Selection for virulence in the potato cyst nematode Globodera pallida.
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ABSTRACT:
PROVIDER: PRJEB41175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4804760_1.fastq.gz | Fastqsanger.gz | |||
| ERR4804760_2.fastq.gz | Fastqsanger.gz | |||
| ERR4804770_1.fastq.gz | Fastqsanger.gz | |||
| ERR4804770_2.fastq.gz | Fastqsanger.gz | |||
| ERR4804761_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:As part of the Globodera pallida (potato cyst nematode) genome project weare profiling the transcriptome of the parasite across its life cycle usingRNA-Seq. . This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2012-11-28 | E-ERAD-55 | biostudies-arrayexpress
Project description:Sets of seven 2-week old potato plants carrying the nematode resistance gene H1, grown from tuber ‘chits’ in sandy loam at a constant temperature of 20 ºC and a light cycle of 16 hour light/8 hour dark, were each inoculated in the roots evenly with 2000 juveniles of the virulent potato cyst nematode Globodera pallida, or with the avirulent G. rostochiensis pathotype Ro1, or with water. Plants were manually watered throughout the duration of the experiment. 5, 17 and 33 days after inoculation, the roots were carefully washed and root tissue samples were individually flash-frozen in liquid nitrogen and stored at –80 ºC. Total RNA isolations were performed using the Qiagen RNeasy kit. All samples were treated with DNase. The experiment was replicated twice. Keywords: Direct comparison
2007-09-01 | GSE8220 | GEO
Project description:Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest (including desiccation, cryopreservation, hatching inhibition and dauer stages) are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in a dessicated state unhatched nematodes within the egg dispersal unit inside the cyst. Long term survival seems to be associated primarily with species that have a very restricted host range which requires surviving unhatched in the absence of the host for extended periods of time. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G.pallida to hydration and following exposure to tomato root diffusate using microarray gene expression analysis from a broad set of genes. Surprisingly, many unique genes were activated in the population of diapaused eggs. Transport activity was activated in both quiescent and diapaused eggs; however, the transport function genes were very different between them. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long term survival.
2016-02-01 | E-MTAB-3824 | biostudies-arrayexpress
Project description:Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii
| PRJEB73769 | ENA
Project description:Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.
| S-EPMC7760817 | biostudies-literature
Project description:Globodera pallida genomic sequencing
| PRJEB2242 | ENA
Project description:The mitochondrial genome (mtDNA) of the plant parasitic nematode Globodera pallida exists as a population of small, circular DNAs that, taken individually, are of insufficient length to encode the typical metazoan mitochondrial gene complement. As far as we are aware, this unusual structural organization is unique among higher metazoans, although interesting comparisons can be made with the multipartite mitochondrial genome organizations of plants and fungi. The variation in frequency between populations displayed by some components of the mtDNA is likely to have major implications for the way in which mtDNA can be used in population and evolutionary genetic studies of G. pallida.
| S-EPMC1460896 | biostudies-other
Project description:BACKGROUND:The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure - the syncytium - which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium. RESULTS:The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure. CONCLUSION:This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.
| S-EPMC4213498 | biostudies-literature
Project description:TaxonomyPhylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera.BiologyPotato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy-between 4 and 6 weeks in total-is almost unparalleled in plant-pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs.Host rangeThe host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007).Disease symptomsSymptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers.Disease controlResistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks.Useful websitesGenomic information for PCN is accessible through WormBase ParaSite.
| S-EPMC8035638 | biostudies-literature