The genome sequence for the potato cyst nematode Globodera pallida and its utilisation for improved control

Lead Research Organisation: University of Leeds
Department Name: Ctr for Plant Sciences

Abstract

The aim of this project is to define bases for novel control and enhanced pest management of the potato cyst nematode, Globodera pallida by obtaining and utilising the full genome sequence. The British Potato Council estimates the UK potato production, processing and retail markets to be worth c. £3 billion p.a. and the potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are the most economically important nematode problems of this industry. They occur in 65% of UK potato land with G. pallida present at 92% of these sites. PCN impose an annual cost in excess of £50 million on UK potato growers and threaten the future of the crop for many growers. Breeding for resistance since the mid 1950s has produced few commercially acceptable varieties with resistance to G. pallida. Currently used chemical control methods are under increasing pressure due to cost, environmental and health concerns and there are no benign alternatives to the currently used compounds. Control of G. pallida is an essential requirement to maintain the competitiveness of U.K. production. For example, the consumer demand for food with no pesticide residues has resulted in Waitrose sourcing all its potatoes from crops that have not received a nematicide treatment (www.waitrose.com). This requires imports from countries with a lower PCN incidence or requires a more extensive agricultural system in the UK. Consumer support is likely for UK produce that avoids pesticide residues or environmental harm and is soundly based on a sustainable approach. This proposal underpins the innovation needed to reach that outcome. Over the next 5 years, Wellcome Trust Sanger Institute will undertake a major genome sequencing programme aimed at nematodes and other helminths that are human or veterinary-important parasites. WTSI is willing to sequence this plant parasitic nematode for comparative genomic studies. Gene identification will be carried out ab initio and by experimental analysis. The scienfic outputs of the proposed work will be of relevance to plant nematologists and to the wider scientific community. A G. pallida genome sequence will allow the UK plant nematology community to remain internationally competitive and will enable new collaborative links to be built with researchers working in other fields including plant development, molecular plant pathology and evolution of resistance. The proposal has broad support. The British Potato Council will independently support CASE awards for postgraduate students that will be aligned with the project. Other support is evident from the letters of support from both industry and the scientific community.

Technical Summary

The aim of this project is to define bases for novel control and enhanced pest management of the potato cyst nematode, Globodera pallida, by obtaining the full genome sequence. The UK potato production, processing and retail markets are worth c. £3 billion p.a. and the potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are the most economically important nematode problems of this industry. They occur in 65% of UK potato land with G. pallida present at 92% of these sites. Breeding for resistance has produced few commercially acceptable varieties with resistance to G. pallida. Currently used chemical control methods are under increasing pressure due to cost, environmental and health concerns. Control of G. pallida is an essential requirement to maintain the competitiveness of U.K. production. Over the next 5 years, Wellcome Trust Sanger Institute will undertake a major genome sequencing programme aimed at nematodes and other helminths that are human or veterinary-important parasites. WTSI is willing to sequence this plant parasitic nematode for comparative genomic studies. The sequencing strategy can be considered as comprising several stages: (1) 1.9 million whole genome shotgun sequencing reads (~8x coverage), 20000 BAC end and 50000 fosmid end reads will be produced (2) initial assembly into contigs (3) generation of larger scaffolds (linked contigs) by automated resequencing (50,000 reads) from selected shotgun clones to extend the length of contigs that were truncated by the presence of GC-rich sequences, secondary structure, etc (4) assembly refinement and annotation. Gene identification will be carried out ab initio and by experimental analysis using tiling arrays.
 
Description The potato cyst nematode Globodera pallida is a major agricultural pathogen, threatening the £3 billion UK potato industry. Potato cyst nematodes are present on 65% of UK potato land, and controlling them costs UK growers in excess of £50 million annually. Mainstream commercial potato varieties show no resistance to Globodera pallida, and increasing controls on the use of nematicides, and increasing concern on the part of consumers about pesticide residues, mean that these nematodes threaten the future of the potato crop for many growers. Novel control and pest management approaches are thus urgently needed for this nematode.

The principal output from this research is a high-quality draft genome sequence of the potato cyst nematode Globodera pallida, which will prove a major resource in developing novel approaches to control this important plant pathogen. It will also be a valuable tool for researchers working with other parasitic nematode species for comparative genomic studies. Sequencing the genome of Globodera pallida proved challenging, as there was significant genetic diversity within the parasite population, confounding standard approaches to assembling the short sequencing 'reads' generated into a single sequence. Producing data from a range of different sequencing platforms allowed us to circumvent this problem and produce a draft sequence for the entire genome.

