The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

BACKGROUND: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. RESULTS: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. CONCLUSIONS: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.SE-vdA is supported by BBSRC grant BB/M014207/1. Sequencing was funded by BBSRC grant BB/F000642/1 to the University of Leeds and grant BB/F00334X/1 to the Wellcome Trust Sanger Institute). DRL was supported by a fellowship from The James Hutton Institute and the School of Biological Sciences, University of Edinburgh. GK was supported by a BBSRC PhD studentship. The James Hutton Institute receives funding from the Scottish Government. JAC and NEH are supported by the Wellcome Trust through its core funding of the Wellcome Trust Sanger Institute (grant 098051). This work was also supported by funding from the Canadian Safety and Security Program, project number CRTI09_462RD

Les nématodes des légumineuses alimentaires à grosses graines dans le bassin méditerranéen

National audienc

Identification of Ditylenchus species associated with Fabaceae seeds based on a specific polymerase chain reaction of ribosomal DNA-ITS regions

International audienceA technique based on the use of specific primers for polymerase chain reaction (PCR) was developed for the identification of the stem and bulb nematode belonging to the Ditylenchus dipsaci species complex. The internal transcribed spacer re-ion ITS1 and ITS2, the genes 5.8 S and part of genes 18 S and 26 S of twenty populations of the D. dipsaci species complex belonging to both D. dipsaci sensu stricto and Ditylenchus sp. B (corresponding to populations of giant individuals associated to Vicia faba) and three congeneric species were amplified with two universal ribosomal primers. PCR-amplified DNA samples were digested with five restriction enzymes in order to reveal some polymorphism allowing the identification of D. dipsaci populations associated with Fabaceae seeds. The polymorphism among species was confirmed by the sequencing of the PCR products. A primer (DdpS2) was designed in a region conserved in all populations of both D. dipsaci sensu stricto and D. sp. B studied in the present work. The other Anguinidae species (except a few species from Central Asia associated to Astereaceae and D. sp. G associated to Plantago maritima) differ in two to four nucleotides at the 3' extremity of this region. This sequence portion coincides with a TspEI restriction site. In combination with a primer located in the ribosomal region, this first primer is a good candidate for identification by PCR of populations of the D. dipsaci species complex found in Fabaceae seeds. A second primer (DdpS1) was designed in a similar way and was specific to D. dipsaci sensu stricto. The utility of these two sets of primers is discussed against the background of quarantine regulatio

NEMATOOLS : Développement d’outils pour la maîtrise durable du risque nématodes en plant de pomme de terre et cultures en rotation

Nematools project aimed at reinforcing prophylactic methods to prevent introduction and disseminationof regulated phytoparasites nematodes Meloidogyne chitwoodi, M. fallax, Globodera pallida and G.rostochiensis which are serious threats for potato crops and to improve the control strategies in order to preserve the privileged health status of the French territory. This project made it possible to developnew molecular tools for the detection of root-knot nematodes in soil samples, and later their validationon a collection of nematode populations established during the project. The risk analysis on thedissemination of nematodes related to agricultural practices have led firstly to the development of aconceptual model for the identification of management strategies for the use of agricultural equipment atrisk and on the other hand to highlight and to quantify the importance of cyst nematodes dispersal bythe soil practices and by soil-adhering to agricultural machinery at the field and at the farm scale. Theactions carried out in partnership with industrials and with experimental stations made it possible toproduce a user-friendly risk analysis tool characterizing the critical phases of different waste and effluenttreatment processes and providing answers on the sanitizing performances of different decontaminationprocesses such as composting, lagooning, anaerobic digestion, chlorination, and heat treatment. Thisproject also allowed to screen, under controlled conditions, plant species which are not conducive to thedevelopment and propagation of root-knot nematodes such as M. chitwoodi and M. fallax and may beproposed as rupture plants on contaminated sitesLes actions conduites dans le cadre du projet de recherche Nematools visaient à renforcer lesméthodes prophylactiques pour prévenir l’introduction et la dissémination des nématodesphytoparasites réglementés Meloidogyne chitwoodi, M. fallax, Globodera pallida et G. rostochiensis.Ces nématodes constituent des menaces sérieuses pour diverses cultures, dont la pomme de terre, etconduisent à repenser les stratégies de lutte afin de préserver l’état sanitaire privilégié du territoirenational. Le projet a permis le développement de nouveaux outils moléculaires de détection desnématodes à galle dans des échantillons de sol, outils validés sur une collection de populations denématodes constituée pendant la durée du projet. Les travaux portant sur l’analyse du risque dedissémination des nématodes, associés aux pratiques agricoles, ont conduit (1) à l’élaboration d’unmodèle conceptuel permettant d’identifier les stratégies de gestion du matériel agricole à risque et (2) àmettre en évidence et à quantifier l’importance de la dispersion des nématodes à kyste par les travauxdu sol et par le matériel agricole à l’échelle parcellaire et inter-parcellaire. Les travaux menés enpartenariat avec des industriels ainsi qu’en stations expérimentales ont permis la production d’un outilinteractif d’analyse de risque caractérisant les phases critiques de différents process de traitements desdéchets et d’effluents. Il apporte des éléments de réponse sur les performances d’assainissement dedifférents procédés de décontamination comme le compostage, le lagunage, la méthanisation, lachloration et le traitement thermique. Ce projet a aussi permis de cribler, en conditions contrôlées, desespèces végétales non favorables à la multiplication des nématodes à galle M. chitwoodi et M. fallax etpouvant être proposées comme plantes de rupture sur des sites contaminés

MUSCLE COMPOSITION IN RESPIRATORY ACIDOSIS

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategie