Identification of the pathotype of <i>Synchytrium endobioticum,</i> causal agent of potato wart disease, present in Georgia

Sikharulidze, Z.; Ghoghoberidze, Sopio; Mentink, N. M.; Meparishvili, G.; Tsetskhladze, T.; Leeuwen, G. C. M. van

doi:10.1111/epp.12582

Cited by 5 publications

(2 citation statements)

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“…Pathotype 38(Nevşehir) was previously reported from Bulgaria (van de Vossenberg et al, 2020a), Georgia (Sikharulidze et al, 2019) and Turkey (Çakır et al, 2009)and isolates from the latter two countries were included in our analysis. All sequenced pathotype 38(Nevşehir) isolates contain the specific combination of structural variants β and δ in highly varying compositions.…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

Vossenberg

Gent

Meffert

et al. 2022

Preprint

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Synchytrium endobioticum (Schilb.) Perc. is a chytrid fungus causing potato wart disease and is one of the most important quarantine diseases on cultivated potato. Infected host tissues develop warts rendering the crop unmarketable. Resting spores that can remain viable and infectious for decades are formed in warted tissues which are released into the surrounding soil when the host tissue decays. To better understand the pathogen’s diversity and to potentially uncover pathways of migrations and introduction events, molecular characterization was performed on the historical S. endobioticum resting spore collection of the Dutch National Plant Protection Organization. Mitochondrial genomes were assembled and annotated, and four novel structural variants were identified from these materials with intronic presence-absence variation in cox1 or cob genes and structural variation in the dpoB – TIR region. Several fungal isolates were shown to contain mixtures of structural variants. We analyzed the mitogenomic sequences obtained from recent potato wart disease findings in Canada and the Netherlands in the context of the historical materials and found that fungal isolates from the new Dutch outbreak contained a specific mixture of mitogenomic variants previously not observed in the Netherlands. Based on the mitogenomic profile, pathotype 38(Nevşehir) was suspected which was later verified by pathotyping. To further facilitate dissemination of data and interactive visual analytics we created a public Nextstrain webpage with S. endobioticum mitogenomic sequences and associated metadata on their geographic origin, pathotype identity and (mixture) of mitogenomic variants ( https://nextstrain.nrcnvwa.nl/Sendo ).

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Section: Discussionmentioning

confidence: 99%

Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

Vossenberg

Gent

Meffert

et al. 2022

Preprint

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“…S. endobioticum was reported from Georgia for the fi rst time in 2014, but was already observed since 2009, possibly 2006 (Gorgiladze L et al, 2014;Sikharulidze ZV, 2019) By 2019 the potato wart spread to two municipalities (23 villages) and is listed as an A2 pest by the Ministry of Agriculture of Georgia (Ghoghoberidze S et al, 2019). The isolates of S. endobioticum obtained from the villages of Skvana, Uchkho, and Dzirkvadzeebi, Khulo municipality (Georgia) belonged to pathotype 38 (Nevşehir), widespread in Turkey (Ghoghoberidze S et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Efficiency of detecting resting spores of Synchytrium endobioticum (potato wart disease) in infested sites of Ukraine and Georgia

Zelya¹,

Janse²,

Janse³

et al. 2021

Agric. sci. pract.

