Comparative genomics among three cyst nematode species reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs

Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are an essential handle for PCN control. However, the poor delineation of G. pallida pathotypes hampers the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCN after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression (DOG boxes) were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Re-sequencing of PCN populations with deviant virulence characteristics will allow for the linking of these characteristics with the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.

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The ability of rhizosphere bacteria isolated from nematode host and non-host plants to influence the hatch in vitro of the two potato cyst nematode species, Globodera rostochiensis and G. pallida

Nematology ◽

10.1163/1568541042360528 ◽

2004 ◽

Vol 6 (3) ◽

pp. 375-387 ◽

Cited By ~ 5

Author(s):

N. Aileen Ryan ◽

Peter Jones

Keyword(s):

Sugar Beet ◽

Host Plant ◽

Host Plants ◽

Nematode Species ◽

Cyst Nematode ◽

Potato Cyst Nematode ◽

Globodera Pallida ◽

Bacterial Isolates ◽

Bacillus Spp

AbstractSeventy bacteria, isolated from the rhizosphere of the potato cyst nematode (PCN) host plant, potato, were cultured in the presence and absence of potato root leachate (PRL) and the resultant culture filtrates were analysed for their ability to affect the hatch in vitro of the two PCN species. Of the isolates tested, nine had a significant effect on PCN hatch. Six affected Globodera pallida hatch and three affected G. rostochiensis hatch. Five of the isolates significantly increased hatch only when cultured in the presence of PRL. Three of the isolates decreased PCN hatch significantly in PRL. Only one isolate increased hatch significantly in the absence of PRL. No isolate affected the hatch of both species. Six of the nine isolates that significantly affected PCN hatch had been pre-selected by culturing on PRL. Bacterial isolates from PCN non-hosts (14 from wheat, 17 from sugar beet) were also tested for hatching activity. The principal effect of the hatch-active isolates from the PCN non-host plants was to increase PCN hatch in the presence of PRL. In contrast to the host bacteria results, the isolates from non-host plants affected only G. rostochiensis hatch (three wheat isolates and four sugar beet isolates significantly increased G. rostochiensis hatch); no such isolate affected G. pallida hatch significantly in the presence of PRL. Ten isolates (32%) from non-host plants had the ability to increase significantly the hatch of PCN in the absence of PRL (eight of these affected G. rostochiensis hatch and four affected G. pallida hatch), compared to only one bacterial isolate (1%) from a host plant. The majority of the isolates from non-hosts produced PCN species-specific effects, as with the bacteria isolated from potatoes, although two wheat isolates increased the hatch of both species significantly in the absence of PRL. Of 20 hatch-active bacterial isolates (from all three plants) identified, 70% were Bacillus spp. Other genera identified were Arthrobacter , Acinetobacter and Staphylococcus .

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Immunochemical studies on pathotypes of the potato cyst nematodes, Globodera rostochiensis and G. pallida

Parasitology ◽

10.1017/s0031182000055475 ◽

1985 ◽

Vol 90 (3) ◽

pp. 471-483 ◽

Cited By ~ 4

Author(s):

P. C. Fox ◽

H. J. Atkinson

Keyword(s):

Nematode Species ◽

Cyst Nematode ◽

Globodera Pallida ◽

Potato Cyst Nematodes ◽

Cyst Nematodes ◽

Crossed Immunoelectrophoresis ◽

Specific Antigens ◽

And Cluster Analysis ◽

Species Specific ◽

Micro Organisms

The potential of antigenic differences for discriminating pathotypes of the potato cyst nematodes Globodera pallida and G. rostochiensis has been examined by the use of an antiserum raised to a homogenate of potato cyst nematode larvae. Species-specific antigens were detected among reference pathotypes but more variability was detected among field populations, and cluster analysis was used to interpret the precipitation are pattern produced by Laurell crossed-immunoelectrophoresis. A division into species was seen with this analysis but no definite pathotype groupings were detected. Cross-reaction with other cyst-nematode species was limited to general non-specific precipitation. The antigens were all proteinaceous, did not arise from micro-organisms within the cyst and were mainly hydrophilic with an acidic isoelectric point. Peptidase and acid phosphatase activity was detected in some precipitation arcs but this was not species specific.

