A synthetic biology approach to develop durable disease resistance in crops
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
A billion people alive today are undernourished. Crop losses due to pests and diseases are a major obstacle towards achieving global food security. In developing countries, pests and diseases account for up to half of crop losses. In developed countries, the use of pesticides, fungicides, and other chemicals for agriculture are heavily restricted due to EU directives. New, durable, sustainable, 'green' control measures are urgently needed.
Plants in the field are often under simultaneous attack from many different types of pathogens. Some of these are from above ground (i.e. the potato late blight pathogen Phytophthora infestans), and some are from below ground (i.e. microscopic nematode worms that parasitise plant roots). Both types of pathogens 'inject' proteins into the plant to hi-jack plant machinery to benefit themselves and help spread infection. These proteins (known as effectors) often interact with normal crop proteins, and in some way modify them to help the pathogen. The key research questions remain:
1) How do effectors modify host proteins to promote infection?
2) Do different types of pathogens target the same host proteins?
3) Can our understanding of the molecular interaction allow us to disrupt it, favouring plant immunity?
I aim to determine how pathogen effectors physically interact with plant proteins in order to direct changes to the latter so that the pathogens can no-longer manipulate them. To accomplish this I propose a collaboration between the University of Dundee in Scotland and the John Innes Centre in Norwich. The University of Dundee Division of Plant sciences, together with the James Hutton Institute, aim to apply aspects of plant breeding, pathology and ecology to allow fundamental research to be readily translated to end-users. The John Innes Centre has extensive experience of structural biology, in particular in the area of plant-pathogen interactions. Bringing together these complementary institutes is vital to achieve the aims.
Potential applications and benefits:
The proposed work will provide a new understanding of how pathogens can manipulate and infect their host. With this understanding, the informed re-design of specific plant proteins so they can no-longer be targeted by pathogens will undermine and prevent infection. Proteins targeted by multiple pathogens are likely to be very important to successful infection. Modifying these by editing the plant DNA will help to create a durable 'green' solution to the use of pesticides against multiple different pathogens. This could help to ensure food production and security in developing and developed countries.
Plants in the field are often under simultaneous attack from many different types of pathogens. Some of these are from above ground (i.e. the potato late blight pathogen Phytophthora infestans), and some are from below ground (i.e. microscopic nematode worms that parasitise plant roots). Both types of pathogens 'inject' proteins into the plant to hi-jack plant machinery to benefit themselves and help spread infection. These proteins (known as effectors) often interact with normal crop proteins, and in some way modify them to help the pathogen. The key research questions remain:
1) How do effectors modify host proteins to promote infection?
2) Do different types of pathogens target the same host proteins?
3) Can our understanding of the molecular interaction allow us to disrupt it, favouring plant immunity?
I aim to determine how pathogen effectors physically interact with plant proteins in order to direct changes to the latter so that the pathogens can no-longer manipulate them. To accomplish this I propose a collaboration between the University of Dundee in Scotland and the John Innes Centre in Norwich. The University of Dundee Division of Plant sciences, together with the James Hutton Institute, aim to apply aspects of plant breeding, pathology and ecology to allow fundamental research to be readily translated to end-users. The John Innes Centre has extensive experience of structural biology, in particular in the area of plant-pathogen interactions. Bringing together these complementary institutes is vital to achieve the aims.
Potential applications and benefits:
The proposed work will provide a new understanding of how pathogens can manipulate and infect their host. With this understanding, the informed re-design of specific plant proteins so they can no-longer be targeted by pathogens will undermine and prevent infection. Proteins targeted by multiple pathogens are likely to be very important to successful infection. Modifying these by editing the plant DNA will help to create a durable 'green' solution to the use of pesticides against multiple different pathogens. This could help to ensure food production and security in developing and developed countries.
Technical Summary
Multiple phylogenetically diverse pathogens that have co-evolved with the same host, and that require similar manipulations of that host, are likely to have targeted the same pathways and proteins. This proposal will analyse the structural basis of the interactions between effectors and host targets with the aim of using synthetic biology to design modified targets that evade disruption by effectors. The main aims will be:
1. Identification of potato host proteins that are common targets of Phytophthora infestans and potato cyst nematode effectors by Y2H, using known P. infestans effector targets to identify corresponding nematode effectors. Subsequent validation in planta by Bimolecular fluorescence complementation and co-immunoprecipitation will be performed.
