Limited morphological,physiological and genetic diversity of Phytophthora palmivora from cocoa in Papua New Guinea

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.     

Cryptic species and population genetic structure of Plasmopara viticola in São Paulo State,Brazil

Downy mildew (Plasmopara viticola) is one of the most important diseases in grape-growing areas worldwide, including Brazil. To examine pathogen population biology and structure, P. viticola was sampled during the 2015/16 growing season from 516 lesions on nine grape cultivars in 11 locations in subtropical areas of São Paulo State, Brazil. For identification of cryptic species, a subsample of 130 isolates was subjected to cleaved amplified polymorphic sequence (CAPS) analysis, and for 91 of these isolates the ITS1 region was sequenced. These analyses suggest that the population of P. viticola in São Paulo State consists of a single cryptic species, P. viticola clade aestivalis. Seven microsatellite markers were used to determine the genetic structure of all 516 P. viticola isolates, identifying 23 alleles and 55 multilocus genotypes (MLGs). Among these MLGs, 34.5% were clonal and represented 93% of the isolates sampled. Four dominant genotypes were present in at least five different locations, corresponding to 65.7% of the isolates sampled. Genotypic diversity (Ĝ = 0.21–0.89) and clonal fraction (0.58–0.96) varied among locations (populations). Most populations showed significant deviation from Hardy–Weinberg expectations; in addition, excess of heterozygosity was verified for many loci. However, principal coordinate analysis revealed no clusters among locations and no significant isolation by distance was found, suggesting high levels of migration. The results indicate that downy mildew epidemics result from multiple clonal infections caused by a few genotypes of P. viticola, and reproduction of P. viticola in São Paulo State is predominantly asexual.     

Genotypic and phenotypic characterization of Phytophthora infestans populations on Java,Indonesia

Phytophthora infestans is endemic to Indonesia and can infect potato crops at any stage in the growing season. Little is known about P. infestans populations in Indonesia. The objectives of this study were first to identify the genotypes causing late blight in the main potato-growing regions on Java in Indonesia, and secondly to examine genotypic diversity in the P. infestans populations in those regions. Samples were collected on FTA cards (n = 140) or in tubers (n = 6) from 15 locations in nine regencies over four years (2016–2019). Microsatellite analysis revealed that late blight outbreaks in these regencies were caused by EU_2_A1 and other genotypes that are unique to Indonesia. Eighty percent of the samples that amplified with CAPS markers were the A1 mating type. Cultures of six isolates were determined to be the A1 mating type based on the pairing test, and of these, two isolates were intermediate and four were sensitive to metalaxyl-M (mefenoxam). The mode of reproduction of the P. infestans population on Java, Indonesia, was found to be clonal. However, as the sample size in this study was small, more isolates need to be tested to confirm this. Microsatellite analysis revealed that 90% of Indonesian samples had trisomic loci. A high number of multilocus genotypes (MLGs) were found in all nine regencies (131 MLGs out of 146 samples). Results indicate that there is ongoing polyploidization in these populations due to a high mutation rate and no selection pressure from the susceptible potato hosts that are being grown in Indonesia.     

High genetic and virulence diversity detected in Neofusicoccum luteum and N. australe populations in New Zealand vineyards

Genotypic and virulence diversity of Neofusicoccum luteum and N. australe isolates recovered from grapevines displaying symptoms of dieback and decline in New Zealand were investigated. The universally primed PCR (UP‐PCR) method was used to investigate the genetic diversity of 40 isolates of N. luteum and 33 isolates of N. australe. Five UP‐PCR primers produced a total of 51 loci from N. luteum and 57 from N. australe with a greater number of polymorphic loci produced in N. australe (86%) compared with N. luteum (69%). Analysis of UP‐PCR data showed both species found in New Zealand vineyards were genetically diverse at both the inter‐ and intra‐vineyard levels with only a single pair of clonal isolates in N. luteum. Cluster analysis of UP‐PCR data produced four genetic groups in N. luteum and 10 in N. australe (P < 0.05). For both species, there was no relationship between the genetic groups and the origin of isolates. The mean genetic diversity (H) of N. luteum was less than for N. australe, being 0.1791 and 0.2417, respectively. Pathogenicity assays of both species using isolates from either the same or different genetic groups inoculated onto either green shoots or grapevine trunks, showed virulence diversity within the population; however, no correlation was identified between genetic groups and virulence.     