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Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. rostochiensis and Heterodera schachtii

Nematology ◽

10.1163/15685411-00003086 ◽

2017 ◽

Vol 19 (7) ◽

pp. 789-804 ◽

Cited By ~ 5

Author(s):

Sylvie Gamel ◽

Aude Letort ◽

Didier Fouville ◽

Laurent Folcher ◽

Eric Grenier

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Limit Of Detection ◽

Simultaneous Detection ◽

Nematode Species ◽

Globodera Pallida ◽

Heterodera Schachtii ◽

Cyst Nematodes ◽

Detection And Identification ◽

Template Dna

Considering the growing trade of seed potato, reliable diagnostic protocols are required for the detection of regulated nematode species. In this study, a specific and sensitive multiplex Taqman-based real-time PCR method was developed in order to detect and identifyGlobodera pallida,G. rostochiensisandHeterodera schachtii. The newly designed primers and probes enabled the detection of all the target populations tested and with no cross-reaction for closely related non-target species (55 populations tested). The limit of detection (LOD) was one juvenile forG. rostochiensisandG. pallidaand five juveniles forH. schachtii. For monitoring potato cyst nematodes, this analytical tool would extend the number of cyst investigated as five juveniles can be detected among 50 cysts in a sample. Furthermore, this multiplex assay detects DNA of the three targeted species in template DNA obtained directly from float material after nematode extraction from soil.

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Hatching Induction of Cyst Nematodes in Bare Soils Drenched With Root Exudates Under Controlled Conditions

Frontiers in Plant Science ◽

10.3389/fpls.2020.602825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Bruno Ngala ◽

Nicolas Mariette ◽

Mélina Ianszen ◽

Pauline Dewaegeneire ◽

Marie-Christine Denis ◽

...

Keyword(s):

Soil Moisture ◽

Root Exudates ◽

Root Exudate ◽

Soil Depth ◽

Cyst Nematode ◽

Globodera Pallida ◽

Heterodera Schachtii ◽

Cyst Nematodes ◽

Host Root

Cyst nematodes account for substantial annual yield losses in crop production worldwide. Concerns over environmental and health issues due to the use of chemical nematicides mean alternative sustainable and integrated solutions are urgently required. Hatch induction of encysted eggs in the absence of host plants, i.e., ‘suicide-hatching,’ could be a sustainable alternative in reducing population densities of cyst nematodes in infested soils. Here we examined in situ hatching of encysted eggs of Globodera pallida, Heterodera carotae, and Heterodera schachtii at varying soil depths, following exogenous applications of host root exudates in repeated glasshouse experiments. Cysts were retrieved 30 or 43 days post-incubation depending on the nematode species and assessed for hatching rates relative to the initial number of viable eggs per cyst. Hatching of the potato cyst nematode G. pallida depended on both soil moisture and effective exposure to root exudates, and to a lesser extent on exudate concentration. The carrot cyst nematode H. carotae had over 75% hatched induced by root exudate irrespective of the concentration, with better hatch induction at 20 cm as compared with 10 cm soil depth. Hatching of the beet cyst nematode H. schachtii largely depended on the soil moisture level at constant temperature, rather than the type or concentration of root exudates applied. As a conclusion, exogenously applied host root exudates may play a major role in inducing in situ hatch of encysted eggs of potato and carrot cyst nematodes in the absence of host plant under favorable soil temperature/moisture conditions. To improve such strategy, the characterization of chemical profiles of the root exudate composition and field validation are currently ongoing.

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Occurrence and molecular characterization of cyst nematode species (Globodera spp.) associated with potato crops in Colombia

PLoS ONE ◽

10.1371/journal.pone.0241256 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0241256

Author(s):

Daniela Vallejo ◽

Diego A. Rojas ◽

John A. Martinez ◽

Sergio Marchant ◽

Claudia M. Holguin ◽

...

Keyword(s):

Management Strategies ◽

Nematode Species ◽

Globodera Pallida ◽

Rrna Gene ◽

Potato Cyst Nematodes ◽

28S Rrna ◽

Cyst Nematodes ◽

Nucleotide Substitutions ◽

Internal Transcribed Spacer Region ◽

The Status

Potato cyst nematodes (PCN) from the genus Globodera spp. cause major losses in the potato (Solanum tuberosum) industry worldwide. Despite their importance, at present little is known about the status of this plant pathogen in cultivated potatoes in Colombia. In this study, a total of 589 samples collected from 75 geographic localities in nine potato producing regions of Colombia (Cundinamarca, Boyacá, Antioquia, Nariño, Santander, Norte de Santander, Tolima, Caldas and Cauca) were assayed for the presence of potato cyst nematodes. Fifty-seven percent of samples tested positive for PCN. Based on phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rRNA gene and D2-D3 expansion segments of the 28S rRNA gene, all populations but one were identified as Globodera pallida. Sequences of G. pallida from Colombia formed a monophyletic group closely related to Peruvian populations, with the lowest average number of nucleotide substitutions per site (Dxy = 0.002) and net nucleotide substitutions per site (Da = 0.001), when compared to G. pallida populations from Europe, South and North America. A single sample formed a well-supported subclade along with G. rostochiensis and G. tabacum from Japan, USA and Argentina. To our knowledge this is the first comprehensive survey of Globodera populations from Colombia that includes genetic data. Our findings on species diversity and phylogenetic relationships of Globodera populations from Colombia may help elucidate the status and distribution of Globodera species, and lead to the development of accurate management strategies for the potato cyst nematodes.

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The beet cyst nematode (Heterodera schachtii): an ancient threat to sugar beet crops in Central Europe has become an invisible actor.

10.1079/9781789247541.0055 ◽

2021 ◽

pp. 394-399

Author(s):

Matthias Daub

Keyword(s):

Sugar Beet ◽

Integrated Management ◽

Nematode Species ◽

Cyst Nematode ◽

Heterodera Schachtii ◽

Future Research ◽

Parasitic Nematodes ◽

Beet Cyst Nematode ◽

Management Optimization ◽

Damage Symptoms

Abstract The beet cyst nematode (BCN) was one of the first discovered plant parasitic nematodes. Heterodera schachtii was observed in 1859 in Halle in Central Germany by the botanist Herman Schacht and described later by Adolf Schmidt in 1871, who named this cyst nematode species after its original discoverer. Partly due to the lack of knowledge about the effect of sugar beet monocultures on the population build-up of BCN, this nematode had a devastating impact on sugar production in 1876 that led to the shutdown of 24 sugar factories in Germany. This chapter discusses the economic importance, distribution, host range, damage symptoms, biology and life cycle, interactions with other nematodes and pathogens, recommended integrated management, and management optimization of H. schachtii. Future research requirements and future developments are also mentioned.

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First Report of the Pale Potato Cyst Nematode Globodera pallida from Bosnia and Herzegovina

Plant Disease ◽

10.1094/pdis-07-13-0739-pdn ◽

2014 ◽

Vol 98 (4) ◽

pp. 575-575 ◽

Cited By ~ 1

Author(s):

B. Nježić ◽

B. Gerič Stare ◽

S. Širca ◽

N. Grujić

Keyword(s):