2. Determine the three-dimensional structures of host targets in effector-bound and effector-unbound states.
3. Elucidate the biology of effector-target interactions using a combination of biophysical and molecular biological analytical techniques. Provide high-throughput bioassays that will monitor the effectiveness of perturbing these molecular interactions.
4. Use knowledge of structure-function relationships between effectors and their targets to re-design target proteins to undermine effector binding/activity yet retain endogenous function.
Understanding the structural basis of how an effector-bound target functions differently to promote pathogen success, with sufficient detail to undermine the interaction, can be applied directly to crop species using synthetic biology genome editing tools.
1. Identification of potato host proteins that are common targets of Phytophthora infestans and potato cyst nematode effectors by Y2H, using known P. infestans effector targets to identify corresponding nematode effectors. Subsequent validation in planta by Bimolecular fluorescence complementation and co-immunoprecipitation will be performed.
2. Determine the three-dimensional structures of host targets in effector-bound and effector-unbound states.
3. Elucidate the biology of effector-target interactions using a combination of biophysical and molecular biological analytical techniques. Provide high-throughput bioassays that will monitor the effectiveness of perturbing these molecular interactions.
4. Use knowledge of structure-function relationships between effectors and their targets to re-design target proteins to undermine effector binding/activity yet retain endogenous function.
Understanding the structural basis of how an effector-bound target functions differently to promote pathogen success, with sufficient detail to undermine the interaction, can be applied directly to crop species using synthetic biology genome editing tools.
Planned Impact
In addition to the numerous and diverse academic beneficiaries detailed in the appropriate section, the proposed work will generate data with strong translational potential that meets societal needs of relevance to the Food Security Strategic Priority area of the BBSRC.
Although a challenging aim, the long-term goal of the research is to develop approaches with the potential to reduce pesticide use and increase agricultural stability. This may benefit commercial farmers by limiting the need for repeated spraying of pesticides, as well as subsistence farming where growers do not have access to means of chemical disease control. Consistent agricultural production in the UK is critical to maintain a position of economic competitiveness, particularly in light of recent reductions of pesticide use by EU legislation (91/414/EEC). In addition, the substantial gross value added to the economy for every pound invested in JIC science represents the wide indirect benefit of the research.
The economic and farming impact will need to be realised through industry. Biotechnology industry will benefit from the research, and the UK is well positioned to ensure effective exploitation. This will be carried out through the extensive network of industrial partners associated with the host institution and group.
Realising the potential impact of the proposal will rely on the extensive public engagement activities detailed in the pathways to impact. In summary, taking advantage of the resources available at two geographically distinct locations, with exceptional track records of public engagement, will ensure the broadest possible impact. Through engagement with schools, the education sector has the potential to benefit from the research through knowledge exchange. Especially relevant is the long-term potential of the research to contribute to food security, global sustainability (limiting potentially damaging chemical inputs into the environment) and to enthusing the next generation of scientists. Synthetic biology in particular is in its infancy. Promoting this discipline to the public, starting at a young age, will allow the UK to make the most of the opportunities it provides. Promoting doctors in science in local schools, with an emphasis on gender equality, will aim to address some of the general issues in science.
Although a challenging aim, the long-term goal of the research is to develop approaches with the potential to reduce pesticide use and increase agricultural stability. This may benefit commercial farmers by limiting the need for repeated spraying of pesticides, as well as subsistence farming where growers do not have access to means of chemical disease control. Consistent agricultural production in the UK is critical to maintain a position of economic competitiveness, particularly in light of recent reductions of pesticide use by EU legislation (91/414/EEC). In addition, the substantial gross value added to the economy for every pound invested in JIC science represents the wide indirect benefit of the research.
The economic and farming impact will need to be realised through industry. Biotechnology industry will benefit from the research, and the UK is well positioned to ensure effective exploitation. This will be carried out through the extensive network of industrial partners associated with the host institution and group.