Evidence of low levels of genetic diversity for the Phytophthora austrocedrae population in Patagonia,Argentina

Phytophthora austrocedrae is a recently discovered pathogen that causes severe mortality of Austrocedrus chilensis in Patagonia. The high level of susceptibility of the host tree, together with the distribution pattern of the pathogen, have led to the hypothesis that P. austrocedrae was introduced into Argentina. The aim of this study was to assess the population structure of P. austrocedrae isolates from Argentina in order to gain an understanding of the origin and spread of the pathogen. Genetic diversity was determined based on amplified fragment length polymorphisms (AFLPs). In total, 48 isolates of P. austrocedrae were obtained from infected A. chilensis trees, representing the geographical range of the host. Four primer combinations were used for the AFLP analysis. Of the 332 scored bands, 12% were polymorphic. Gene diversity (h) ranged from 0·01 to 0·03; the Shannon index (I) ranged from 0·01 to 0·04. A high degree of genetic similarity was observed among the isolates (pairwise S values = 0·958–1; 0·993 ± 0·009, mean ± SD). A frequency histogram showed that most of the isolate pairs were identical. Principal coordinate analysis using three‐dimensional plots did not group any of the isolates based on their geographical origin. The low genetic diversity (within and between sites) and absence of population structure linked to geographic origin, together with the aggressiveness of the pathogen and the disease progression pattern, suggest that P. austrocedrae might have been introduced into Argentina.     

Pineapple heart rot isolates from Ecuador reveal a new genotype of Phytophthora nicotianae

Pineapple heart rot disease, caused by Phytophthora nicotianae (syn. P. parasitica), is responsible for significant annual reductions in crop yield due to plant mortality. In Ecuador, new infections arise during the rainy season and increase production costs due to the need for biocontrol and fungicide applications. Studies of P. nicotianae population structure suggest that certain genetic groups are associated with host genera; however, it is not clear how many host‐specific lineages of the pathogen exist or how they are related. The objectives of this study were to determine the level of genetic variation in the P. nicotianae population causing heart rot disease of pineapple in Ecuador and compare the genotypes found on pineapple to those previously reported from citrus, tobacco and ornamentals. Thirty P. nicotianae isolates collected from infected pineapple leaves from four farms were genotyped using nine simple sequence repeat loci. In addition, the DNA sequences of mitochondrial loci cox2 + spacer and trnG‐rns were analysed. Together, these loci supported a single clonal lineage with two multilocus genotypes differing in a single allele and low mitochondrial diversity. This lineage was distinct but closely related to isolates collected from vegetables and ornamentals in Italy. The results support the hypothesis of host specialization of P. nicotianae in intensive cropping systems and contribute to the understanding of population structure of this important pathogen.     

Genetic diversity of Botrytis in New Zealand vineyards and the significance of its seasonal and regional variation

Species‐ and population‐specific differences in fungicide resistance and aggressiveness within Botrytis makes basic data on genetic diversity important for understanding disease caused by this fungus. Genetic diversity of Botrytis was surveyed between 2008 and 2012 from grapes from five New Zealand wine‐growing regions. A total of 1226 isolates were gathered from symptomless flower buds at the start of the growing season and 1331 isolates from diseased fruit at harvest. Two species were found, B. cinerea and B. pseudocinerea. Botrytis pseudocinerea was common in both Auckland vineyards sampled, and infrequent elsewhere. However, even in Auckland, it was rarely isolated from diseased fruit. The presence of the Boty and Flipper transposons was assessed. Isolates with all four transposon states (Boty only, Flipper only, both Boty and Flipper, no transposons) were found for both species. Both vineyards in the Auckland region had high numbers of Flipper‐only isolates at flowering; both vineyards from the Waipara region had high numbers of Boty‐only isolates at flowering. Most isolates from diseased fruit at harvest contained both transposons. These observations suggest that B. pseudocinerea, and isolates with one or both of the transposons missing, may be less aggressive than B. cinerea, or than isolates with both transposons present. Two clades were resolved within B. pseudocinerea, only one of which has been reported from European vineyards. Phylogenetic diversity within B. cinerea in New Zealand was similar to that known from Europe, including isolates that appear to match Botrytis ‘Group S’. The taxonomic implications of this genetic diversity are discussed.     

Outcome of sexual reproduction in the <Emphasis Type="Italic">Phytophthora infestans</Emphasis> population in Estonian potato fields

In this study, the Estonian population of Phytophthora infestans was characterized with mating type, sensitivity to metalaxyl, virulence on 11 potato R-gene differentials and 12 SSR markers to show the outcome of potential sexual reproduction in the population. During the three years 2010–2012, 141 P. infestans isolates, collected from 23 potato fields, showed quite a high and stable frequency of the A2 mating type, 48% of the total population. In 87% of all sampled potato fields, both mating types were recorded, suggesting continuous sexual reproduction of P. infestans and possible oospore production. Metalaxyl-sensitive isolates prevailed in all three years (68 out of 99 isolates). Amongst the 95 isolates tested, 51 virulence races were found. The race structure was diverse, and most pathotypes were unique, appearing only once; the two most common pathotypes, 1.2.3.4.6.7.10.11 and 1.2.3.4.7.10.11, comprised 35% of the population. The P. infestans population was genetically highly diverse and most of the multilocus genotypes (MLGs) appeared only once. Furthermore, all of the MLGs appeared in only one of the three sampling years. Our results confirm that the high diversity in the Estonian P. infestans population is most likely the result of frequent sexual reproduction, which benefits the survival, adaptability and diversity of the pathogen in the climate of North-Eastern Europe.     

The morphology,behaviour and molecular phylogeny of Phytophthora taxon Salixsoil and its redesignation as Phytophthora lacustris sp. nov.

Since its first isolation from Salix roots in 1972, isolates of a sexually sterile Phytophthora species have been obtained frequently from wet or riparian habitats worldwide and have also been isolated from roots of Alnus and Prunus spp. Although originally assigned to Phytophthora gonapodyides on morphological grounds, it was recognized that these isolates, informally named P. taxon Salixsoil, might represent a separate lineage within ITS Clade 6. Based on phylogenetic analyses and comparisons of morphology, growth‐temperature relationships and pathogenicity, this taxon is formally described here as Phytophthora lacustris sp. nov. Isolates of P. lacustris form a clearly resolved cluster in both ITS and mitochondrial cox1 phylogenies, basal to most other Clade 6 taxa. Phytophthora lacustris shares several unusual behavioural properties with other aquatic Clade 6 species, such as sexual sterility and tolerance of high temperatures, that have been suggested as adaptations to riparian conditions. It appears to be widespread in Europe and has also been detected in Australia, New Zealand and the USA. It was shown to be weakly or moderately aggressive on inoculation to Alnus, Prunus and Salix. The extent of P. lacustris’ activity as a saprotroph in plant debris in water and as an opportunistic pathogen in riparian habitats needs further investigation. Its pathogenic potential to cultivated fruit trees also deserves attention because P. lacustris has apparently been introduced into the nursery trade.     

Genetic diversity,sensitivity to phenylamide fungicides and aggressiveness of Phytophthora ramorum on Camellia,Rhododendron and Viburnum plants in Spain

Phytophthora ramorum has been detected in official plant health surveys on Rhododendron, Viburnum and Camellia in ornamental nurseries in northern Spain since 2003. A collection of 94 isolates of P. ramorum was obtained from 2003 to 2008 from plants with symptoms at different geographical locations. Isolates were identified based on morphology and sequence of the rDNA ITS region. Mating type, genetic variation, sensitivity to phenylamide fungicides and aggressiveness of these isolates were determined. All isolates belonged to the A1 mating type, ruling out the possibility of genetic recombination. Seven microsatellite markers were used to study genetic diversity; three out of the seven microsatellite markers were polymorphic within the Spanish population of P. ramorum. This study confirms that all Spanish isolates of P. ramorum belonged to the EU1 lineage. Twelve intralineage genotypes were detected, five that are unique to Spain (EU1MG38, EU1MG41, EU1MG37, EU1MG39 and EU1MG40) and seven that are also present in at least one other European country (EU1MG1, EU1MG29, EU1MG22, EU1MG13, EU1MG2, EU1MG18 and EU1MG26). Genotypes EU1MG37, EU1MG39 and EU1MG40 were isolated from Rhododendron from one region; EU1MG38 and EU1MG41 were isolated from Camellia from two different regions. Isolates of genotype EU1MG38 were resistant to metalaxyl and mefenoxam. The level of genetic diversity within the Spanish population of P. ramorum is limited and indicates a relatively recent clonal expansion.     