Bosnia And Herzegovina ◽

Potato Production ◽

Cyst Nematode ◽

Soil Samples ◽

Potato Cyst Nematode ◽

Globodera Pallida ◽

Economic Losses ◽

Cyst Nematodes ◽

Seed Potatoes ◽

Infested Field

Potato cyst nematodes (PCN), the golden cyst nematode Globodera rostochiensis (Woll.) Bahrens, and the pale potato cyst nematode G. pallida (Stone) stand out by their remarkable and efficient parasitic adaptations causing high economic losses in potato production worldwide. They are A2 quarantine pests in EPPO countries as well as in Bosnia and Herzegovina. Up to now, only G. rostochiensis was reported from Bosnia and Herzegovina in 2011 (1). A systematic survey on the presence of PCN on entire territory of Bosnia and Herzegovina started in 2011. During the PCN survey, each year 120 soil samples of 1.5 liters were collected in the Republic of Srpska, one of the two entities of Bosnia and Herzegovina. The samples were collected by soil auger 10 cm in length with a diameter of 1.5 cm consisting of 100 cores. Entire samples were processed by Seinhorst elutriator (4). In autumn of 2012, PCN viable cysts were found in two soil samples originating from one field. From one sample, 12 cysts were extracted, and 2 from another sample. The morphology of cysts and second stage juveniles and molecular analysis established the identity of this species as pale cyst nematode G. pallida (3). In addition, the sequencing of the ribosomal DNA region revealed unequivocal similarity to G. pallida (GenBank Accession No. HF968449), while PCR-RFLP analysis (2) showed European type of G. pallida. The infested field is located in Rogatica, 70 km east of Sarajevo, which is one of the main seed and potato production areas in Bosnia and Herzegovina. The field history revealed that farm-propagated, farm-saved seed potatoes could spread the nematodes to other fields as well. Therefore, 26 additional samples were taken from the fields that belong to the infested field owner and the surrounding fields, but no cysts were found in additional samples. To determine infestation focus and its size, the infested field (1.1 ha) was divided into 46 plots (25 × 10 m) and resampled by taking samples of 60 cores per plot. The detailed sampling of the field revealed a high infestation of 1 cyst per gram of soil in the infestation focus. The high infestation level and the propagation of farm-own seed potatoes suggest that the introduction of G. pallida might have occurred several years ago, probably with imported seed potatoes. The infested field was subjected to the phytosanitary measure of banning potato production for a period of 6 years with the possibility of its prolongation, if cysts with live content are found afterward. It is expected that the nematode is present in other fields due to the farmer's practices of propagating farm-saved seed potatoes and deficient field machinery hygiene. Therefore, the whole area will be intensively monitored for the presence of PCN in the future. An adequate pest management plan will be prepared after PCN pathotype identification. To our knowledge, only one field was found infested with G. pallida during the 3-year PCN survey in Bosnia and Herzegovina. Strict phytosanitary measures for preventing further PCN introductions and spreading should be intensified. References: (1) I. Ostojić et al. Plant Dis. 95:883, 2011. (2) S. Širca et al. Phytopathol. Mediterr. 49:361, 2010. (3) A. M. Skantar et al. J. Nematol. 39:133, 2007. (4) J. van Bezooijen. Methods and Techniques for Nematology, Wageningen University, 2006.

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Morphological characteristics and distribution of Globodera species in Slovenia

Plant Protection Science ◽

10.17221/10488-pps ◽

2017 ◽

Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽

pp. 354-357

Author(s):

G. Urek ◽

S. Širca ◽

V. Meglič

Keyword(s):

Hot Spot ◽

Morphological Characteristics ◽

Globodera Rostochiensis ◽

Cyst Nematode ◽

Soil Samples ◽

Globodera Pallida ◽

Cyst Nematodes ◽

First Time ◽

Austrian Border ◽

Central Slovenia

Surveillance on cyst nematodes in Slovenia started already in 1963. We have found Globodera rostochiensis for the first time in 1971 and for the second time in 1975 (two cysts). In 1999 cysts of yellow potato cyst nematode were found again. A small hot spot was detected along the Slovene Austrian border. Cysts of Globodera rostochiensis were extracted from samples taken in 1.6 hectare field. In 2001 we surveyed 194 fields with the surface of 468.29 ha. We discovered another hot spot of Globodera rostochiensis in the Central Slovenia. Cysts of Globodera achilleae are seldom discovered in Slovenia. During the period between 1980 and 2000 we extracted altogether 206 cysts. In 2001 we found three fields where we extracted at first seven cysts. With more detailed survey we extracted another 30 cysts. In a few soil samples taken from the imported potatoes from Italy we have intercepted cysts of Globodera pallida. For that reason shipments were returned. In a similar way in 2002 shipments from Croatia were returned because of G. rostochiensis presence. Specimens of Globodera rostochiensis and G. achilleae species found in Slovenia were morphometricaly handeled.

