Comparative analysis of pathogenic and nonpathogenic Fusarium oxysporum populations associated with banana on a farm in Minas Gerais,Brazil

Fusarium wilt is one of the most devastating diseases on banana. The causal agent, Fusarium oxysporum f. sp. cubense (Foc) is genetically diverse and its origin and virulence are poorly understood. In this study, pathogenic Foc isolates and nonpathogenic F. oxysporum isolates from Minas Gerais in Brazil were compared using EF‐1α and IGS sequences. This allowed the examination of the origin and evolutionary potential of Foc in a country outside the region of origin of the banana plant. Two different sequence types were found among Foc isolates. One appeared to be of local origin because it was identical to the sequence type of the largest group of nonpathogenic isolates. To explore if the ‘local’ Foc isolates had acquired pathogenicity either independently through coevolution with the host, or through horizontal gene transfer (HGT) of pathogenicity genes from other, probably introduced, Foc isolates, the presence and sequence of putative SIX effector genes were analysed. Homologues of SIX1, SIX3 and SIX8 were found. SIX1 sequences were identical and exclusively found in all pathogenic isolates, while variable ratios of sequences of multicopy gene SIX8 were found among nonpathogenic and different pathogenic isolates. This observation supports the HGT hypothesis. Horizontal transfer of genes between isolates of F. oxysporum has important implications for the development of reliable diagnostic tools and effective control measures. Full genome sequencing is required to confirm HGT and to further unravel the virulence mechanisms of forma specialis cubense.     

Variation in potential effector genes distinguishing Australian and non‐Australian isolates of the cotton wilt pathogen Fusarium oxysporum f.sp. vasinfectum

This study identified genes that distinguish Australian Fusarium oxysporum f.sp. vasinfectum (Fov) isolates from related co‐localized non‐pathogenic F. oxysporum isolates and from non‐Australian Fov isolates. One gene is a homologue of the F. oxysporum f.sp. lycopersici (Fol) effector gene SIX6, encoding a 215‐residue cysteine‐rich secreted protein. The Six6 proteins from Fol and Fov contained eight conserved cysteine residues, five of which occurred in the highly diverged 48‐amino‐acid region where FovSix6 differs from FolSix6 at 32 residues. Two other potential effector genes, PEP1 and PEP2, were identified in a cDNA library of Fov genes expressed during infection of cotton. The presence of FovSIX6 and other differences in DNA fingerprints clearly distinguished Australian Fov isolates from non‐Australian Fov isolates and these differences further support the hypothesis based on earlier phylogenetic analysis that Australian Fov is different from Fov in other cotton‐growing areas. A specific diagnostic for Fov based on FovSIX6 is described.     

Morphology,phylogeny and pathogenicity of Fusarium species from Sansevieria trifasciata in Malaysia

Leaf blight is a common disease affecting Sansevieria trifasciata in many countries, including Malaysia. In the present study, Fusarium isolates were consistently recovered from the diseased leaves collected from various locations throughout the country. Based on morphology and multigene phylogenetic analysis using mitochondrial small subunit (mtSSU), intergenic spacer region (IGS) and translation elongation factor 1-α (TEF1-α) gene sequences, seven Fusarium species were identified, with F. oxysporum being the most prevalent (67.6%) among 34 isolates. Pathogenicity tests resulted in the discovery of pathogenic isolates that belonged to F. oxysporum, F. proliferatum, and F. pseudocircinatum, whereas all isolates of F. brachygibbosum, F. concentricum, F. mangiferae, and F. solani were nonpathogenic. The results suggest that several Fusarium species are accountable for causing disease on S. trifasciata in Malaysia.     