A phylogenetically distinct lineage of Pyrenopeziza brassicae associated with chlorotic leaf spot of Brassicaceae in North America

Light leaf spot, caused by the ascomycete Pyrenopeziza brassicae, is an established disease of Brassicaceae in the United Kingdom (UK), continental Europe, and Oceania (OC, including New Zealand and Australia). The disease was reported in North America (NA) for the first time in 2014 on Brassica spp. in the Willamette Valley of western Oregon, followed by detection in Brassica juncea cover crops and on Brassica rapa weeds in northwestern Washington in 2016. Preliminary DNA sequence data and field observations suggest that isolates of the pathogen present in NA might be distinct from those in the UK, continental Europe, and OC. Comparisons of isolates from these regions using genetic (multilocus sequence analysis, MAT gene sequences, and rep-PCR DNA fingerprinting), pathogenic (B. rapa inoculation studies), biological (sexual compatibility), and morphological (colony and conidial morphology) analyses demonstrated two genetically distinct evolutionary lineages. Lineage 1 comprised isolates from the UK, continental Europe, and OC, and included the P. brassicae type specimen. Lineage 2 contained the NA isolates associated with recent disease outbreaks in the Pacific Northwest region of the USA. Symptoms caused by isolates of the two lineages on B. rapa and B. juncea differed, and therefore “chlorotic leaf spot” is proposed for the disease caused by Lineage 2 isolates of P. brassicae. Isolates of the two lineages differed in genetic diversity as well as sensitivity to the fungicides carbendazim and prothioconazole.     

Phytophthora infestans populations in central,eastern and southern African countries consist of two major clonal lineages

Limited knowledge is available on Phytophthora infestans populations in Sub‐Saharan Africa (SSA). Therefore, and in response to recent severe late blight epidemics, P. infestans isolates from potato, tomato and Petunia × hybrida from eight SSA countries were characterized. Isolates were characterized with ‘old’ markers, including mating type (176 isolates), mitochondrial DNA haplotype (mtDNA) (281 isolates), glucose‐6‐phosphate isomerase (Gpi) (70 isolates), restriction fragment length polymorphism analysis with probe RG‐57 (49 isolates), and by metalaxyl sensitivity (64 isolates). Most isolates belonged to the US‐1 genotype or its variants (US‐1.10 and US‐1.11). The exceptions were genotype KE‐1 isolates (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and unique RG‐57 genotype), identified in two fields in Kenya, which are related to genotypes previously identified in Rwanda (RW‐1 and RW‐2), Ecuador and Europe. Metalaxyl‐resistant P. infestans isolates from potato were present in all the countries except Malawi, whereas all the isolates from tomato were sensitive. Genotyping of 176 isolates with seven simple sequence repeat (SSR) markers, including locus D13 that was difficult to score, revealed 79 multilocus genotypes (MLGs) in SSA. When this locus was excluded, 35 MLGs were identified. Genetic differentiation estimates between regional populations from SAA were significant when locus D13 was either excluded (P = 0·05) or included (P = 0·007), but population differentiation was only low to moderate (F_ST = 0·044 and 0·053, respectively).     

Temporal disease dynamics and relative importance of sexual and asexual reproduction of grape downy mildew (Plasmopara viticola) in an isolated vineyard in the North Georgia Mountains,USA