Realising the potential impact of the proposal will rely on the extensive public engagement activities detailed in the pathways to impact. In summary, taking advantage of the resources available at two geographically distinct locations, with exceptional track records of public engagement, will ensure the broadest possible impact. Through engagement with schools, the education sector has the potential to benefit from the research through knowledge exchange. Especially relevant is the long-term potential of the research to contribute to food security, global sustainability (limiting potentially damaging chemical inputs into the environment) and to enthusing the next generation of scientists. Synthetic biology in particular is in its infancy. Promoting this discipline to the public, starting at a young age, will allow the UK to make the most of the opportunities it provides. Promoting doctors in science in local schools, with an emphasis on gender equality, will aim to address some of the general issues in science.
Organisations
- University of Dundee (Lead Research Organisation)
- Science and Advice for Scottish Agriculture (Collaboration)
- Government of Canada (Collaboration)
- James Hutton Institute (Collaboration)
- Iowa State University (Collaboration)
- University of Warwick (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- John Innes Centre (Collaboration)
- University of Ghent (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
- Wageningen University & Research (Collaboration)
- University of Bristol (Collaboration)
- University of St Andrews (Collaboration)
- University of Hull (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- University of California, Davis (Collaboration)
- National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) (Collaboration)
- North Carolina State University (Collaboration)
- King Abdulaziz University (Collaboration)
- Agriculture and Agriculture-Food Canada (Collaboration)
- University of Illinois Urbana-Champaign (Collaboration)
- University of Cambridge (Fellow)
People |
ORCID iD |
Sebastian Eves-Van Den Akker (Principal Investigator / Fellow) |
Publications
Eves-Van Den Akker S
(2015)
A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual.
in Molecular ecology
Eves-Van Den Akker S
(2016)
Functional C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis.
in Molecular plant pathology
Eves-Van Den Akker S
(2016)
The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.
in Genome biology
Description | Plant-parasitic nematodes precisely coordinate the infection process using a suite of "molecular tools", termed effectors. Such effectors are delivered directly into the plant through a needle-like stylet to suppress plant immunity, and are central in dictating the outcome of infection. A high impact output from 2016 was the discovery of a "parasitism promoter" in the plant-parasitic nematode G. rostochiensis. This motif, termed the "DOG box", is associated with, and thus can be used to predict, Effectors. For the first time, we are able to predict effectors in silico and have massively expanded the known effector repertoire for a number of related species. This discovery was critically important for progression through the objectives: nematode effectors are the main focus of the fellowship, and identification thereof is rate limiting to progress. |
Exploitation Route | The ability to predict effectors in silico will expedite research into a number of economically important plant pathogens in the UK and abroad. Further, the presence of one motif that unifies hundreds of sequence-unrelated effectors implies the existence of a master regulator that binds this motif, and thus orchestrates the parasitism process. In a spotlight article highlighting the implications of the DOG box, the existence of such a "single point of failure" was predicted and named (DOG Master-Regulator (DOGMR)), with the aim of providing a high-value focal point for future research. |
Sectors | Agriculture Food and Drink Chemicals Environment |
URL | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0985-1 |
Description | The key findings have been highlighted in a white paper entitled: "Foundational and translational research opportunities to improve plant health." to be presented to research councils in the UK and the US to influence funding policy. |
First Year Of Impact | 2017 |
Sector | Agriculture, Food and Drink |
Impact Types | Policy & public services |
Description | UK-US plant health workshop and white paper (currently under revision). |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Membership of a guideline committee |
Description | BBSRC International Worksop |
Amount | £9,527 (GBP) |
Funding ID | BB/N021908/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2016 |
End | 12/2016 |
Description | BSPP Undergraduate Vacation Bursary Fund |
Amount | £2,500 (GBP) |
Organisation | British Society of Plant Pathoogy |
Sector | Learned Society |
Country | United Kingdom |
Start | 04/2016 |
End | 08/2016 |
Description | David Phillips Fellowship |
Amount | £979,232 (GBP) |
Funding ID | BB/R011311/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2018 |
End | 05/2023 |
Description | Institutional Strategic Support Fund |
Amount | £10,000 (GBP) |
Organisation | University of Dundee |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2017 |
End | 04/2017 |