The elegans fusaria causing wilt disease of carnation. II. Distinction of vegetative compatibility groups

The vegetative compatibility patterns among isolates ofElegans fusaria causing wilt disease of carnation were investigated. Nitrate non-utilizing mutants were generated from 16 isolates labelledF. redolens, nine of which came from carnation, and from 33 isolates labelledF. oxysporum, 19 of which came from carnation. Pairings of the mutants revealed five vegetative compatibility groups among the isolates from carnation, corresponding withF. oxysporum f.sp.dianthi race 1 (VCG1), race 2 (VCG2) and race 4 (VCG3),F. redolens f.sp.dianthi (VCG4) andF. redolens isolates from foot rot-diseased carnations (VCG5). Besides three isolates typical ofF. redolens, VCG4 comprised a now slightly deviating subculture of the type isolate ofF. redolens f.sp.dianthi of which the cultural characteristics correspond toF. oxysporum instead ofF. redolens. This observation may be taken to support previous conclusions that the distinction between both taxa is not justified. Otherwise, the compatibility patterns did not provide decisive evidence to accept or reject conspecificity of both taxa. Isolates from carnation did not form heterokaryons with other formae speciales ofF. oxysporum.Samenvatting De vegetatieve compatibiliteitspatronen bij isolaten vanElegans-fusaria die verwelkingsziekte bij anjer veroorzaken werden onderzocht. Van 16 isolaten vanF. redolens, waarvan negen afkomstig van anjers, en van 33 isolaten vanF. oxysporum, waarvan 19 afkomstig van anjers, werden mutanten gegenereerd die zonder een organische stikstofbron geen luchtmycelium meer konden vormen. Paringen tussen mutanten van isolaten afkomstig van anjers brachten een vijftal vegetatieve compatibiliteitsgroepen aan het licht, die overeenkwamen metF. oxysporum f.sp.dianthi fysio 1 (VCG 1), fysio 2 (VCG 2) en fysio 4 (VCG3),F. redolens f.sp.dianthi (VCG4) enF. redolens isolaten afkomstig van aan voetrot lijdende anjers (VCG5). Naast drie voorF. redolens karakteristieke isolaten omvatte VCG4 ook een afwijkende subculture van het type-isolaat vanF. redolens f.sp.dianthi, die in cultuureigenschappen overeen kwam metF. oxysporum in plaats vanF. redolens. Deze waarneming geeft enige steun aan eerdere conclusies dat het onderscheid tussen beide taxa niet gerechtvaardigd is. Daarbuiten gaven de compatibiliteitspatronen geen uitsluitsel over de mogelijke conspecificiteit van beide taxa. Isolaten afkomstig van anjers vormden geen heterokaryons met andere formae speciales vanF. oxysporum.     

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense

Fusarium oxysporum f. sp. cubense (Foc), causal agent of fusarium wilt of banana, is among the most destructive pathogens of banana and plantain. The development of a molecular diagnostic capable of reliably distinguishing between the various races of the pathogen is of key importance to disease management. However, attempts to distinguish isolates using the standard molecular loci typically used for fungal phylogenetics have been complicated by a poor correlation between phylogeny and pathogenicity. Among the available alternative loci are several putative effector genes, known as SIX genes, which have been successfully used to differentiate the three races of F. oxysporum f. sp. lycopersici. In this study, an international collection of Foc isolates was screened for the presence of the putative effector SIX8. Using a PCR and sequencing approach, variation in Foc‐SIX8 was identified which allowed race 4 to be differentiated from race 1 and 2 isolates, and tropical and subtropical race 4 isolates to be distinguished from one another.     