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Aim. To determine the occurrence and persistence of Synchytrium endobioticum, resting spore contamination in a small survey of (known infested) potato plots in Ukraine and Georgia; to compare the detection efficiency for resting spores (winter sporangia) of S. endobioticum using an extraction method, routinely applied in Ukraine, based on the use of sodium iodide (NaI) and an extraction method largely based on EPPO Standard PM 7/28(2) (2017), using kaolin and calcium chloride (CaCl2) for extraction. Methods. The examination of fields, aimed at detecting of S. endobioticum in 22 infested plots in Georgia, was conducted following the standard European Plant Protection Organisation (EPPO) phytosanitary procedure PM 3/59(3) (2017), and in Ukraine in 11 plots according to the Ukrainian Standard ‘Methodological recommendations on sampling during quarantine inspection and evaluation’ (Omeluta V P et al, 1996). Resting spores were extracted using kaolin and CaCl2 (following largely EPPO Standard PM 7/28(2) 2017), and floatation in a solution of NaI (Zelya et al, 2005), respectively. The content of soil organic matter (SOM), collected in potato wart infested plots in Ukraine and Georgia, was determined according to the ‘Method of laboratory determination of the content of organic matter’, largely following the method of Tyurin to determine total soil organic carbon (Jankauskas B et al, 2006). The persistence or decline of potato wart in infested plots was evaluated, based on our own observations and the data of the national phytosanitary services (https://dpss.gov.ua; http://agr.georgia.gov). The results of the study were subjected to statistical analysis, using Statistica 5 software. Results. It was found that under a low up to high level of organic matter in soil samples (2.0–2.7 and 3.1–3.9 %, respectively) and a moderate to high level of inoculum in soil (3–15 up to 41–65 resting spores/g soil, respectively) there were no significant differences in the efficiency of two extraction methods under consideration: the floatation in a solution of NaI and the application of kaolin and CaCl2. However, at a low number of resting spores present in soil (1–2 resting spores/g soil), the efficiency of the method using NaI decreased statistically significant by 20–30 % as opposed to the method using kaolin/CaCl2. A relatively high level of soil contamination with resting spores was found in 11 investigated plots of 4 Ukrainian regions: 41–46 resting spores/g soil in the Ivano-Frankivsk Region, 49 in the Lviv Region, 40–65 in the Zakarpattia and 52–65 Chernivtsi Regions. The majority of the 22 investigated Georgian plots showed a low inoculum level (1–7 resting spores/g soil) and only in one village their level amounted to 15 resting spores/g soil (Uchguli village, Mestia municipality). Conclusions. The method applying sodium iodide was found to be comparable to the method applying kaolin and CaCl2 under conditions of moderate to high inoculum levels (15–65 resting spores/g soil) but the latter method was more efficient under conditions of high content of organic matter and very low inoculum level (

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Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

Vossenberg¹,

Gent

Meffert³

et al. 2023

J Plant Pathol

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Synchytrium endobioticum (Schilb.) Perc. is a chytrid fungus causing potato wart disease and is one of the most important quarantine diseases on cultivated potato. Infected host tissues develop warts rendering the crop unmarketable. Resting spores, that can remain viable and infectious for decades, are formed in warted tissues and are released into the surrounding soil when host tissue decays.To better understand the pathogen’s diversity and to potentially uncover pathways of migrations and introduction events, molecular characterization was performed on the historical S. endobioticum resting spore collection of the Dutch National Plant Protection Organization. Mitochondrial genomes were assembled and annotated, and four novel structural variants were identified from these materials with intronic presence-absence variation in cox1 or cob genes and structural variation in the dpoB – TIR region. Several fungal isolates were shown to contain mixtures of structural variants. We analyzed the mitogenomic sequences obtained from recent potato wart disease findings in Canada and the Netherlands in the context of the historical materials and found that fungal isolates from the new Dutch outbreak contained a specific mixture of mitogenomic variants previously not observed in the Netherlands. Based on the mitogenomic profile, pathotype 38(Nevşehir) was suspected which was later verified with the Spieckermann bioassay. To further facilitate dissemination of data and interactive visual analytics we created a public Nextstrain webpage with S. endobioticum mitogenomic sequences and associated metadata on their geographic origin, pathotype identity and (mixture) of mitogenomic variants (https://nextstrain.nrcnvwa.nl/Sendo).

show abstract

Identification of the pathotype of Synchytrium endobioticum, causal agent of potato wart disease, present in Georgia

Cited by 5 publications

References 11 publications

Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

Efficiency of detecting resting spores of Synchytrium endobioticum (potato wart disease) in infested sites of Ukraine and Georgia

Molecular characterization and comparisons of potato wart (Synchytrium endobioticum) in historic collections to recent findings in Canada and the Netherlands

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