Showing papers on "Globodera rostochiensis published in 2016"

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

Abstract: 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. 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. 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.

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

Abstract: For each gene, lists the normalized expression data for each life stage, and (if significantly differentially expressed) which expression super cluster it is grouped into.

Identification, distribution and genetic diversity of the golden potato cyst nematode (Globodera rostochiensis) in Java Indonesia

Abstract: Golden potato cyst nematode (Globodera rostochiensis (Wollenweber) Behrens) is a nematode species which has worldwide regulatory concern. This nematode causes serious economic problem of potato losses in Indonesia. To study the distribution and genetic diversity of G. rostochiensis, 30 soil samples were collected from Java island, Indonesia. Seventeen out of thirty samples were infected by G. rostochiensis obtained from Pangalengan West Java, Wonosobo Central Java, Banjarnegara Central Java, Probolinggo East Java and Malang East Java. PCR assay with specific primers for G. rostochiensis (PITSr3) produced a single band of 434 base pairs (bp) length from all samples. The internal transcribed spacer (ITS1 and ITS5) regions were subjected to direct sequencing to study the genetic diversity of these populations. Five representative isolates were sequenced and compared with the sequences which available in GenBank. The sequencing data showed that all of the five population represented the same species, G. rosto...

Additional file 15: Figure S7. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Abstract: BackgroundThe 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.ResultsWe 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.ConclusionsThese 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.

Agricultural waste amendments improve inundation treatment of soil contaminated with potato cyst nematodes, Globodera rostochiensis and G. pallida.

Abstract: Potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are major constraints to potato production. They are distributed passively with soil adhering to farm machinery and harvested tubers, but also by waste soil from trading and processing plants. Inundation is considered an environmentally save method for disinfestation of waste soil. We investigated if agro-industrial waste products accelerate this disinfestation process by studying PCN survival, hatching and infectivity over time. Experiments were conducted in 2-L containers filled with 1.5 L non-amended soil, soil amended with steamed or fresh potato peels, calcium sulphate, steamed potato peels mixed with calcium sulphate, or leek leaves. In each container, cysts of G. rostochiensis or G. pallida were buried in the soil in retrievable bags and 400 ml water was added. Non-amended and non-inundated soils were the controls. It took 8 weeks of inundation of non-amended soil to reduce nematode survival by 72 %, while in amended soils survival was reduced up to 99.9 % after 4 weeks. After 1 week, fewer second-stage juveniles (J2) hatched and infected roots in inundated amended soil than in inundated non-amended soil. Host finding ability of surviving J2 was not affected. To understand mechanisms of nematode suppression, concentrations of short chain fatty acids (SCFA), gases (O2, CO2, H2S, CH4, and N2) and phospholipid fatty acids (PLFAs) were determined. Higher concentrations of SCFA and carbon dioxide and lower levels of oxygen were detected in amended treatments. H2S was occasionally detected in the leek-amended soil. The microbial biomass changed significantly in potato peels-amended soils.

Adverse effects of brassica green manures on encysted eggs, infective second-stage juveniles and the reproduction of Globodera rostochiensis

Abstract: Potato cyst nematodes (PCN), Globodera spp., are major pests of potato worldwide. In this study, the toxicity of an aqueous extract (1 g/ml) of fresh leaves of brassica species (savoy cabbage, cauliflower, broccoli, red cabbage, turnip, white mustard and edible radish) was tested on G. rostochiensis encysted eggs and infective, second-stage juveniles (J2) in vitro. Soil infested with cysts (Pi 20 eggs/g soil) was either fumigated with metham sodium and/or biofumigated with 2 % green manure of brassica and wheat under glasshouse conditions. More than 99 % of the J2 were paralysed after 24 h and <1 % of J2 hatched from encysted eggs during a 6-week exposure to brassica extracts. Nematode reproduction on the susceptible potato cv. Marfona was reduced by green manure amendments, the numbers of new cysts was reduced by between 60 % in radish- and 33 % in cauliflower-treated soil. The reproduction rate of G. rostochiensis was reduced to less than 1, and final populations of eggs and J2/g soil were reduced by between 73 % (white mustard) and 92 % (edible radish). Likewise, green manure of wheat and metham sodium fumigation decreased potato cyst nematode reproduction rates to below one, new cysts by 50 and 42 %, and final eggs/g soil by 81 and 88 %, respectively. In infested soil, total fresh weight of aerial parts and roots of potato was decreased by 64 %, while total weight of plants was increased between 21 and 74 % in brassica amended soil, and 56 and 76 % in wheat and metham sodium-treated soil, respectively.