The Elegans fusaria causing wilt disease of carnation. I. Taxonomy

The distinction of the wilt disease pathogen of carnationFusarium (oxysporum var.)redolens fromF. oxysporum (var.oxysporum) is considered. Previous reports that isolates of both taxa cause indistinguishable diseases in carnation are confirmed.F. (oxysporum var.)redolens andF. oxysporum were found to form one variable complex on morphological criteria. Apparently, host specialization rather than morphological variation reflects the evolutionary relationships in theFusarium sectionElegans. The distinction ofF. redolens fromF. oxysporum does therefore not seem justified, neither at specific nor at varietal level.Samenvatting Het onderscheid tussenFusarium (oxysporum var.)redolens enF. (oxysporum var.)oxysporum als verwekkers van verwelkingsziekte bij anjer wordt ter discussie gesteld. Fytopathologisch onderzoek bevestigde vermeldingen in de literatuur dat voor anjer pathogene isolaten van beide soorten ziekten veroorzaken die niet te onderscheiden zijn; dit is ook bekend voor andere gewassen. Op morfologische gronden blekenF. (oxysporum var.)redolens enF. oxysporum één variabel complex te vormen. Kennelijk geeft de pathogene specialisatie inFusarium sectieElegans de evolutionaire verwantschappen beter weer dan de morfologische variatie. Het onderscheiden vanF. redolens naastF. oxysporum is daarom noch als soort, noch als variëteit gerechtvaardigd.     

Characterisation ofFusarium oxysporum isolated from carnation in Australia based on pathogenicity,vegetative compatibility and random amplified polymorphic DNA (RAPD) assay

Isolates ofF. oxysporum collected from symptomless carnation cuttings from Australian carnation growers properties, together with isolates from national collections, were screened for pathogenicity and grouped according to vegetative compatibility and random amplified polymorphic DNA (RAPD) patterns. The collection of 82 Australian isolates sorted into 23 different vegetative compatibility groups (VCGs). Of 69 isolates tested for pathogenicity, 24 were pathogenic to carnations, while the remaining 45 were non-pathogenic. All pathogenic isolates were within two VCGs, one of which was also compatible with an isolate obtained from an international culture collection, and which is known to represent VCG 0021 and race 2. Race status of the two pathogenic VCGs remains unknown. The RAPD assay revealed distinct DNA banding patterns which could distinguish pathogenic from non-pathogenic isolates as well as differentiate between isolates from the two pathogenic VCGs.     

Fusarium Redolens f.sp asparagi, Causal Agent of Asparagus Root Rot, Crown Rot and Spear Rot

Two Fusarium species, F. oxysporum f.sp. asparagi and F. proliferatum, are known to be involved in the root and crown rot complex of asparagus. We have investigated reports on the involvement of F. redolens, a third species, which until recently was considered conspecific with F. oxysporum because of morphological similarities. RFLP analysis of the rDNA internal transcribed spacer region and AFLP fingerprinting identified eight strains from asparagus unambiguously as F. redolens. Four of these were tested and found to be pathogenic to asparagus either in this study (two strains) or in a previous one in which they were classified as F. oxysporum (three strains). Disease symptoms and disease development were the same as with F. oxysporum f.sp. asparagi and F. proliferatum. Present data and literature reports identify F. redolens as a host-specific pathogen involved in root, crown and spear rot of asparagus. The pathogen is formally classified as F. redolens Wollenw. f.sp. asparagi Baayen.     

Phylogenetic relationships and virulence assays of Fusarium secorum from sugar beet suggest a new look at species designations

Fusarium spp. are responsible for significant yield losses in sugar beet (Beta vulgaris) with Fusarium oxysporum f. sp. betae most often reported as the primary causal agent. Recently, a new species, F. secorum, was reported to cause disease in sugar beet but little is known on the range of virulence within F. secorum or how this compares to the virulence and phylogenetic relationships previously reported for Fusarium pathogens of sugar beet. To initiate this study, partial translation elongation factor 1-α (TEF1) sequences from seven isolates of F. secorum were obtained and the data were added to a previously published phylogenetic tree that includes F. oxysporum f. sp. betae. Unexpectedly, the F. secorum strains nested into a distinct group that included isolates previously reported as F. oxysporum f. sp. betae. These results prompted an expanded phylogenetic analysis of TEF1 sequences from genomes of publicly available Fusarium spp., resulting in the additional discovery that some isolates previously reported as F. oxysporum f. sp. betae are F. commune, a species that is not known to be a sugar beet pathogen. Inoculation of sugar beet with differing genetic backgrounds demonstrated that all Fusarium strains have a significant range in virulence depending on cultivar. Taken together, the data suggest that F. secorum is more widespread than previously thought. Consequently, future screening for disease resistance should rely on isolates representing the full diversity of the Fusarium population that impacts sugar beet.     

