列为TBRV运动蛋白基因的部分序列，在系统关系树上与TBRV的其它分离物形成一簇，表明所建立的RT-PCR和IC-RT-PCR检测方法是可靠的。  相似文献   

8.
The β‐proteobacterium Ralstonia solanacearum causes bacterial wilt of many plant species. Knowledge of phylotype and sequevar variability in populations of this microorganism is useful for implementing control measures, particularly host resistance. To this end, 301 isolates of R. solanacearum were collected from different geographic regions and hosts in Brazil. Their phylotype and sequevar characterization was used to determine the amount and distribution of phenetic and phylogenetic variability. Isolates were classified into phylotypes I (n = 48), clade 1; and phylotype II, clades 2–5. Phylotype II was divided into subclusters IIA (n = 112) and IIB (n = 141). Phylotype II was widely distributed, whereas phylotype I isolates were found in Central, Northern, and Northeastern regions of Brazil. There were 108 haplotypes identified among endoglucanase (egl) gene sequences from 301 isolates and 32 haplotypes among DNA repair (mutS) gene regions from 176 isolates. The egl and mutS sequence analyses identified eight known (1, 4, 7, 18, 27, 28, 41 and 50) and four new (54, 55, 56 and 57) sequevars. Phylotype IIB showed high diversity in sequevars and host range. Multiplex PCR, using primers specific to the Moko ecotype, characterized banana and long pepper isolates as sequevar 4 and 4/NPB, respectively. This constitutes the first report of the emergent ecotype IIB/4NPB in a new host, long pepper. The majority of sequevars were associated with geographic regions. This high variability of R. solanacearum in Brazil suggests use of host resistance to control bacterial wilt should be mainly focused by region.  相似文献   

9.
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10.
The aim of this study was to develop new polymorphic markers for analysis of genetic diversity in the fungal soilborne plant pathogen Verticillium dahliae. Twelve polymorphic markers (five microsatellites and seven polymorphic sequences) were developed from a genomic library enriched for microsatellites. Screening of polymorphic loci was done using a collection of 25 V. dahliae isolates of diverse geographic origins, host sources and vegetative compatibility groups (VCGs). Three methods were used to score alleles: polyacrylamide gel electrophoresis (PAGE), sequencing of PCR‐amplified loci, and capillary electrophoresis. The new markers were used to assess genetic differentiation between isolates associated with different host plants. Two collections of isolates were analysed, obtained from artichoke (30 isolates) and potato (20 isolates) from crops grown in rotation located in the same area in eastern‐central Spain. The resolution of genetic differentiation between these two collections using the new markers was compared to that provided by other often‐used markers (SCARs and VCGs). Sequence analysis of the alleles proved to be the most unambiguous technique for scoring microsatellite data. The relatively high genetic differentiation observed between isolates from different crops (genetic differentiation coefficient, GST = 0·24) and their high genotypic diversity suggest a divergence between V. dahliae from artichoke and potato. It is hypothesized that evolution of V. dahliae from the local resident population in association with the two host crops has occurred. The new markers are useful for resolving population structure within V. dahliae and may contribute to a better understanding of the population biology of this fungus.  相似文献   

11.
ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P < 0.05) and populations from different host genotypes (P < 0.02). In the geographic populations, most of populations from cultivated and wild P. virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P < 0.02), except there was no differentiation between the Shubert Select and wild chokecherry populations (>P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow existed between populations from different regions and host species. Gene flow rates (Nm) varied from <1 to 12.5, with higher gene flow rates among population pairs from the same host species (P = 1.000). The analysis of molecular variance revealed that a major genetic variance source came from the genetic variation among isolates within populations regardless of the origin and host genotype of the population. Although some locations had a limited number of isolates, the results of this study clearly showed that the genetic diversity and population differentiation of A. morbosa were closely associated with host genotypes and geographic locations, but mostly with the former.  相似文献   

12.
In Papua New Guinea (PNG) cocoa (Theobroma cacao) is one of the most important cash crops grown in the tropical lowland and island regions. As in most cocoa‐growing areas, phytophthora black pod and canker cause significant yield losses. Cocoa breeding activities in PNG are focused in East New Britain province where disease control recommendations are also developed. This study tested the hypothesis that there was no diversity in the Phytophthora palmivora population causing black pod on cocoa by characterizing the variation in pathogen populations within and between the five major cocoa‐growing areas. Diseased pods were sampled hierarchically from the five locations and additional isolates were collected from soil, stem and leaf lesions, or retrieved from culture collections. Morphological characters showed continuous variation within the range described for P. palmivora. Genetic analysis revealed that the isolates belonged to one dominant clonal lineage, with restricted distributions of several other subpopulations. Lowest diversities were found in the geographically isolated Karkar Island and East Sepik province. Soil isolates showed greater genetic diversity than isolates from cocoa lesions. Intra‐farm variation was as much as inter‐farm or inter‐province variation. Both mating types were detected, although no strong evidence of sexual recombination was observed. The analysis revealed limited geographic, temporal or host specialization, suggesting continuous selection for pathogenicity from a genetic pool of P. palmivora. These findings have significant implications on the deployment of cocoa genotypes, enforcement of inter‐province quarantine and sustainable disease management strategies.  相似文献   