Genome sequence data itself is of little use without some 'annotation', indicating the putative function of different elements of the sequence, and in particular, which parts of the sequence are predicted to be genes - transcribed as RNA and then (for the most part) translated to produce proteins. To aid this gene finding, we sequenced RNA from two samples for each of eight key stages of the Globodera pallida life cycle, allowing us to unambiguously identify genes. As an additional benefit, these data allow us to infer exactly when each gene is turned on and off, an important clue to the function of the genes.

Advances in sequencing technologies allowed additional sequence data to be generated over and above that originally planned in the project. We have generated sequence for a number of additional G. pallida populations. These include four UK populations that differ in their virulence. We have also generated sequence data from from the closely related species of potato cyst nematode, G. rostochiensis, which differs in its virulence against a key resistance gene found in some potato cultivars.

We have characterised the transcriptomic response of infective juveniles of G. pallida to seven chemical compounds, including nematicides. Expression analysis was carried out after appropriate exposures to chloroquine, dazomet, imidacloprid, thiabendazole, levamisole, fluoxetine and ivermectin, considerably broadening the applied impact of the research.
Exploitation Route Complete knowledge of the genes expressed by potato cyst nematode at the various stages of its lifecycle will provide many opportunites for the development of new management or control strategies for this important crop pest.
Analysis of the data has produced a catalogue of candidate genes involved in initiation of the parasitic interaction with the host potato plant. Such genes will be important targets for the disruption of this process that could lead to plant resistance. One route for achieving this would be to develop plants that produce molecules to specifically target and suppress these genes or others known to be essential to the viability of the nematode.
The data that we have generated characterising the transcriptomic response of infective juveniles of G. pallida to seven chemical compounds, including nematicides, considerably broadens the applied impact of the research. Analysis of the gene complement of the nematode may provide additional targets for the development of new, biosafe nematicides. All of the genomic data is available to the scientific community and its analysis will continue to provide insights into the biology of Globodera pallida and the molecular basis of its pathology for many years. The transcriptome sequence from eight stages around the Globodera pallida lifecycle and in response to seven chemicals, including nematicides, allows global comparative gene expression to be analysed. Together, this provides probably the most comprehensive transcriptomic dataset for a nematode other than Caenorhabditis elegans and is a major resource for further functional analysis of genes.
The comparative genome and transcriptome sequence produced for more than six populations of G. pallida plus the closely related species G. rostochiensis will provide insights into key determinants of nematode virulence.
Molecular understanding of the interaction between potato cyst nematodes and their host will have important implications for our understanding of plant development, and of how plant development can be controlled. Disrupting this reprogramming process will also be an important target for control of the nematode.
Sectors Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

URL http://www.sanger.ac.uk/resources/downloads/helminths/globodera-pallida.html
 
Description Potato cyst nematode (PCN), a microscopic worm that attacks potato plants, costs the UK potato industry £43 million/year. Control of PCN relies on chemicals that are often essential for economic cropping in the UK. EU legislation has already resulted in the recent loss of two nematicides in response to environmental concerns. There is severe doubt that future pesticides with appropriate environmental safety can reach the high control levels that are required. Having the genome sequence of PCN underpins new long-term strategies to design novel, benign methods of control. As the first genome sequence available for any cyst nematode, it also provides valuable information for understanding the important cyst nematode pests of other crops such as soybean, sugar beet and wheat. The sequence data from this project is publicly available and has already been utilised by nematologists around the world. It has provided the foundation for further funding, leading to research grants and at least four PhD studentships at institutions in the UK. It has directly led to the formation of an international consortium of researchers from both academia and government bodies who are using the sequence data generated for Globodera rostochiensis to understand important aspects of its biology, determine differences between pathotypes that may be associated with virulence and undertake comparative genomics with other Globodera species.
First Year Of Impact 2013
Sector Agriculture, Food and Drink,Environment
Impact Types Economic,Policy & public services

 
Description China Scholarship
Amount £72,000 (GBP)
Organisation University of Leeds 
Department China Scholarship Council
Sector Academic/University
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description Potato Crops Small Research Grant
Amount £3,232 (GBP)
Organisation Scottish Crop Research Institute (SCRI) 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2014 
End 04/2015
 
Title G. pallida genome assembly 
Description BLASTable database of predicted genes, proteins and assembly scaffolds of the Globodera pallida genome assembly. All data is also available for FTP download. All data is available directly through the website of the Wellcome Trust Sanger Institute and also through WormBase ParaSite, that allows integration with other parasitic nematode genome resources. 
Type Of Material Database/Collection of data 
Year Produced 2011 
Provided To Others? Yes  
Impact The data has been instrumental in subsequent research carried out by the original research team to investigate, for example, effectors involved in the plant-nematode interaction; components of neuronal signalling; and genes involved in dormancy and the response to heat. As all data are publicly available, they have also been used by many other groups around the world. As the first complete sequence data for a cyst nematode, the data set has been particularly used in comparative genomics studies. 
URL http://www.sanger.ac.uk/resources/downloads/helminths/globodera-pallida.html
 