Molecular characterisation of vegetative compatibility groups in Fusarium oxysporum f. sp. radicis-lycopersici and f. sp. lycopersici by random amplification of polymorphic DNA and microsatellite-primed PCR

Random amplification of polymorphic DNA (RAPD-PCR) analysis was conducted on 48 isolates of Fusarium oxysporum f. sp. radicis-lycopersici (F.o.r.l.) from different geographic regions, representing all known vegetative compatibility groups (VCGs) except VCG 0097 and VCG 0099 and on eight isolates of F.oxysporum f. sp. lycopersici (F.o.l.), representing VCGs 0030, 0031, 0032 and 0033. Upon UPGMA (unweighted pair-group method with arithmetic averages) analysis of 86 RAPD-PCR markers generated by 16 informative primers and 44 markers obtained with eight microsatellite primers, a close relatedness was evident for F.o.r.l. isolates in VCGs 0090, 0092, 0096, and, to a lesser extent, for those in VCG 0093. Representatives of VCG 0091 formed a distinct group, while F.o.r.l. isolates in VCGs 0094 and 0098 were not distinguishable by the tested markers, most of which were also shared by F.o.l. isolates belonging to VCGs 0031 and 0033. F.o.l. isolates in VCGs 0030 and 0032 shared most of the molecular markers. The correlation between RAPD-PCR and microsatellite genetic distance was highly significant (R² = 0.77; P by Mantel test < 0.001). The molecular variability observed in both formae speciales is discussed in relation to the development of F.o.r.l.- and F.o.l.-specific diagnostic tools.     

Phylogenetic relationships between the lettuce root rot pathogen Fusarium oxysporum f. sp. lactucae races 1, 2, and 3 based on the sequence of the intergenic spacer region of its ribosomal DNA

The genetic relationship between the vegetative compatibility groups (VCGs) and between physiological races of Fusarium oxysporum f. sp. lactucae (FOL), the causal pathogen of lettuce root rot, was determined by analyzing the intergenic spacer (IGS) region of its ribosomal DNA. A total of 29 isolates containing a type strain were tested: 24 Japanese isolates, 2 Californian isolates, and 3 Italian isolates. Three races (races 1, 2, and 3) were found in Japan, and race 1 was also distributed in California and Italy. Races 1, 2, and 3 each belonged to a distinct VCG: VCG-1, VCG-2, and VCG-3 (VCG-3-1, VCG-3-3), respectively. Phylogenetic (neighbor-joining) analysis of the IGS sequences revealed that races 1, 2, and 3 coincided with three phylogenetic groups (PG): PG-1, PG-2, and PG-3, respectively. These results indicate that the three races are genetically quite different and have a strong correlation with VCGs and phylogenetic groupings. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession no. AB195218     

Identification,pathogenicity and community dynamics of fungi and oomycetes associated with pea root rot in northern France

The pea root rot complex is a major concern for green pea production worldwide. This study aimed at characterizing its composition and dynamics throughout a cropping season in northern France. To this end, fungi and oomycetes were isolated from green pea plant roots with symptoms sampled at the flowering stage in 22 fields in 2017, and at the pea emergence, elongation and flowering stages in two fields in 2018. Out of 646 isolates collected, 317 were identified using molecular markers. Fusarium oxysporum, F. solani and F. redolens were highly predominant. Pathogenicity tests separated the isolates into four aggressiveness groups. F. solani isolates were the most aggressive. Phylogenetic analysis of their TEF1 sequences showed that they mainly belonged to the F. pisi lineage, and that F. oxysporum isolates were genetically close to isolates from the UK that did not belong to the forma specialis pisi. In addition, several Clonostachys rhizophaga isolates are reported for the first time to cause pea root rot. The oomycetes were rarely found and were represented by a few Pythium spp. isolates. Lastly, this study shows that the fungal and oomycete communities associated with pea root rot change during the cropping season. The level of dissimilarity of the root-rot-associated communities decreased throughout the cropping season towards a more similar composition at the flowering stage, dominated by F. solani, F. oxysporum and F. redolens. The proportion of nonpathogenic to weakly pathogenic isolates decreased progressively during the growing season in favour of moderately to highly pathogenic isolates.     

