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Plant pathogens secrete effector molecules during host invasion to promote colonization. However, some of these effectors become recognized by host receptors to mount a defence response and establish immunity. Recently, a novel resistance was identified in wild tomato, mediated by the single dominant V2 locus, to control strains of the soil-borne vascular wilt fungus Verticillium dahliae that belong to race 2. With comparative genomics of race 2 strains and resistance-breaking race 3 strains, we identified the avirulence effector that activates V2 resistance, termed Av2. We identified 277 kb of race 2-specific sequence comprising only two genes encoding predicted secreted proteins that are expressed during tomato colonization. Subsequent functional analysis based on genetic complementation into race 3 isolates and targeted deletion from the race 1 isolate JR2 and race 2 isolate TO22 confirmed that one of the two candidates encodes the avirulence effector Av2 that is recognized in V2 tomato plants. Two Av2 allelic variants were identified that encode Av2 variants that differ by a single acid. Thus far, a role in virulence could not be demonstrated for either of the two variants.

The host range of Verticillium dahliae, causal agent of verticillium wilt in various dicot plants, differs among strains, but the mechanism responsible for the host-specific pathogenicity of the strains remains unclear. In this study, protoplast fusion of a tomato-pathogenic and a nonpathogenic strain of V. dahliae was used for genetic recombination of the isolates to localize the fungal genomic region involved in the pathogenicity on tomato. Twenty fusion strains resistant to two antibiotics, hygromycin B and geneticin, were obtained by protoplast fusion between two parental strains resistant to one of these antibiotics. Genomic Southern hybridization probed with telomere sequences revealed that these fusion strains were haploid and inherited chromosomes from both parental strains. Eight fusion strains were pathogenic on tomato. In PCR analysis of the fusion strains using DNA markers specific to a parental strain TV103, two DNA markers (T12 and VDA787) were amplified only in strains pathogenic on tomato. The genomic region mapped around these two DNA markers for a parental strain pathogenic on tomato was similar to that on the map for chromosome 3 of a reference strain (JR2). The analysis of 35 fusion strains with additional DNA markers revealed that one of the markers was completely accorded with pathogenicity of the strains on tomato. Therefore, the genomic region around this DNA marker is possibly involved in pathogenicity of V. dahliae on tomato.

Berkeleyomyces rouxiae, a causal agent of black root rot of lettuce, is morphologically and physiologically indistinguishable from the closely related species B. basicola. PCR primers specific for these species were designed based on the nucleotide sequence of genes specific to the species. The primer pair specific to B. rouxiae did not amplify DNA of other plant pathogens that invade root or stem base of lettuce and was useful for diagnosis and quantitating the pathogen from lettuce root tissue.

In August 2016, lettuce plants (Lactuca sativa) cultivated in Gunma Prefecture became stunted and often wilted. Dark brown to black lesions were observed on roots of diseased plants. Most small feeder roots were lost. Fungi isolated from lesions on roots were identified as Berkeleyomyces rouxiae based on their morphological and genetic characteristics. Pathogenicity of this fungus on lettuce was confirmed by inoculation and reisolation. This report is the first of black root rot caused by B. rouxiae on lettuce in Japan.

Rosellinia necatrix causes white root rot in various plants, including the Japanese pear. PCR assays using specific primers for R. necatrix detected the fungus on the roots of nine weed species from infested pear orchards. The soil inoculation experiment revealed that the spread of R. necatrix was similar between weed-mowed and non-weed-mowed treatments under field conditions. The spread of R. necatrix was also observed when rescue grass (Bromus catharticus) was grown in planter boxes under greenhouse conditions, but was limited without the grass, suggesting that some weeds facilitate the spread of R. necatrix in soil.

SUMMARYPlant pathogens secrete effector molecules during host invasion to promote host colonization. However, some of these effectors become recognized by host receptors, encoded by resistance genes, to mount defense response and establish immunity. Recently, a novel resistance was identified in tomato, mediated by the single dominant V2 locus, to control strains of the soil-borne vascular wilt fungus Verticillium dahliae that belong to race 2. We performed comparative genomics between race 2 strains and resistance-breaking race 3 strains to identify the avirulence effector that activates V2 resistance, termed Av2. We identified 277 kb of race 2-specific sequence comprising only two genes that encode predicted secreted proteins, both of which are expressed by V. dahliae during tomato colonization. Subsequent functional analysis based on genetic complementation into race 3 isolates confirmed that one of the two candidates encodes the avirulence effector Av2 that is recognized in V2 tomato plants. The identification of Av2 will not only be helpful to select tomato cultivars that are resistant to race 2 strains of V. dahliae, as the corresponding V2 resistance gene has not yet been mapped, but also to monitor adaptations in the V. dahliae population to deployment of V2-containing tomato cultivars in agriculture.