Description | Research Incentive Grant |
Amount | £7,466 (GBP) |
Funding ID | 70741 |
Organisation | Carnegie Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2017 |
End | 01/2018 |
Title | DOG box prediction |
Description | The ability to identify plant-parasitic nematode effectors by association with a promoter motif. For the first time we are able to predict nematode effector in silico, rapidly expediting one of the major rate limiting steps in progress. |
Type Of Material | Biological samples |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | A spotlight article highlighting the various implications of this method followed the primary publication, and has lead to a number of novel research directions and collaborations. |
URL | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0985-1 |
Title | Additional file 10: Table S3. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | High confidence effectors. (XLSX 13 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_Table_S3_of_The_genome_of_th... |
Title | Additional file 10: Table S3. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | High confidence effectors. (XLSX 13 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_Table_S3_of_The_genome_of_th... |
Title | Additional file 12: Table S4. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Genes acquired via HGT in other cyst and root-knot nematodes also found in the genome of G. rostochiensis. (XLSX 21 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_12_Table_S4_of_The_genome_of_th... |
Title | Additional file 12: Table S4. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Genes acquired via HGT in other cyst and root-knot nematodes also found in the genome of G. rostochiensis. (XLSX 21 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_12_Table_S4_of_The_genome_of_th... |
Title | Additional file 13: Table S5. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Variants summary. (XLSX 11 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_13_Table_S5_of_The_genome_of_th... |
Title | Additional file 13: Table S5. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Variants summary. (XLSX 11 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_13_Table_S5_of_The_genome_of_th... |
Title | Additional file 14: Table S6. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Molecular markers of pathotypes Ro1, 4 and 5. (XLSX 24 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_14_Table_S6_of_The_genome_of_th... |
Title | Additional file 14: Table S6. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Molecular markers of pathotypes Ro1, 4 and 5. (XLSX 24 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_14_Table_S6_of_The_genome_of_th... |
Title | Additional file 16: Table S7. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | SNP allele frequency correlation with virulence in non-effectors. (XLSX 15 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_16_Table_S7_of_The_genome_of_th... |
Title | Additional file 16: Table S7. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | SNP allele frequency correlation with virulence in non-effectors. (XLSX 15 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_16_Table_S7_of_The_genome_of_th... |
Title | Additional file 18: Table S8. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Effector islands. (XLSX 13 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_18_Table_S8_of_The_genome_of_th... |
Title | Additional file 18: Table S8. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Effector islands. (XLSX 13 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_18_Table_S8_of_The_genome_of_th... |
Title | Additional file 1: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S1. List of verified effector genes from Bursaphelenchus xylophilus used for the analysis of the promoter regions using the differential motif discovery algorithm HOMER. The venny diagram compares the genes in the input effector list with the results from the first output from FIMO analysis. The motif STATWWAWRS is present in the promoter region of 26 genes verified effector genes, which represents approximatly 62% of the genes. (XLSX 102 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 1: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S1. List of verified effector genes from Bursaphelenchus xylophilus used for the analysis of the promoter regions using the differential motif discovery algorithm HOMER. The venny diagram compares the genes in the input effector list with the results from the first output from FIMO analysis. The motif STATWWAWRS is present in the promoter region of 26 genes verified effector genes, which represents approximatly 62% of the genes. (XLSX 102 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 21: Table S9. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. rostochiensis putative DOG effectors. (XLSX 36 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_21_Table_S9_of_The_genome_of_th... |
Title | Additional file 21: Table S9. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. rostochiensis putative DOG effectors. (XLSX 36 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_21_Table_S9_of_The_genome_of_th... |
Title | Additional file 22: Table S10. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. pallida putative DOG effectors. (XLSX 44 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_22_Table_S10_of_The_genome_of_t... |