Fusarium commune associated with wilt and root rot disease in rice

Wilt and root rot disease in plants has been caused mainly by Fusarium species. Previous studies reported that members of the Fusarium oxysporum species complex (FOSC) were usually associated with this disease, but there has been no report of it being caused in rice by specific Fusarium species. However, in this study, Fusarium commune was identified and characterized as a causal agent of wilt and root rot disease of rice. Four Fusarium isolates (BD005R, BD014R, BD019R, and BD020R) were obtained from different parts (root, stem, and seeds) of diseased rice plants. In morphological studies, these isolates produced key characteristics of F. commune, such as long and slender monophialides, polyphialides, and abundant chlamydospores. In molecular studies, the isolates were identified as F. commune based on sequences of the translation elongation factor 1-α (TEF1) gene that had 99.7%–100% sequence identity with the reference strain F. commune NRRL 28058. The phylogenetic tree showed that all four isolates belonged to the F. commune clade. A mating type test determined that three isolates carried MAT1-2. Their teleomorph stage was still unknown. Pathogenicity assays showed that all the isolates produced wilt and root rot symptoms and the isolate BD019R was observed as the most virulent among the isolates. To our knowledge, this is the first report of F. commune causing wilt and root rot disease on rice.     

Phylogenetic relationships of Fusarium oxysporum f. sp. melonis in Iran

Fusarium wilt of melon caused by Fusarium oxysporum f. sp. melonis is a destructive fungal disease in melon growing regions. Isolates of F. oxysporum obtained from six major melon producing provinces in Iran, from melons and other hosts, were characterized based on pathogenicity to melon, vegetative compatibility groups (VCGs) and nuclear ribosomal DNA intergenic spacer (IGS) sequencing. Thirty-four of 41 isolates from Iran in this study were identified as race 1,2 which belonged to either VCG 0134 or an unassigned VCG, which based on IGS sequencing grouped with the VCG 0135 tester isolate. The seven remaining isolates were identified as nonpathogenic to melon belonging to two undescribed VCGs. Based on sequence analyses of the IGS region of Iranian and foreign isolates, nine lineages were identified, each including one VCG. The separation of VCGs into distinct lineages based on IGS sequences is mostly consistent with Repetitive extragenic palindromic PCR (Rep-PCR) results. Exceptions are VCGs 0130 and 0131, which could be differentiated with IGS sequences, but not with Rep-PCR. Different races from the USA, France and Iran associated with VCG 0134 grouped into one IGS lineage but could be differentiated with Rep-PCR, suggesting that this VCG is more diverse than previously thought. Given the long history of melon cultivation in Iran and the Rep-PCR diversity of isolates belonging to this VCG, it could be speculated that VCG 0134 perhaps evolved in Iran.     