Verticillium wilt is a major concern in vegetable production due to its broad host range, world-wide distribution, vascular colonization, and resilient microsclerotia. This study was conducted to evaluate the growth and tolerance to Verticillium dahliae in two tomato cultivars inoculated with arbuscular mycorrhizal fungi (AMF)- Rhizophagus intraradices 15S-1 and an endophytic fungus- Penicillium pinophilum EU0013. In a randomized factorial layout, seedlings of tomato cultivars (Momotaro, Rodeo) were inoculated with beneficial microbes and V. dahliae pathogen and raised until maturity under greenhouse condition. In vitro dual culture indicated the growth inhibition of V. dahliae by P. pinophilum after one month on PDA media. Root colonization by R. intraradices and P. pinophilum were modulated in response to V. dahliae in a cultivar-dependent manner. While Momotaro showed greater foliar and internal disease symptoms than Rodeo, P. pinophilum and R. intraradices significantly reduced disease incidence, compared to control. Verticillium-induced reductions in root and fruit dry weights in Rodeo and Momotaro were reduced by P. pinophilum, while AMF generally boosted fruit weights. Co-inoculation of R. intraradices and P. pinophilum did not consistently improve host growth indices compared to single inoculation, and modulations in mineral element nutrition by both beneficial microbes in response to V. dahliae was cultivar dependent. In Momotaro, R. intraradices and P. pinophilum increased SlSOD2, SlSOD5 and SlSOD9 gene expression, but this was not generally the case in Rodeo, where lower expression levels were observed. Cultivar-dependent modulation of root colonization, element nutrition, and SlSODs gene expression, by R. intraradices and P. pinophilum underpin their promotion of host growth and tolerance to verticillium wilt.

Plectosphaerella rot affects hydroponically grown lettuce, especially those grown using deep flow technique. Plectosphaerella species such as P. pauciseptata and P. cucumerina are reported as causal agents of this disease. However, the relation between fungal lineage and pathogenicity on lettuce has been unclear. From inoculation tests, we discovered that various lineages of Plectosphaerella can infect lettuce tissues. Even strains isolated from non-lettuce plants were pathogenic on lettuce. Furthermore, various lettuce cultivars were equally susceptible to a particular strain. These results indicate that strains from a wide lineage of Plectosphaerella can be pathogenic on various lettuce cultivars.

Unknown spot diseases were observed on calla lily leaves and spathes in Japan. Fungi isolated from spots were identified as Plectosphaerella sp. based on morphological characteristics. Inoculation and reisolation confirmed the pathogenicity of the fungi on calla lily. The fungi were distinct from known species of Plectosphaerella in terms of rDNA nucleotide sequences, growth rate, and specific pathogenicity on Zantedeschia species. This report is the first in the world literature of a spot disease of calla lily caused by Plectosphaerella sp. Management of this pathogen is important for calla lily cultivation because it degrades spathes having high commercial value.

Severe fruit rot of sweet pepper was found in Shimane, Hyogo, Chiba, Toyama, and Nagano prefectures, Japan from 2005 to 2011. Dark, sunken spots with concentric rings of orange conidial masses appeared on fruits. Pathogenic isolates from diseased fruits in the prefectures were identified as Colletotrichum scovillei. This species was added to the pathogens of sweet pepper anthracnose in Japan. The representative isolate was pathogenic to sweet pepper, tomato and chili pepper fruits, kidney bean pod, azuki bean, pea and strawberry leaves, but a caused no symptoms on cucumber or carrot in inoculation tests.