Title | Additional file 22: Table S10. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. pallida putative DOG effectors. (XLSX 44 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_22_Table_S10_of_The_genome_of_t... |
Title | Additional file 23: Table S11. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. rostochiensis genome libraries. (XLSX 9 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_23_Table_S11_of_The_genome_of_t... |
Title | Additional file 23: Table S11. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | G. rostochiensis genome libraries. (XLSX 9 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_23_Table_S11_of_The_genome_of_t... |
Title | Additional file 25: Table S12. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Microsatellite abundance. (XLSX 8 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_25_Table_S12_of_The_genome_of_t... |
Title | Additional file 25: Table S12. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Microsatellite abundance. (XLSX 8 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_25_Table_S12_of_The_genome_of_t... |
Title | Additional file 2: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S2. Nematode genes that have at least one occurence (repetition) of the motif STATAWAARS in the promoter region. The predicted presence or absence of the signal peptide is indicated by 1 or 0 (zero), respectively. (XLSX 48 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_2_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 2: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S2. Nematode genes that have at least one occurence (repetition) of the motif STATAWAARS in the promoter region. The predicted presence or absence of the signal peptide is indicated by 1 or 0 (zero), respectively. (XLSX 48 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_2_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 3: Table S1. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Genome annotation. (XLSX 9 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_Table_S1_of_The_genome_of_the... |
Title | Additional file 3: Table S1. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Genome annotation. (XLSX 9 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_Table_S1_of_The_genome_of_the... |
Title | Additional file 5: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S5. Limited overlap (venny diagram) between the top most abundant thirty genes represented in the gland cells and the list of 42 genes used for the discovery of DNA sequence motif. (XLSX 68 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 5: of STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus |
Description | Table S5. Limited overlap (venny diagram) between the top most abundant thirty genes represented in the gland cells and the list of 42 genes used for the discovery of DNA sequence motif. (XLSX 68 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_STATAWAARS_a_promoter_motif_associ... |
Title | Additional file 7: File S1. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Clusters and normalised expression tables. (XLSX 956 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_7_File_S1_of_The_genome_of_the_... |
Title | Additional file 7: File S1. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Clusters and normalised expression tables. (XLSX 956 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_7_File_S1_of_The_genome_of_the_... |
Title | Additional file 9: Table S2. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Alien indices. (XLSX 81 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_9_Table_S2_of_The_genome_of_the... |
Title | Additional file 9: Table S2. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence |
Description | Alien indices. (XLSX 81 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_9_Table_S2_of_The_genome_of_the... |
Title | Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual |
Description | Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK, and adopt a metagenetics approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one fifth contain a mix of mitotypes, and less than 3 % contain all three mitotypes. Within mixed fields we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying "pathoscape". Finally, we assess mitotype distribution at the level of the individual cyst, and provide evidence of "hybrids". This study provides a method for accurate, quantitative and high throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant-parasite. |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.pd7r6 |
Title | Data from: Effector gene birth in plant parasitic nematodes: neofunctionalization of a housekeeping glutathione synthetase gene |