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Using a selective fast turn-around bioassay for population density determination of Heterodera schachtii

Nematology ◽

10.1163/15685411-00002720 ◽

2013 ◽

Vol 15 (7) ◽

pp. 809-819 ◽

Cited By ~ 1

Author(s):

Annabell Meinecke ◽

Andreas Hermann ◽

Andreas Westphal

Keyword(s):

Sugar Beet ◽

Globodera Pallida ◽

Heterodera Schachtii ◽

Soil Types ◽

Meloidogyne Hapla ◽

Cyst Nematodes ◽

Soil Extraction ◽

Easy Method ◽

Wide Range ◽

Field Samples

In Central Europe, Heterodera schachtii is kept below threshold levels by cover-cropping with resistant crucifers and crop rotation with non-hosts. Determining population densities of H. schachtii in soil is critical when implementing resistant and tolerant sugar beet cultivars in integrated pest management (IPM) programmes. Soil extraction of the cysts followed by egg counts or extraction of the second-stage juveniles (J2) facilitated by the chemical stimulant acetox can be unsatisfactory in mixed field populations of cyst nematodes. In contrast to H. schachtii, nematodes typically present in sugar beet soils, e.g., Globodera pallida, G. rostochiensis, H. avenae, H. filipjevi, Meloidogyne hapla, M. incognita and Pratylenchus penetrans, rarely penetrated radish roots. In this bioassay, equivalents of 50 g of soil dry weight were adjusted to 10-20% moisture, seeded with Raphanus sativus cv. Saxa 3, and incubated at a day-night (16:8 h) cycle of 28/23°C for 4 days before J2 in radish roots were enumerated. In different soil types, penetration by H. schachtii reflected the inoculation levels. When inoculated with mixes of H. schachtii with H. avenae or H. filipjevi, counts of H. schachtii were similar to those in soils with H. schachtii only. When comparing three methods in three soils spiked with H. schachtii cysts, the bioassay and the extraction method were lightly impacted by the soil texture but results of the acetox method varied with texture. When implemented for field samples from Franconia, the radish bioassay and the acetox method provided results related to cyst and egg extraction data. The radish bioassay provided a quick and easy method for quantifying H. schachtii in the presence of other nematode species in a wide range of soil types. Including this assay in IPM programmes may serve as an alternative to standard methods and will improve the decision making in sustainable production systems.

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Isolation and localisation of an annexin gene (gp-nex) from the potato cyst nematode, Globodera pallida

Nematology ◽

10.1163/156854101300106883 ◽

2001 ◽

Vol 3 (1) ◽

pp. 45-54 ◽

Cited By ~ 18

Author(s):

Andrew Warry ◽

Rosane Curtis ◽

Andrew Porter ◽

Luca Fioretti ◽

Patrick Haydock

Keyword(s):

Amino Acid ◽

Nematode Species ◽

Globodera Pallida ◽

Predicted Amino Acid Sequence ◽

Cyst Nematodes ◽

Expression Library ◽

Calcium Dependent ◽

Secretion Signal ◽

Second Stage ◽

Annexin Gene

AbstractA full length cDNA clone was isolated by screening a mixed stage Globodera pallida expression library using the monospecific polyclonal antibody IACR-PC320. Sequence comparison indicated that the predicted 332 amino acid protein encoded by the cDNA was a member of the annexin gene family named gp-nex and very similar to annexins found in other nematode species. Annexins are calcium-dependent phospholipid binding proteins characterised by four repeated domains approximately 70 amino acids in length. The predicted amino acid sequence of the protein did not contain an N-terminal secretion signal peptide; however, the protein was shown to be present in excretory/secretory products from G. pallida second stage juveniles treated with the neurotransmitter 5 methoxy-N, N dimethyl tryptamine. Gp-nex encodes a protein of 35 kDa and was immunolocalised in the amphids, genital primordium and in the constraining muscles above and below the metacorpus pump chamber of G. pallida second stage juveniles. It is also present in eggs and adult females of the two species of the potato cyst nematodes.

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