Fusarium oxysporum,F. proliferatum and F. redolens associated with basal rot of onion in Finland

In recent years in Finland, Fusarium infections in onions have increased, both in the field and in storage, and Fusarium species have taken the place of Botrytis as the worst pathogens causing post‐harvest rot of onion. To study Fusarium occurrence, samples were taken from onion sets, harvested onions and also from other plants grown in the onion fields. Isolates of five Fusarium species found in the survey were tested for pathogenicity on onion. Fusarium oxysporum was frequently found in onions and other plants, and, of the isolates tested, 31% caused disease symptoms and 15% caused growth stunting in onion seedlings. Fusarium proliferatum, a species previously not reported in Finland, was also identified. Over 50% of the diseased onion crop samples were infected with F. proliferatum, and all the F. proliferatum isolates tested were pathogenic to onion. Thus, compared to F. oxysporum, F. proliferatum seems to be more aggressive on onion. Also some of the F. redolens isolates were highly virulent, killing onion seedlings. Comparison of the translation elongation factor 1α gene sequences revealed that the majority of the aggressive isolates of F. oxysporum f. sp. cepae group together and are distinct from the other isolates. Incidence and relative proportions of the different Fusarium species differed between the sets and the mature bulbs. More research is required to determine to what extent Fusarium infections spoiling onions originate from infected onion sets rather than the field soil.     

Genetic diversity and pathogenicity of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> isolated from wilted Welsh onion in Japan

Thirty isolates of Fusarium oxysporum from wilted Welsh onion plants were examined for their diversity in nucleotide sequences of the ribosomal DNA (rDNA) intergenic spacer (IGS) region and for pathogenicity with regard to five Welsh onion cultivars. Phylogenetic analysis based on the IGS sequences revealed polyphyletic origins of the isolates and a relationship between phylogeny and pathogenicity; low virulence isolates differed genetically from those with high and moderate virulence. Mating type analysis revealed that all F. oxysporum isolates were MAT1-1 idiomorphs, suggesting that the pathogens may be clonal in the fields examined.     

Germination of Fusarium oxysporum in root exudates from tomato plants challenged with different Fusarium oxysporum strains

The response of microconidia from pathogenic and non-pathogenic Fusarium oxysporum to root exudates from tomato plants inoculated with different pathogenic and non-pathogenic F. oxysporum strains was studied. Root exudates from non-inoculated tomatoes highly stimulated the microconidial germination of the two tomato pathogens, F. oxysporum f.sp. lycopersici strain Fol 007 and F. oxysporum f.sp. radicis-lycopersici strain Forl 101587. In root exudates from tomato plants challenged with the pathogen Fol 007 the microconidial germination of Fol 007 was increased, whereas in root exudates from plants challenged with Forl 101587 the microconidial germination of Fol 007 was reduced. Root exudates of tomato plants challenged with the non-pathogenic unspecific F. oxysporum strain Fo 135 and the biocontrol strain Fo 47 clearly reduced microconidial germination of the pathogenic strain Forl 101587. Moreover, the microconidial germination rate of the biocontrol strain Fo 47 was increased in the presence of root exudates of tomato plants challenged with the tomato wilt pathogen Fol 007. These results indicate that pathogenic and non-pathogenic F. oxysporum strains alter the root exudation of tomato plants differently and consequently the fungal propagation of pathogenic and non-pathogenic F. oxysporum strains in the rhizosphere is affected differently.     

Genetic diversity and pathogenicity of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> isolated from wilted rocket plants in Italy

Thirty-six isolates of Fusarium oxysporum originated from Eruca vesicaria and Diplotaxis tenuifolia together with eight reference strains belonging to the formae speciales raphani, matthioli and conglutinans, typical on the Brassicaceae family, were tested for pathogenicity on two species of rocket plants (E. vesicaria L., syn. E. sativa, cv. ‘Rucola coltivata’; and D. tenuifolia cv. ‘Winter’) cultivated in the glasshouse. The results showed that different isolates were slightly, moderately or highly virulent. The strains were examined for differences in the nucleotide sequence of the ribosomal DNA (rDNA) intergenic spacer (IGS) region, about 2.5 kb long. The phylogenetic (neighbor-joining) analysis performed on the isolates enabled identification of four different groups, named I, II, III and IV. Thirty-one isolates out of 36 clustered in group I and were genetically similar to F. oxysporum f.sp. raphani. By considering the pathogenicity of the strains included in Group I, a partial host specialization could be observed: the average disease index of the isolates from D. tenuifolia was higher on wild rocket, whereas the average disease index of the isolates from E. vesicaria was higher on cultivated rocket. Moreover, isolates from cultivated rocket showed, on average, a higher degree of aggressiveness than the isolates from wild rocket. Concerning Group I, the sequence analysis confirmed the homogeneity of the population, with only five parsimony-informative SNPs and five haplotypes. Twenty-six out of 31 isolates belonged to haplotype 1. Groups II and III were genetically similar to strains of F. oxysporum f.sp. matthioli. Three other strains, not pathogenic or with a medium level of virulence, clustered together in Group 4, but their sequence was distant from that of other formae speciales. The pathogenicity and IGS analysis confirmed the presence of virulence variation and genetic diversity among the F. oxysporum isolates studied. To our knowledge, this is the first report of differentiation of formae speciales of F. oxysporum on rocket plants by IGS analysis.     