Description | Plant pathogens and parasites are a major threat to global food security. Plant parasitism has arisen four times independently within the phylum Nematoda, resulting in at least one parasite of every major food crop in the world. Some species within the most economically important order (Tylenchida) secrete proteins termed effectors into their host during infection to re-programme host development and immunity. The precise detail of how nematodes evolve new effectors is not clear. Here we reconstruct the evolutionary history of a novel effector gene family. We show that during the evolution of plant parasitism in the Tylenchida, the housekeeping glutathione synthetase (GS) gene was extensively replicated. New GS paralogues acquired multiple dorsal gland promoter elements, altered spatial expression to the secretory dorsal gland, altered temporal expression to primarily parasitic stages, and gained a signal peptide for secretion. The gene products are delivered into the host plant cell during infection, giving rise to "GS-like effectors". Remarkably, by solving the structure of GS-like effectors we show that during this process they have also diversified in biochemical activity, and likely represent the founding members of a novel class of GS-like enzyme. Our results demonstrate the re-purposing of an endogenous housekeeping gene to form a family of effectors with modified functions. We anticipate that our discovery will be a blueprint to understand the evolution of other plant-parasitic nematode effectors, and the foundation to uncover a novel enzymatic function. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.7vd0160 |
Title | Data from: Functional C-terminally encoded peptide (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis |
Description | Sedentary plant-parasitic nematodes (PPNs) induce and maintain an intimate relationship with their host, stimulating cells adjacent to root vascular tissue to re-differentiate into unique and metabolically active 'feeding sites'. The interaction between PPNs and their host is mediated by nematode effectors. We describe the discovery of a large and diverse family of effector genes, encoding C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone mimics (RrCEPs), in the syncytia-forming plant parasite Rotylenchulus reniformis. The particular attributes of RrCEPs distinguish them from all other CEPs, regardless of origin. Together with the distant phylogenetic relationship of R. reniformis to the only other CEP-encoding nematode genus identified to date (Meloidogyne), this suggests that CEPs probably evolved de novo in R. reniformis. We have characterized the first member of this large gene family (RrCEP1), demonstrating its significant up-regulation during the plant-nematode interaction and expression in the effector-producing pharyngeal gland cell. All internal CEP domains of multi-domain RrCEPs are followed by di-basic residues, suggesting a mechanism for cleavage. A synthetic peptide corresponding to RrCEP1 domain 1 is biologically active and capable of up-regulating plant nitrate transporter (AtNRT2.1) expression, whilst simultaneously reducing primary root elongation. When a non-CEP-containing, syncytia-forming PPN species (Heterodera schachtii) infects Arabidopsis in a CEP-rich environment, a smaller feeding site is produced. We hypothesize that CEPs of R. reniformis represent a two-fold adaptation to sustained biotrophy in this species: (i) increasing host nitrate uptake, whilst (ii) limiting the size of the syncytial feeding site produced. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.q8h75 |
Title | Data from: Identification of candidate effector genes of Pratylenchus penetrans |
Description | Pratylenchus penetrans is one of the most important species among root lesion nematodes (RLNs) due to the detrimental and economic impact that it causes in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbors a significant number of secreted proteins that play key roles during parasitism. Here we combined spatially and temporally resolved next generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the esophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen. This article is protected by copyright. All rights reserved. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.4h44313 |
Title | G. rostochiensis genome |
Description | Genome and transcriptome sequence for potato cyst nematode Globodera rostochiensis. all scripts (https://github.com/DRL/GenomeBiology2016_globodera_rostochiensis), raw data (PRJNA305631), and crucially all analysed data (http://dx.doi.org/10.5061/dryad.4s5r6), were made available to the scientific community. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | N/A |
URL | http://datadryad.org/resource/doi:10.5061/dryad.4s5r6 |
Description | BBSRC-AFLF: UoD-JIC |
Organisation | John Innes Centre |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Proteins of interest and in vivo studies |
Collaborator Contribution | Crystallisation platform and in vitro studies |
Impact | Still active. Multi disciplinary: Cell biology Biochemistry/structural biology Plant pathology |
Start Year | 2015 |
Description | Metagenetics of G. pallida |
Organisation | James Hutton Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Coordinating the project and carrying out the research |
Collaborator Contribution | Leeds: equipment and financial SASA: samples JHI: equipment UoE: sequencing |