We developed a real-time PCR assay using a TaqMan probe (TM-qPCR) for specific detection and quantification of Phomopsis sclerotioides, causal agent of black root rot of cucurbit crops. The design of the primer sets and hybridization probe was based on the internal transcribed spacer region of the ribosomal DNA. The TM-qPCR assay was compared with a conventional, standard PCR (sPCR) assay and on a quantitative real-time PCR (SG-qPCR) assay based on SYBR Green I. The TM-qPCR assay had a detection limit of ca. 0.4 fg of P. sclerotioides DNA, which was approximately 100 times more sensitive than the sPCR assay and almost equivalent to the SG-qPCR assay. The TM-qPCR and SG-qPCR assays both were able to detect various quantities of P. sclerotioides DNA from diseased plants and infested soils, including DNA levels that were not detectable by the sPCR assay. However, the TM-qPCR was advantageous for samples containing PCR-inhibiting substances because its multiplex real-time PCR function allows the adjustment of cycle threshold values with an internal control. Based on the high specificity and sensitivity required for analyzing DNA in natural samples, the newly developed TM-qPCR assay was the most reliable tool for rapidly detecting and quantifying P. sclerotioides in plant and soil samples.

Although wilt diseases of various plants by Verticillium dahliae occur worldwide, Verticillium wilt of lettuce is relatively new and rare. In 2009, this disease appeared suddenly in commercial fields in Ibaraki Prefecture, Japan. To investigate the cause of the disease, we characterized each lettuce isolate for pathogenicity, mating types, and genetic characteristics and found two types of V. dahliae. A population that included at least two types of V. dahliae was the putative infection source of the disease. Effective management systems against V. dahliae isolates of different races and having different host ranges are necessary.

Rot diseases of hydroponically cultured leaf lettuce, coriander, and chervil were found in Chiba Prefecture, Japan. Stems and petioles of the three diseased plants became brown or black with a soft rot, and vascular parts of the stems became discolored. Seemingly similar fungi were isolated from the diseased plants. Pathogenicity of these fungal isolates to each plant was demonstrated by inoculation tests. The fungi were identified as Plectosphaerella pauciseptata based on morphological and cultural characters. This identification was supported by phylogenetic analysis with rDNA ITS1-5.8S-ITS2 regions. The diseases were named Plectosphaerella rot (Plectosphaerella huhai-byo in Japanese) of lettuce, coriander, and chervil.

The pea pathogen Fusarium oxysporum f. sp. pisi is able to detoxify pisatin produced as a defense response by pea, and the gene encoding this detoxification mechanism, FoPDA1, was 82% identical to the cytochrome P450 pisatin demethylase PDA1 gene in Nectria haematococca. A survey of F. oxysporum f. sp. pisi isolates demonstrated that, as in N. haematococca, the PDA gene of F. oxysporum f. sp. pisi is generally located on a small chromosome. In N. haematococca, PDA1 is in a cluster of pea pathogenicity (PEP) genes. Homologs of these PEP genes also were found in the F. oxysporum f. sp. pisi isolates, and PEP1 and PEP5 were sometimes located on the same small chromosomes as the FoPDA1 homologs. Transforming FoPDA1 into a pda– F. oxysporum f. sp. lini isolate conferred pda activity and promoted pathogenicity on pea to some transformants. Different hybridization patterns of FoPDA1 were found in F. oxysporum f. sp. pisi but these did not correlate with the races of the fungus, suggesting that races within this forma specialis arose independently of FoPDA1. FoPDA1 also was present in the formae speciales lini, glycines, and dianthi of F. oxysporum but they had mutations resulting in nonfunctional proteins. However, an active FoPDA1 was present in F. oxysporum f. sp. phaseoli and it was virulent on pea. Despite their evolutionary distance, the amino acid sequences of FoPDA1 of F. oxysporum f. sp. pisi and F. oxysporum f. sp. phaseoli revealed only six amino acid differences, consistent with a horizontal gene transfer event accounting for the origin of these genes.