13.
The genetic variability and aggressiveness of Brazilian Erwinia psidii isolates from Eucalyptus spp. was studied and compared with reference isolates from guava (Psidium guajava). Repetitive element sequence (rep)-based PCR markers of 101 isolates from Eucalyptus spp. and five from guava showed that the populations of E. psidii displayed a relatively low genetic variability. No correlation of genetic clustering based on rep-PCR analysis with geographic origin or host of origin was observed, indicating that genome rearrangements associated with adaptation to a particular host were not detected by these molecular markers. A higher genotypic richness was detected in the Mato Grosso do Sul population, probably reflecting a pathogen dissemination associated with the recent expansion in eucalypt plantations. Wilcoxon and ANOVA tests of disease severity data indicated differences in aggressiveness among isolates and an isolate × clone interaction. The area under the disease progress curve (AUDPC) and disease severity for some isolates were significantly different between two susceptible clones tested. Notably, isolate LPF681 from guava was not able to cause disease on a susceptible Eucalyptus urophylla clone, suggesting that some co-evolution between pathogen and host has taken place. The variability in aggressiveness and virulence among isolates of E. psidii observed in this study will be important for the establishment of appropriate screening approaches to select for disease resistance.  相似文献   

14.
Calonectria leaf blight, caused by Calonectria pteridis, is currently one of the main foliar diseases in eucalypt plantations in Brazil. In warm and high rainfall regions, the disease can be a limiting factor for eucalypt production when planting susceptible genotypes. The most effective method for controlling this disease in the field is the use of resistant genotypes, which requires knowledge of the genetic variability and aggressiveness of the pathogen population for effective deployment of plant resistance. This work evaluated the genetic diversity and aggressiveness of C. pteridis populations obtained from infected eucalypt plants in Monte Dourado (Pará state) and Imperatriz (Maranhão state), Brazil. To study the genetic diversity, 16 ISSR primers were tested, five of which amplified polymorphic, reproducible and informative bands. Thirty-one closely related genotypes were identified from 84 isolates studied, indicating that the population has a low genetic diversity. The aggressiveness of seven isolates, selected according to geographic origin and their clustering in the ISSR-based dendogram, was determined by inoculation of a hybrid Eucalyptus grandis × E. urophylla clone under controlled conditions. Disease severity was assessed by both measuring the percentage of plant defoliation and assigning a score according to a diagrammatic scale of symptoms. A high correlation between the two evaluation methods was observed, which revealed significant differences in aggressiveness among the isolates. The diagrammatic scale is recommended for disease evaluation because results are obtained much faster, before the occurrence of severe defoliation. No correlation between clustering in the ISSR-based phylogenetic analysis and aggressiveness was observed.  相似文献   

15.
The random amplified polymorphic DNA (RAPD) method was used to investigate the genetic variability and population structure of Fusarium culmorum isolated from wheat stem bases. A total of 108 isolates, representing seven geographically distinct populations, was collected from five climatic regions in Tunisia. Pseudo-allelic frequencies were estimated at each of the 25 putative RAPD loci analyzed by scoring for the presence or absence of amplified fragments; 92 haplotypes were found among the 108 strains. The analysis of the population structure did not reveal any trend with regard to geographic origin. Total gene diversity (HT * = 0.318) was mostly attributable to diversity within populations (HS * = 0.308). Analysis of molecular variance confirmed that most of the genetic variability was within populations. Genetic differentiation among populations was low to moderate (GST * ranged from 0 to 0.190 and averaged 0.041 over all loci). Cluster analysis with UPGMA using genetic distances did not reveal any spatial clustering of the isolates collected from the different geographic regions. Based on these results, we conclude that the F. culmorum isolates recovered from different regions in Tunisia might be part of a single population pool.  相似文献   