Impact | Publication attracted media attention from 11 media outlets: www.farminguk.com Researchers make technological breakthrough against potato cyst nematode http://www.farminguk.com/News/Researchers-make-technological-breakthrough-against-potato-cyst-nematode_37583.html www.dundeeandanguschamber.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.dundeeandanguschamber.co.uk/news/James-Hutton-News_0_3067.html phys.org Researchers make technological breakthrough against potato cyst nematode http://phys.org/news/2015-11-technological-breakthrough-potato-cyst-nematode.html www.hortweek.com Match potato varieties to local nematode populations, say researchers http://www.hortweek.com/match-potato-varieties-local-nematode-populations-say-researchers/edibles/article/1370971 www.agcc.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.agcc.co.uk/news-article/researchers-make-technological-breakthrough-against-potato-cyst-nematode www.stackyard.com Breakthrough against potato cyst nematode http://www.stackyard.com/news/2015/11/crop/01_james_hutton_pcn.html www.fwi.co.uk Scientists make breakthrough in potato pest control http://www.fwi.co.uk/arable/scientists-make-breakthrough-in-potato-pest-control.htm The Courier (Main Edition) Researchers breaking new ground with G pallida fight The Courier (Dundee Edition) Researchers breaking new ground with G pallida fight www.farmingfutures.org.uk Breakthrough against potato cyst nematode http://www.farmingfutures.org.uk/blog/breakthrough-against-potato-cyst-nematode Farmers Guardian Research breakthrough in the battle against PCN |
Start Year | 2014 |
Description | Metagenetics of G. pallida |
Organisation | Science and Advice for Scottish Agriculture |
Country | United Kingdom |
Sector | Public |
PI Contribution | Coordinating the project and carrying out the research |
Collaborator Contribution | Leeds: equipment and financial SASA: samples JHI: equipment UoE: sequencing |
Impact | Publication attracted media attention from 11 media outlets: www.farminguk.com Researchers make technological breakthrough against potato cyst nematode http://www.farminguk.com/News/Researchers-make-technological-breakthrough-against-potato-cyst-nematode_37583.html www.dundeeandanguschamber.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.dundeeandanguschamber.co.uk/news/James-Hutton-News_0_3067.html phys.org Researchers make technological breakthrough against potato cyst nematode http://phys.org/news/2015-11-technological-breakthrough-potato-cyst-nematode.html www.hortweek.com Match potato varieties to local nematode populations, say researchers http://www.hortweek.com/match-potato-varieties-local-nematode-populations-say-researchers/edibles/article/1370971 www.agcc.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.agcc.co.uk/news-article/researchers-make-technological-breakthrough-against-potato-cyst-nematode www.stackyard.com Breakthrough against potato cyst nematode http://www.stackyard.com/news/2015/11/crop/01_james_hutton_pcn.html www.fwi.co.uk Scientists make breakthrough in potato pest control http://www.fwi.co.uk/arable/scientists-make-breakthrough-in-potato-pest-control.htm The Courier (Main Edition) Researchers breaking new ground with G pallida fight The Courier (Dundee Edition) Researchers breaking new ground with G pallida fight www.farmingfutures.org.uk Breakthrough against potato cyst nematode http://www.farmingfutures.org.uk/blog/breakthrough-against-potato-cyst-nematode Farmers Guardian Research breakthrough in the battle against PCN |
Start Year | 2014 |
Description | Metagenetics of G. pallida |
Organisation | University of Edinburgh |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Coordinating the project and carrying out the research |
Collaborator Contribution | Leeds: equipment and financial SASA: samples JHI: equipment UoE: sequencing |
Impact | Publication attracted media attention from 11 media outlets: www.farminguk.com Researchers make technological breakthrough against potato cyst nematode http://www.farminguk.com/News/Researchers-make-technological-breakthrough-against-potato-cyst-nematode_37583.html www.dundeeandanguschamber.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.dundeeandanguschamber.co.uk/news/James-Hutton-News_0_3067.html phys.org Researchers make technological breakthrough against potato cyst nematode http://phys.org/news/2015-11-technological-breakthrough-potato-cyst-nematode.html www.hortweek.com Match potato varieties to local nematode populations, say researchers http://www.hortweek.com/match-potato-varieties-local-nematode-populations-say-researchers/edibles/article/1370971 www.agcc.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.agcc.co.uk/news-article/researchers-make-technological-breakthrough-against-potato-cyst-nematode www.stackyard.com Breakthrough against potato cyst nematode http://www.stackyard.com/news/2015/11/crop/01_james_hutton_pcn.html www.fwi.co.uk Scientists make breakthrough in potato pest control http://www.fwi.co.uk/arable/scientists-make-breakthrough-in-potato-pest-control.htm The Courier (Main Edition) Researchers breaking new ground with G pallida fight The Courier (Dundee Edition) Researchers breaking new ground with G pallida fight www.farmingfutures.org.uk Breakthrough against potato cyst nematode http://www.farmingfutures.org.uk/blog/breakthrough-against-potato-cyst-nematode Farmers Guardian Research breakthrough in the battle against PCN |
Start Year | 2014 |
Description | Metagenetics of G. pallida |
Organisation | University of Leeds |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Coordinating the project and carrying out the research |
Collaborator Contribution | Leeds: equipment and financial SASA: samples JHI: equipment UoE: sequencing |