We developed polymerase chain reaction (PCR) assays to detect and quantify Phomopsis sclerotioides, the causal agent of black root rot of cucurbits. We used internal transcribed spacers 1 and 2 of the ribosomal DNA (rDNA) from representative isolates to search for target sequences. Primer pairs were selected after testing against 40 fungal isolates including 13 Ph. sclerotioides isolates, 9 Phomopsis isolates other than Ph. sclerotioides, and 18 soilborne fungi that were either pathogenic or nonpathogenic to cucurbits. Conventional PCR assays with the primer pair of CPs-1 (forward) and CPs-2 (reverse) produced target DNA amplicons from all Ph. sclerotioides isolates but none of the other isolates tested. From soil and root samples collected from fields naturally infested with black root rot of cucumber and melon, the CPs-1/CPs-2 primer pair successfully amplified target DNA fragments in conventional PCR assays. Moreover, we applied the CPs-1/CPs-2 primer pair in a real-time PCR assay with SYBR Green I, and PCR-amplified products were successfully quantified by reference to a standard curve generated by adding known amounts of target DNA. Target Ph. sclerotioides DNA fragments were similarly detected in artificially inoculated roots of cucumber, melon, pumpkin, and watermelon, but quantities of Ph. sclerotioides DNA in their hypocotyls of the hosts varied as follows: melon ≥ cucumber ≥ watermelon > pumpkin. These results suggest that Ph. sclerotioides infection is not species-specific but the rate of infection may differ among host species.

Verticillium dahliae, a soilborne plant pathogen, causes wilt disease in many important crops. We reported previously that the mating type gene MAT1-2-1 is spread to isolates of this asexual fungus. However, we did not determine whether V. dahliae is homothallic or heterothallic because the opposite mating type gene, MAT1-1-1, had not been identified. In the present study, we identified the MAT1-1-1 gene from an isolate lacking MAT1-2-1 and the mating type idiomorphs of V. dahliae. Each isolate we tested contained either the MAT1-1 or MAT1-2 idiomorph, indicating that the asexual fungus V. dahliae is potentially heterothallic.

Mating type genes of Verticillium dahliae, a wilt pathogen affecting many plant species, were identified to examine sexual recombination between Japanese pathotypes. We amplified a DNA sequence encoding high mobility group (HMG) box from V. dahliae using PCR. A cloned genomic DNA fragment included a sequence homologous to MAT1-2-1 gene. Despite that sequence's presence in all V. dahliae isolates we used, MAT1-1-1 (an opposite mating type gene) was never amplified. We concluded that V. dahliae is potentially heterothallic. Furthermore, sexual bias practically obviates sexual recombination between Japanese pathotypes. This report describes, for the first time, a mating type gene of phytopathogenic Verticillium.

The chromosome number and electrophoretic karyotype of Japanese isolates of Verticillium dahliae were investigated. In a genomic Southern blot analysis of seven isolates probed with a telomere consensus sequence (TTAGGG)5, 12 or 14 bands were observed. Furthermore, pulsed-field gel electrophoresis (PFGE) of these isolates revealed five or six chromosomal bands. A band (approx. 3.5 Mbp) common to all isolates apparently contained more than two chromosomes. From these results, we concluded that each isolate’s chromosome number is six (an eggplant pathotype isolate) or seven (all isolates of tomato and sweet pepper pathotypes). Although the chromosome sizes differed among isolates, karyotypes were similar within tomato and sweet pepper pathotypes. A small chromosome (approx. 1.8 Mbp) was observed only in the sweet pepper pathotype. Subsequent PFGE-Southern hybridization analyses revealed that the three DNA fragments specific to tomato pathotype are located on the same chromosome. These results suggest that the tomato-pathotype-specific DNA sequences might coexist on one chromosome.

Japanese isolates of Verticillium dahliae, a causal agent of wilt disease in many plants, are classifiable into pathotypes based on their pathogenicity. Because these pathotypes are morphologically indistinguishable, establishing a rapid identification method is very important for the control of this pathogen in Japan. For cloning DNA fragments that are useful for identification and specific detection of V. dahliae pathotypes, we performed random amplified polymorphic DNA (RAPD) analyses using various isolates. One polymerase chain reaction (PCR) product, E10-U48, was specific to isolates pathogenic to sweet pepper. The other product, B68-TV, was specific to race 1 of isolates pathogenic to tomato. The specificity of these sequences was confirmed by genomic Southern hybridization. Further analyses revealed that the region peripheral to B68-TV obtained from the genomic DNA library includes the sequence specific to all isolates pathogenic to tomato (races 1 and 2). Moreover, sequence tagged site (STS) primers designed from B68-TV and its peripheral region showed race-specific and pathotype-specific amplification in a PCR assay. The probes and primers obtained in this study are likely to be useful tools for the identification and specific detection of pathotypes and races of V. dahliae.

Although the causal agent of black root rot of Cucurbitaceae in Japan has been proposed as Phomopsis sclerotioides, the species identification of the pathogen has remained inconclusive because of a lack of spore formation. We confirmed that a Japanese isolate of Phomopsis sp. obtained from a diseased pumpkin root produced pycnidia containing α spores in sterilized bean pods. In phylogenetic analyses of rDNA-ITS regions, nine Japanese Phomopsis sp. isolates from melon, watermelon grafted onto bottle gourd, and pumpkin diagnosed with black root rot, formed a single clade with P. sclerotioides standard isolates. We identified the causal agent of the black root rot of melon, pumpkin, bottle gourd, and watermelon in Japan as P. sclerotioides and propose the Japanese name “Phomopsis-negusare-byo” for the disease. Patterns of random amplified polymorphic DNA (RAPD) of these Japanese isolates were also similar to those of P. sclerotioides, thus supporting the species identification. However, mycelial incompatibilities were found for many combinations among these P. sclerotioides isolates, suggesting some genotypic variations of this fungus in Japan at a level that the RAPD analyses cannot discriminate.

Using differential hybridization, two DNA fragments, VDf35 and VDf90, specific to Verticillium dahliae, were isolated. These fragments contained truncated open reading frames (ORFs) homologous to the gypsy-type retrotransposon. The ORFs of VDf35 and VDf90 were pol and gag homologs, respectively. In addition, VDf90 had a pol homolog without an ORF sequence. The pol homologs in VDf35 and VDf90 were similar to each other, and these two DNA fragments had completely identical sequences. Genomic Southern analysis revealed that numerous copies of these homologs existed in V. dahliae, suggesting that V. dahliae carries a gypsy-like retroelement. Genomic Southern and polymerase chain reaction (PCR) analysis also indicated that a large number of these homologs exist in V. longisporum as well as in V. dahliae, but only a few were present in V. albo-atrum. No homolog was found in either V. nigrescens or V. tricorpus. The uneven distribution of these homologs of the retroposon-like elements among Verticillium species suggested a close genetic kinship between V. dahliae and V. longisporum. PCR primers designed from VDf35 showed species- or pathotype-specific amplification. Therefore, this sequence may be useful as a DNA marker to identify species and pathotypes of V. dahliae. This is the first report on a retrotransposon-like sequence in the genome of phytopathogenic Verticillium species.

緑肥エンバク野生種の栽培・すき込み後のトマト土壌病害の発生をピシウム苗立枯病,リゾクトニア苗立枯病,萎凋病,半身萎凋病および青枯病を対象に調査した結果,半身養凋病のような進行の遅い土壌病害の発生が抑制され,特に非殺菌時にその効果が顕著に認められた.その原因として,エンバク野生種栽培・すき込みに伴う土着の土壌微生物相の量的および質的変化による影響が,希釈平板法,微生物活性量およびPCR-DGGE法から示唆された.また,エンバク野生種由来の化学物質の抗菌性が関係している可能性も示した.

Verticillium dahliaeは多犯性の土壌伝染性植物病原菌であるが,その宿主範囲は菌株ごとに異なっており,いくつかの病原性系統に分けられている.本菌の各菌株のゲノムをRAPDにより解析したところ,トマト・ピーマン系はトマト系とピーマン系の遺伝的雑種である可能性が示唆された.本菌は不完全菌類であり有性生殖による交雑は行わないが,菌株間において擬有性生殖による組換えが生じることが知られている.そこで,本菌のトマト系とピーマン系の間で組換えが生じるかどうかを調査するため,それぞれ異なる遺伝子に変異を持つトマト系とピーマン系のnit変異株を混合培養し,得られた分生胞子を最少培地で培養した.その結果,22菌株の原栄養株が得られ,そのうちの1菌株はトマトとピーマンに病原性を併せ持っていた.また,RAPD解析により,本菌株はトマト系とピーマン系の遺伝的雑種であることが示された.以上の結果より,V. dahliaeにおいては病原性系統間で遺伝的組換えが生じ,新たな宿主範囲を持つ菌株が発生し得ることが示唆された.