Title G. rostochiensis genome 
Description As part of the project to sequence the genome of the potato cyst nematode Globodera pallida, genomic data was also generated for the sister species G. rostochiensis. This sequence was assembled and a consortium was subsequently formed to annotate the genome and make the data more widely available. The genome assembly together with predicted genes and proteins is now available with facilities for BLAST search, key word search of annotations, InterPro domains etc. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The database has been used widely both within our group and those of numerous collaborators to identify genes involved in a range of important aspects of nematode biology such as those encoding effector proteins, receptors involved in neurotransmission, or with a role in the response to temperature and other stresses. This data is then feeding in to a range of other research projects. For example, analysis of effector genes has identified a promoter motif associated with specific expression in a single nematode gland cell that can be used to predict novel effectors. 
URL http://globodera.bio.ed.ac.uk/
 
Description Globodera rostochiensis genome annotation 
Organisation Agriculture and Agri-Food Canada
Country Canada 
Sector Public 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation French National Institute of Agricultural Research
Department INRA Rennes Centre
Country France 
Sector Public 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation French National Institute of Agricultural Research
Department INRA Sophia Antipolis
Country France 
Sector Public 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation Government of Canada
Country Canada 
Sector Public 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation James Hutton Institute
Country United Kingdom 
Sector Public 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Globodera rostochiensis genome annotation 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution The collaboration was set up to analyse and annotate the genome of the golden potato cyst nematode Globodera rostochiensis. The foundation for this was a genome assembly produced as part of our BBSRC grant BB/F000642/1 for which the focus was the sister species G. pallida. Transcriptome data for two life stages was also contributed by our team. One member of our team initiated and coordinates the collaboration and took a major role in preparing the genome assembly for group manual annotation. Four members of our research team have been actively involved in the specialist annotation of the genome and the correction of gene models.
Collaborator Contribution Partners at the University of Edinburgh have contributed bioinformatics expertise, use of computing facilities and hosted a group annotation event attended by all members of the collaboration. Partners in Canada have contributed genome and transcriptome data and taken part in genome annotation. All other partners have contributed their specific expertise in manual annotation of particular gene families.
Impact Transcriptome data has been mapped to the genome assembly. Almost 1500 gene models (>10% of the total) have been manually curated and corrected by the collaborators, to act as a training set for improved gene predictions. A promoter motif has been identified that is associated with expression in the main, effector-producing gland cell of potato cyst nematodes. This provides a new route for prediction of novel effectors in cyst nematodes and has formed the basis for further studies by collaborating partners. A manuscript describing the genome and particular features of interest has been published in Genome Biology.
Start Year 2013
 
Description Rotylenchulus transcriptome 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution We have contributed transcriptome sequence data and assemblies for different life stages of the reniform nematode Rotylenchulus reniformis.
Collaborator Contribution The collaborators at USDA have amassed their own set of genome and transcriptome sequence data and are integrating our data set with theirs. This data has already been used to further our research into nematode effectors.
Impact A manuscript describing the genome and transcriptome of Rotylenchulus reniformis is in preparation by our collaborators
Start Year 2014
 
Description Frontier Potato Group Presentation 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk sparked questions and discussion afterwards: possibilities of commercial direction.

The audience were aware of GM technology that could provide a solution to nematode pathogens
Year(s) Of Engagement Activity 2012,2015
 
Description G. rostochiensis genome media 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact The publication of the Globodera rostochiensis genome sequence and its analysis prompted a press release and subsequent articles in a number of media outlets, including Horticulture Week, South East Farmer and online sites such as phys.org, spudsmart.com and seedquest.com
Year(s) Of Engagement Activity 2016
URL http://www.seedquest.com/news.php?type=news&id_article=78208&id_region=&id_category=&id_crop=
 
Description KWS 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Information provided to company regarding new biotechnology

Company were able to make economic decisions
Year(s) Of Engagement Activity 2010
 
Description University Open Days 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The work undertaken by the research team in developing nematode resistant crops was demonstrated to visitors. Visitors were engaged in discussions about the work and GM technology in general. Postgraduate students, postdocs and technicians associated with the grants all took part in either preparing or demonstrating the events.

Prospective students encouraged to apply for courses with an applied biology focus
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013