16.
Meloidogyne ethiopica is an important nematode pathogen causing serious economic damage to grapevine in Chile. In Brazil, M. ethiopica has been detected with low frequency in kiwifruit and other crops. The objectives of this study were to evaluate the intraspecific genetic variability of M. ethiopica isolates from Brazil and Chile using AFLP and RAPD markers and to develop a species‐specific SCAR‐PCR assay for its diagnosis. Fourteen isolates were obtained from different geographic regions or host plants. Three isolates of an undescribed Meloidogyne species and one isolate of M. ethiopica from Kenya were included in the analysis. The results showed a low level of diversity among the M. ethiopica isolates, regardless of their geographical distribution or host plant origin. The three isolates of Meloidogyne sp. showed a high homogeneity and clustered separately from M. ethiopica (100% bootstrap). RAPD screenings of M. ethiopica allowed the identification of a differential DNA fragment that was converted into a SCAR marker. Using genomic DNA from pooled nematodes as a template, PCR amplification with primers designed from this species‐specific SCAR produced a fragment of 350 bp in all 14 isolates of M. ethiopica tested, in contrast with other species tested. This primer pair also allowed successful amplification of DNA from single nematodes, either juveniles or females and when used in multiplex PCR reactions containing mixtures of other root‐knot nematode species, thus showing the sensitivity of the assay. Therefore, the method developed here has potential for application in routine diagnostic procedures.  相似文献   

17.
We collected samples from black, red and white currants showing symptoms of blackcurrant reversion disease (BRD) and full blossom disease (FBD), cultivated in the Czech Republic. Blackcurrant reversion virus (BRV) was detected in all symptomatic plants. After amplification, a substantial part of the 3′ non-translated region (3′-NTR) of RNA2 of 15 new isolates of BRV was sequenced and compared with sequences available in the literature and GenBank. We did not find significant sequence diversity among isolates associated with either FBD or BRD. BRV was graft-transmitted from FBD infected red currant to black currant where symptoms of BRD were observed. Further sequence analysis of BRV isolates resulted in a phylogenetic tree with four branches, each consisting of six to nine isolates. No correlation with geographic origin was visible on the tree as isolates from various countries occurred in all four branches. We also found no correlation between the host and the topology of the tree: most of black currant isolates occurred in branches 3 and 4, but also occurred in branches 1 and 2. Only one white currant and one red currant isolate occurred in branches 3 and 4, respectively. The sequence identity of the Czech isolates in this region ranged from 91.9 to 99.8%. The 17 plant species growing within and in the close vicinity of the BRD-infested plantation were tested negative for BRV by RT-PCR as natural hosts of BRV. BRV was successfully transmitted by mechanical inoculation from black currant to Nicotiana occidentalis and N. tabacum cv. Xanthi, the latter being a new host for BRV. The infection was confirmed by PCR and sequencing.  相似文献   

18.
Alternaria tenuissima is a common pathogen on a number of plants described in several geographic regions of the world. Genetic variation within and between Russian Far East, North West and Caucasus populations of A. tenuissima from wheat was examined. In addition, genetic differences between isolates from various hosts were estimated. In total, 101 isolates of A. tenuissima were studied using amplified fragment length polymorphism (AFLP) with four primer combinations. Wright’s fixation index (F st), gene flow (N m) and gene diversity (H s) were calculated. AFLP banding patterns indicated significant genetic distance and at the same time a low level of gene flow between the Far East and the two other groups of isolates originating from the European part of country. The degree of similarity between the North West and Caucasus populations was very high, as was the migration rate. Isolates analysed by UPGMA-based cluster analysis were grouped according to location of origin but irrespective of plant host. Based on the F st value, the group of isolates originating from wheat and barley were not found to differ significantly from each other.  相似文献   

19.
The geographic incidence, genetic diversity and phylogenetic relationships of Melon necrotic spot virus (MNSV) and Olpidium isolates were studied in three cucurbit species from several Latin American and European countries on different collecting dates. Of the 112 cucurbit samples analysed, 69 from Guatemala, Honduras, Mexico, Panama and Spain were DAS‐ELISA‐positive for MNSV. Olpidium bornovanus and O. virulentus infections, and MNSV infections mixed with these Olpidium species, were observed for all these countries. Twenty‐nine MNSV isolates from all the origins where the virus was detected were selected and amplified by RT‐PCR. The resulting RT‐PCR of the p29, p89, p7A, p7B and p42 proteins was used to estimate the genetic diversity and the phylogenetic relationships of the MNSV population. The sequences obtained in this study were compared with the MNSV sequences of the NCBI database, and three groups were recovered by nucleotide composition according to geographical origins: the EU‐LA genotype group (with two subgroups: EU and LA, European and Latin American isolates, respectively), the JP melon genotype group (Japanese melon reference isolates) and the JP watermelon genotype group (Japanese watermelon reference isolates). The genetic diversity in the entire p7A and p7B proteins of MNSV suggests that these coding regions are under strong selective pressure. Additionally, the rDNA‐ITS region was analysed in 40 O. bornovanus and O. virulentus isolates associated with each geographical location and host examined. Phylogenetic analysis showed two groups for each Olpidium species, and these groupings were related to the host from which they were originally isolated.  相似文献   

20.
Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = ?0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.  相似文献   

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