Klebahn is the causal agent of tomato wilt disease. Isolates of V. dahliae can be classified based on pathogenicity to tomato, but the pathotypes are indistinguishable in morphology. We designed PCR primers for specific detection of isolates pathogenic to tomato (tomato pathotype) from the sequences of a pathotype-specific gene, vdt1. With the primer pair Tg5/Tc3, a PCR product (approximately 3.2 kb) specific to tomato pathotype was amplified from the genomic DNA of isolates. Using the primer pair, a tomato pathotype isolate was specifically detected from hypocotyls of inoculated tomato and eggplant. On the other hand, no amplification was observed from non-tomato pathotype isolates of V. dahliae, some other wilt pathogens of tomato and a healthy host plant. Therefore, the primer pair can be useful for pathotype-specific detection of V. dahliae as well as for diagnosis of wilt disease of tomato plant.

Fungal plant pathogens secrete effector molecules to establish disease on their hosts, and plants in turn use immune receptors to try to intercept these effectors. The tomato immune receptor Ve1 governs resistance to race 1 strains of the soil-borne vascular wilt fungi Verticillium dahliae and Verticillium albo-atrum , but the corresponding Verticillium effector remained unknown thus far. By high-throughput population genome sequencing, a single 50-Kb sequence stretch was identified that only occurs in race 1 strains, and subsequent transcriptome sequencing of Verticillium -infected Nicotiana benthamiana plants revealed only a single highly expressed ORF in this region, designated Ave1 (for A virulence on Ve1 tomato ). Functional analyses confirmed that Ave1 activates Ve1-mediated resistance and demonstrated that Ave1 markedly contributes to fungal virulence, not only on tomato but also on Arabidopsis . Interestingly, Ave1 is homologous to a widespread family of plant natriuretic peptides. Besides plants, homologous proteins were only found in the bacterial plant pathogen Xanthomonas axonopodis and the plant pathogenic fungi Colletotrichum higginsianum , Cercospora beticola , and Fusarium oxysporum f. sp. lycopersici . The distribution of Ave1 homologs, coincident with the presence of Ave1 within a flexible genomic region, strongly suggests that Verticillium acquired Ave1 from plants through horizontal gene transfer. Remarkably, by transient expression we show that also the Ave1 homologs from F. oxysporum and C. beticola can activate Ve1 -mediated resistance. In line with this observation, Ve1 was found to mediate resistance toward F. oxysporum in tomato, showing that this immune receptor is involved in resistance against multiple fungal pathogens.

Efficiency of nonpathogenic Fusarium oxysporum Fo-B2 for the biological control of Fusarium wilt of tomato, caused by F. oxysporum f. sp. lycopersici CU1, was examined in different environments: a growth chamber with sterile soil-less medium, a greenhouse with fumigated or nonfumigated soil, and nonfumigated field plots. Inoculation of Fo-B2 onto tomato roots significantly reduced the severity of disease, but the efficiency of disease suppression decreased as the experimental environment became less controlled. Relationships between the recovery of Fo-B2 from hypocotyls and the disease severity indicated that the biocontrol agent was most effective when it colonized vascular tissues intensively. Moreover, the degree of Fo-B2 colonization was greatly reduced when the seedlings were grown in nonfumigated soil. Dose-response models (negative exponential, hyperbolic saturation, and logistic) were fit to observed data collected over a range of inoculum densities of the pathogen and the antagonist; the logistic model provided the best fit in all environments. The ratios of an 50% effective dose parameter for Fo-B2 to that of CU1 increased as the environment became less controlled, suggesting that environmentally related efficiency reduction impacted the antagonist more than the pathogen. The results suggest that indigenous soil microbes were a primary factor negatively influencing the efficiency of Fo-B2. Therefore, early establishment of the antagonist in a noncompetitive environment prior to outplanting could improve the efficacy of biological control.

Pathogenicity-impaired mutants, B02 and H15, of Fusarium oxysporum f. sp. lycorpersici (FOL) were obtained using restriction enzyme-mediated integration. Disease severities of Fusarium wilt caused by these mutants were significantly reduced, and their disease development rates were correlated with their colonization rates in tomato vessels. Both B02 and H15 produced significantly smaller amounts of extracellular proteins as well as fusaric acid than the wild-type. Southern blot analyses suggested that B02 and H15 likely contain a single and three copies of transformation vector, respectively. These mutants may thus be useful in isolating genes involved in pathogenicity of FOL.