Black root rot of cucurbits caused by Phomopsis sclerotioides in Japan and phylogenetic grouping of the pathogen

Shishido, Masahiro; Yoshida, Nanako; Usami, Toshiyuki; Shinozaki, Takahiro; Kobayashi, Masanobu; Takeuchi, T.

doi:10.1007/s10327-006-0273-0

Cited by 22 publications

(16 citation statements)

References 21 publications

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“…Typically, Diaporthe species are saprobes, endophytes, or plant pathogens (Webber & Gibbs, 1984; Boddy & Griffith, 1989; Udayanga et al, 2011). Some plant pathogenic Diaporthe species are associated with cankers, diebacks, rots, spots and wilts on a wide range of plants, some of which are of economic importance as is the case of citrus, cucurbits, soybeans, eggplant, berries and grapevines (Backman, Weaver & Morgan-Jones, 1985; Merrin, Nair & Tarran, 1995; Farr, Castlebury & Rossman, 2002; Farr et al , 2002; Shishido et al, 2006). Less frequently, Diaporthe species can also cause lupinosis and other health problems in humans and other mammals (Van Warmelo & Marasas, 1972; Sutton et al, 1999; Battilani et al, 2011; Garcia-Reyne et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

Santos

Alves

2017

PeerJ

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BackgroundSpecies identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.MethodsHere we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.ResultsAs expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.DiscussionOur results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

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Section: Introductionmentioning

confidence: 99%

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

Santos

Alves

2017

PeerJ

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“…prior to the real-time PCR, a conventional PCR was conducted to amplify ITS region of ribosomal DNA using the primers of ITS1 (5 0 -TCCGTAGGTGAACC TGCGG-3 0 ) and ITS4 (5 0 -TCCTCCGCTTATTGATATG C-3 0 ) (Glass and Donaldson 1995). The procedure used for the conventional PCR was described in a previous report (Shishido et al 2006). The nested PCR substantially improved sensitivity and reliability by detecting much greater quantities of R. necatrix DNA with standard errors in reasonable ranges (Table 3).…”

Section: Development Of Real-time Pcr Assay Using Taqman Probementioning

confidence: 99%

“…Genomic DNA of each fungal isolate was extracted directly from mycelia by crushing samples in DNA extraction buffer [0.5 M NaCl, 10 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1% (w/v) SDS] using a bead-beater (Model 3110BX, BioSpec Products, Bartlesville, OK, USA) as described in a previous report (Shishido et al 2006). DNA concentration was determined using Quant-iT DNA Assay kit with a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA) by measuring absorbance at 260 nm.…”

Section: Development Of Real-time Pcr Assay Using Taqman Probementioning

confidence: 99%

Development of real-time PCR assay using TaqMan probe for detection and quantification of Rosellinia necatrix in plant and soil

2012

Self Cite

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We developed real-time PCR assays using TaqMan probes to detect and quantify Rosellinia necatrix, the causal agent of white root rot in many plant species. Two sets of PCR primers and TaqMan probe indicated that their detection limits could be as low as 1 fg of template DNA. Using the real-time PCR assays with the TaqMan probes, we were able to quantify R. necatrix DNA in naturally diseased roots of Japanese pear and in artificially infested soil samples. Although the new assays were inadequate for use with naturally infested soil samples, nested PCR procedures improved the detectability of the new assays.

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“…The Cucurbitaceae family includes major vegetable crops that are important sources of foods and fresh products. Black root rot caused by the soilborne fungus Diaporthe sclerotioides , formerly Phomopsis sclerotioides (Udayanga et al ., ), is a devastating root disease of cucurbit crops in temperate regions worldwide (Van Kesteren, ; Cappelli et al ., ; Shishido et al ., ). Symptoms caused by this pathogen in the root system include necrosis and the development of greyish‐ or brownish‐black pseudostromata and pseudomicrosclerotia distributed in the root cortex cells (Van Kesteren, ).…”

Section: Introductionmentioning

confidence: 97%

“…To date, the host range of D. sclerotioides is known to be restricted to cucurbit crops, of which cucumbers, melons, pumpkins and watermelons are agriculturally the most important. In Japan, the disease has been prevalent for almost three decades, resulting in serious economic losses in the yields of these crops (Shishido et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Diaporthe sclerotioides exhibits no host specificity among cucurbit species

Shishido

Ōhashi

Momma³

2014

Plant Pathology

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Plant-fungal specificity between cucurbitaceous crops and Diaporthe sclerotioides, the causal agent of black root rot, was studied using cucumbers (Cucumis sativa), melons (Cucumis melo), pumpkins (Cucurbita maxima), watermelons (Citrullus lanatus) and bottlegourd (Lagenaria siceraria var. gourda). Twelve D. sclerotioides isolates from these cucurbit species were cross-inoculated. The virulence of the isolates was evaluated as the area under the disease progress curve (AUDPC). All cucurbit species were susceptible to each isolate, but AUDPCs were significantly different among the hosts, with the order of greatest to least being melon, cucumber, watermelon, bottlegourd and finally, pumpkin. The infectiveness of isolates was assessed as the quantity of D. sclerotioides DNA detected in the hypocotyls of seedlings 2 weeks after inoculation using a real-time PCR protocol. The fungal DNA quantities varied among the species in the same order as the AUDPCs. Whilst there were statistically significant correlations between the virulence and infectiveness of D. sclerotioides isolates in cucumbers, melons and bottlegourds, their coefficients of determination were not high (r 2 < 0Á6). Orthogonal contrasts indicated no specificity in either the fungal virulence or infectiveness between D. sclerotioides isolates and the cucurbit hosts from which these isolates originated. Thus, although the degree of host susceptibility to D. sclerotioides varies among cucurbit species, the absence of specificity to the host species in either virulence or infectiveness suggests the pathogen may spread via various cucurbit crops, irrespective of their original host species.

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Black root rot of cucurbits caused by Phomopsis sclerotioides in Japan and phylogenetic grouping of the pathogen

Cited by 22 publications

References 21 publications

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

Development of real-time PCR assay using TaqMan probe for detection and quantification of Rosellinia necatrix in plant and soil

Diaporthe sclerotioides exhibits no host specificity among cucurbit species

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