Detection and quantification of Fusarium commune in host tissue and infested soil using real‐time PCR

Fusarium wilt caused by Fusarium commune is a major limiting factor for Chinese water chestnut (Eleocharis dulcis) production in China. A SYBR Green I real‐time quantitative polymerase chain reaction (qPCR) assay was developed based on the mitochondrial small subunit rDNA of F. commune. Assay specificity of the FO1/FO2 primer set was tested on 41 fungal isolates, and only a single PCR band of c. 178 bp from F. commune was amplified. The detection limits of the assay were 1 fg μL^?1 pure F. commune genomic DNA, 1 pg μL^?1 F. commune genomic DNA mixed with host plant genomic DNA (0·5 ng μL^?1), and 1000 conidia/g soil (artificially inoculated). The amount of F. commune DNA in stem tissues detected by qPCR was significantly correlated with the disease severity (DS) ratings; however, the qPCR assay showed no significant positive correlation between spore densities in soil of different fusarium wilt DS groupings and the DS ratings. The qPCR assay was further applied to 76 soil samples collected from commercial fields of E. dulcis during the 2011 and 2012 growing seasons. The spore density of F. commune detected was positively correlated with disease index in the 2012 growing season but not in 2011. The qPCR method can be used for rapid and specific detection of F. commune in plant and soil samples, which will facilitate monitoring of the pathogen and improvement of disease management.     

Phylogenetic position and nucleotide diversity of Fusarium oxysporum f. sp. vanillae worldwide based on translation elongation factor 1α sequences

Fusarium oxysporum f. sp. vanillae is considered the most important fungus affecting vanilla crops around the world, causing rot on vanilla roots and stems. Previous studies showed that the ability to infect vanilla plants is a polyphyletic trait among strains of the Fusarium oxysporum species complex (FOSC). The same studies proposed a single origin for F. oxysporum f. sp. vanillae isolates sampled from Mexico, the centre of origin and distribution of vanilla. The aim of this work was to test the hypothesis of the monophyletic origin of a wider sample of isolates of F. oxysporum f. sp. vanillae infecting Mexican vanilla and estimate nucleotide diversity of pathogen isolates from the main vanilla‐producing countries. Sequence data for the TEF1α gene from 106 isolates was assembled. The phylogenetic analyses suggest that some Mexican isolates of F. oxysporum f. sp. vanillae belong in two well‐supported clades, mixed with isolates from Madagascar, Indonesia, Réunion and Comoros. The phylogenetic position of other Indonesian and Mexican isolates is unresolved. Estimations of nucleotide diversity showed that the population from Mexico is genetically more diverse than the other three populations from Madagascar, Indonesia and Réunion. The results support a polyphyletic origin of vanilla‐infecting isolates of F. oxysporum worldwide, and also reject the proposition that Mexican isolates have a single origin. The phylogenetic optimizations over the strict consensus tree of the ability to infect vanilla plants suggest that pathogenic strains around the world are the product of multiple shifts of pathogenesis and dispersion events.