Evaluation of cultural methods for the management of the golden nematode (Globodera rostochiensis) in Quebec, Canada

Abstract: Potato cyst nematodes are a major threat to potato production worldwide. In 2006, the isolation of the golden nematode, Globodera rostochiensis, in Quebec, Canada, led to the establishment of a quarantine area and the initiation of a research programme for the sustainable management of this regulated pest. In this study, the field efficacy of crop rotations and soil amendments was assessed in microplots for their potential to reduce populations of G. rostochiensis in the quarantine area. Crop rotation with a resistant potato cultivar was very effective in decreasing the population density of G. rostochiensis in soil. A single year with a cultivar carrying the H1 resistance gene reduced nematode populations by 62–95%. After 3 consecutive years of cropping to resistant potato, the number of viable eggs was zero in several microplots, and the overall population reduction was around 95%. Natural population decline with the cultivation of a non-host crop such as corn was around 30% per year. Trap cropp...

Morphological and molecular identification of potato and cereal cyst nematode isolates from Algeria and their phylogenetic relationships with other populations from distant theirgeographical areas

Abstract: A nematode survey conducted in 2013 in Algeria, revealed that potato cyst nematodes (PCN) and cereal cyst nematodes (CCN) are widely distributed in several potato and cereal growing regions of the country. Sixteen PCN populations from five localities and five CCN populations from four of these localities were collected and characterized at the morphological and molecular levels. The PCN populations were identified as Globodera rostochiensis and G. pallida occurring separately or in mixed populations. Two species of CCN were detected. Heterodera avenae was found in four localities, whereas H. hordecalis only in one locality in association with H. avenae. The morphological and morphometric identification of PCN and CCN was confirmed by diagnostic ITS-RFLP profiles and sequencing. Phylogenetic analysis of the ITS, D2-D3 expansion domains of the 28S rRNA gene and 18S rRNA gene was made for PCN and CCN populations. Globodera pallida and G. rostochiensis from Algeria show great similarity with European and South American populations. Because of the high divergence among Algerian populations of G. pallida and G. rostochiensis it can be assumed that they were multi-introduced in Algeria. The most divergent population of G. pallida, that formed a well-separated group with some populations from Chile and Peru, suggests a later or independent introduction of this population into Algeria. Heterodera avenae and H. hordecalis formed a well-supported cluster with the corresponding populations.

Effect of soil and soil bacteria on hatching activity towards potato cyst nematodes ( Globodera spp.)

Abstract: Soil samples taken from the ridge of field-grown potato (cv. British Queen) as well as from bulk soil of the same field were incubated with sterile potato root leachate or water. Samples were filtered and filtrates used in an in vitro bioassay to determine their effect on hatch of potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida . Concurrently, an experiment was established where the sterile potato root leachate or water was incubated with a sterile soil wash. Ridge soil was shown to induce significantly more hatching than bulk soil, indicating the presence of PCN hatching factors. When a soil wash of ridge soil was used it did not increase hatch, suggesting a role for soil microorganisms in the hatching process. Greater hatch of G. rostochiensis in bulk soil compared to G. pallida suggests a role for soil microorganisms in spontaneous hatch of PCN in vivo .

Pathotype and molecular characteristics of some Iranian potato cyst nematode populations, Globodera rostochiensis and impact of the resistant and susceptible potato cultivars on egg hatching *

Abstract: Potato cyst nematode, Globodera rostochiensis was reported from potato fields of Bahar County in Hamadan Province in 2008. In order to determine the pathotype of potato cyst nematode, ten populations of potato cyst nematode were collected from different potato fields in Bahar regions. Species identification was based on the morphological and morphometric characters of second stage juveniles and cysts, and by using species- specific primers and nucleotide sequences of the D2-D3 expansion segments of the 28S rRNA gene. Four potato cultivars viz Desiree, Marfona, Sante and Agria were used for pathotype determination, in pot experiments. The plants were treated by 6 ± 1 eggs and second stage juveniles and maintained in growth chambers at 18-22 °C for three months. Based on the results of resistance assessment and relative susceptibility of the tested cultivars the pathotype of the populations was determined as Ro1. The obtained sequences were compared through BLAST search from the NCBI and the phylogenic tree was depicted. The impact of susceptible cultivars Marfona, Desiree, resistant cultivars sante, and Agria on egg hatching indicated that there is no significant difference among the cultivars in most pot experiments and all the cultivars were placed in the same statistical groups.