The North Georgia Mountains are the southernmost region along the United States East Coast where European wine grapes (Vitis vinifera) are grown commercially. Epidemics of downy mildew, caused by Plasmopara viticola, are frequent and severe, but little is known about the epidemiology and population biology of the pathogen in this region. Disease monitoring in an experimental vineyard from 2015 to 2017 indicated that times of disease onset and progress rates were highly variable across years and cultivars. Oospores were observed microscopically, and simulation with a process-based model indicated presence of conditions favourable for oospore germination in the spring and early summer each year. A total of 409 P. viticola isolates collected over three  years were genotyped with seven microsatellite markers, revealing very high genotypic diversity, which when combined with the observation of oospores is indicative of a sexually reproducing population. Among the 409 isolates, 225 multilocus genotypes (MLGs) were identified, of which 164 were detected only once and 61 were repeated (clonal). Eight MLGs (represented by 28 isolates) were detected across years, suggesting the possibility of asexual overwintering of P. viticola in this region. Across sampling dates, the percentage of isolates belonging to nonrepeated (unique) MLGs ranged from 27.3% to 63.2%. Even towards the end of the annual epidemic, the percentage of isolates in nonrepeated MLGs was still relatively high, around 30%. These MLGs may have originated from oospores germinating late during the growing season, although incomplete sampling at earlier dates and contribution by immigration cannot be fully excluded.     

云南省小麦条锈菌不同地理亚群体的遗传结构分析

为明确云南省小麦条锈菌（Puccinia striiformis f. sp. tritici,Pst）在不同地理环境下的群体遗传结构,通过3种不同地理亚群体划分方式,即以县域（Group C）、区域（Group R）和海拔（Group E）对云南省537个Pst单孢系进行不同层次的群体划分,并利用12对SSR引物对其进行遗传多样性和群体遗传结构分析。结果显示,云南省Pst的遗传多样性水平在Group C的亚群体之间差异最大,且来自滇中及滇东北地区的Pst群体的遗传多样性较高。Group R和Group E的亚群体基因流及遗传分化结果表明,云南省Pst菌源交流频繁、遗传分化较小。系统进化树分析结果显示,滇东北与滇中Pst群体类似,滇东南与滇西Pst群体类似。Pst遗传组分呈现出由东向西、由北向南和自低海拔向高海拔变化的趋势,与云南省自东南向西北逐渐攀升的地形及地势吻合。Mantel检验结果表明地理距离与遗传距离不存在相关性,在8个县域亚群体、2个区域亚群体检测到有性生殖。表明来自滇中和滇东北地区的Pst群体具有更高的遗传多样性,地理隔离可能是滇西地区遗传多样性较低的成因,遗传分化发生在...     

Large subclonal variation in Phytophthora infestans populations associated with Ecuadorian potato landraces

The population of Phytophthora infestans on potato landraces in three provinces (Carchi, Chimborazo and Loja) of Ecuador was analysed. All isolates (n = 66) were of the A1 mating type. Simple sequence repeats (SSR) were used to assess the genetic diversity of the isolates. The P. infestans isolates from the potato landraces grouped in a single clade together with reference isolates belonging to the clonal lineage EC‐1. In the 66 SSR profiles obtained, 31 multilocus genotypes were identified. The 66 isolates constituted 49 different races according to the Solanum demissum differential set ( R1 to R11). The P. infestans population was complex and virulent on 4 to 11 R genes. Analysis showed that the subclonal variation in the Ecuadorian EC‐1 clone is increasing over time and is much larger than clonal variation in lineages in the Netherlands and Nicaragua, suggesting high mutation rates and little or no selection in Ecuador.     

Genetic variation,vegetative compatibility,and aggressiveness diversity of Diplodia bulgarica isolates from apple orchards in West Azarbaijan province of Iran

This study investigated inter-simple sequence repeat (ISSR), vegetative compatibility, and aggressiveness diversity in 101 isolates of Diplodia bulgarica recovered from apple trees displaying symptoms of canker and decline in West Azarbaijan province of Iran. Marker analyses revealed high within population diversity, low genetic differentiation, high gene flow, and sharing of multilocus genotypes (MLGs) among geographic populations. Moreover, clustering and multivariate analyses identified two highly differentiated genetic clusters with limited admixture between them. These findings may suggest that the pathogen has been introduced from two genetically divergent sources and has been moved within the region through infected materials. The large number of MLGs, low clonal fraction, and absence of a widely distributed dominant genotype may explain the occurrence of recombination in this pathogen. However, significant linkage disequilibrium in the populations and limited admixture between genetic clusters may indicate the rare occurrence of recombination in D. bulgarica populations in West Azarbaijan, and that the pathogen has not been in the province long enough to reach equilibrium. Vegetative compatibility analyses revealed the occurrence of anastomosis between nonself pairings and high vegetative compatibility group diversity within populations. All studied MLGs produced necrotic lesions on detached shoots of Red Delicious apple but differed in their aggressiveness levels. Our results provide new insights into genetic and phenotypic variation of D. bulgarica that can assist in developing management strategies. Our findings also highlight the vital need for quarantine measures and the production of healthy plant materials to prevent the introduction and spread of the pathogen in Iran.     

Genetic diversity of the pine pathogen Lecanosticta acicola in Slovenia and Croatia

Brown spot needle blight (BSNB), a disease of pine trees caused by the fungus Lecanosticta acicola, has been known in Slovenia since 2008 and in Croatia since 1975. Recent outbreaks in Slovenia prompted this study to compare L. acicola populations in these two neighbouring European countries. Sixty-nine isolates collected from three pine species (Pinus mugo, P. halepensis and P. nigra) were used to determine the phylogenetic relationships, genetic structure, and reproductive strategy of the pathogen. EF1-α sequences showed that Slovenian and Croatian isolates share a common ancestry with individuals from central and northern Europe. Population structure analysis revealed four distinct population clusters of L. acicola in these two countries, generally corresponding to their respective geographic location and host. An unequal ratio of mating types and a low overall genetic diversity in the population indicated a strong influence of asexual reproduction. Although some of the oldest recorded European occurrences of BSNB are from Croatia, this study provided no evidence that the population studied in Croatia was the source of the sampled outbreaks in Slovenia. Recent outbreaks of L. acicola in Slovenia are most likely due to introductions from other, yet to be identified, sources.     

Development,characterization and application of genomic SSR markers for the oat stem rust pathogen Puccinia graminis f. sp. avenae

Oat stem rust, caused by Puccinia graminis f. sp. avenae (Pga), is one of the most severe diseases of oats worldwide. Population studies are scarce for this pathogen, mainly due to the lack of polymorphic molecular markers suitable for genetic analysis. In this study, an Australian Pga isolate was sequenced, the abundance of simple sequence repeats (SSRs) was determined and PCR‐based polymorphic markers suitable for genetic diversity analysis were developed. The amplification of 194 primer pairs was initially assessed using a set of 12 isolates of different cereal rust species and their formae speciales. A high frequency of cross‐species amplification was observed for most markers; however, 36 SSRs were diagnostic for P. graminis only. A subset of 19 genome‐derived SSRs were deemed useful for genetic diversity analysis of Pga and were assessed on 66 Pga isolates from Australia, Brazil and Sweden. Brazilian and Australian isolates were characterized by one and two predominant clonal lineages, respectively. In contrast, the Swedish isolates, previously shown to undergo sexual recombination, were highly diverse (nine distinct genotypes out of 10 isolates) and divided into two subpopulations. The genome‐derived SSR markers developed in this study were well suited to the population studies undertaken, and have diagnostic capabilities that should aid in the identification of unknown rust pathogen species.     

Genetic structure of Italian populations of Pyrenochaeta lycopersici,the causal agent of corky root rot of tomato

Pyrenochaeta lycopersici is the causal agent of corky root rot, which is a serious disease worldwide that attacks the roots of tomato. A total of 139 isolates were sampled from eight locations in Italy and Israel and assigned to two molecular types (type 1 and type 2) based on internal transcribed spacer (ITS) sequences. These isolates were genotyped using amplified fragment length polymorphisms (AFLPs) to decipher the population structure. Based on this population structure analysis, three groups of P. lycopersici were identified. One group correlated to ITS type 1, while the other two correlated to ITS type 2. amova indicated high genetic divergence (F_ST = 0·40) between the Italian types 1 and 2. These data support the view that the two ITS types represent significant evolutionary entities, although there might be incomplete lineage sorting present. Some isolates of different ITS type were observed to have very similar multilocus AFLP profiles, and some genotypes were intermediate between the two ITS types. This suggests that parasexual hybridization between the two types has had a significant role in shaping the population structure of P. lycopersici. Finally, the average divergence among the populations within the ITS types was very high (F_SC = 0·710, P < 10^?5), probably due to strong genetic drift and founder effects combined with restricted migration.