Impact | Publication attracted media attention from 11 media outlets: www.farminguk.com Researchers make technological breakthrough against potato cyst nematode http://www.farminguk.com/News/Researchers-make-technological-breakthrough-against-potato-cyst-nematode_37583.html www.dundeeandanguschamber.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.dundeeandanguschamber.co.uk/news/James-Hutton-News_0_3067.html phys.org Researchers make technological breakthrough against potato cyst nematode http://phys.org/news/2015-11-technological-breakthrough-potato-cyst-nematode.html www.hortweek.com Match potato varieties to local nematode populations, say researchers http://www.hortweek.com/match-potato-varieties-local-nematode-populations-say-researchers/edibles/article/1370971 www.agcc.co.uk Researchers make technological breakthrough against potato cyst nematode http://www.agcc.co.uk/news-article/researchers-make-technological-breakthrough-against-potato-cyst-nematode www.stackyard.com Breakthrough against potato cyst nematode http://www.stackyard.com/news/2015/11/crop/01_james_hutton_pcn.html www.fwi.co.uk Scientists make breakthrough in potato pest control http://www.fwi.co.uk/arable/scientists-make-breakthrough-in-potato-pest-control.htm The Courier (Main Edition) Researchers breaking new ground with G pallida fight The Courier (Dundee Edition) Researchers breaking new ground with G pallida fight www.farmingfutures.org.uk Breakthrough against potato cyst nematode http://www.farmingfutures.org.uk/blog/breakthrough-against-potato-cyst-nematode Farmers Guardian Research breakthrough in the battle against PCN |
Start Year | 2014 |
Description | The G. rostochiensis genome consortium |
Organisation | Agriculture and Agri-Food Canada |
Country | Canada |
Sector | Public |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | French National Institute of Agricultural Research |
Department | INRA Rennes Centre |
Country | France |
Sector | Public |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | French National Institute of Agricultural Research |
Department | INRA Sophia Antipolis |
Country | France |
Sector | Public |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | Government of Canada |
Department | Canadian Food Inspection Agency (CFIA) |
Country | Canada |
Sector | Public |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | James Hutton Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | King Abdulaziz University |
Country | Saudi Arabia |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) |
Department | Centre National de la Recherche Scientifique Marseille |
Country | France |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | The Wellcome Trust Sanger Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | U.S. Department of Agriculture USDA |
Department | Horticultural Crops Research Laboratory |
Country | United States |
Sector | Public |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | University of Edinburgh |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | University of Hull |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | University of Leeds |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | University of St Andrews |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The G. rostochiensis genome consortium |
Organisation | Wageningen University & Research |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | Leading the consortium |
Collaborator Contribution | Genome annotation and various other analyses specific to each partners area/s of expertise. |
Impact | Eves-van den Akker, S., Laetsch, D. R., Thorpe, P., Lilley, C. J., Danchin, E. G., Da Rocha, M., ... & Grenier, E. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology, 17(1), 124. |
Start Year | 2013 |
Description | The P. penetrans transcriptome |
Organisation | U.S. Department of Agriculture USDA |
Country | United States |
Sector | Public |
PI Contribution | Differential expression analyses |
Collaborator Contribution | Transcriptome sequencing and RNAi |
Impact | Vieira, Paulo, et al. "The Pratylenchus penetrans Transcriptome as a Source for the Development of Alternative Control Strategies: Mining for Putative Genes Involved in Parasitism and Evaluation of in planta RNAi." PloS one 10.12 (2015): e0144674. |
Start Year | 2014 |
Description | The genome of the soybean cyst nematode Heterodera glycines |
Organisation | Iowa State University |
Department | Department of Plant Pathology and Microbiology |
Country | United States |
Sector | Academic/University |
PI Contribution | Explore effector regulation and regulatory motifs. |
Collaborator Contribution | Genome sequencing, transcriptome sequencing (temporal and spatially separated) |
Impact | Publication R. Masonbrink, T.R. Maier, U. Muppirala, A.S. Seetharam, E. Lord, P.S. Juvale, J. Schmutz, N.T. Johnson, D. Korkin, M.G. Mitchum, B. Mimee, S. Eves-van den Akker, M. Hudson, A.J. Severin, T.J. Baum. (2019). The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes (2019) BMC Genomics 20 (1), 119. |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | French National Institute of Agricultural Research |
Country | France |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | Iowa State University |
Department | Department of Plant Pathology and Microbiology |
Country | United States |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | James Hutton Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | North Carolina State University |
Department | Plants for Human Health Institute |
Country | United States |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Bristol |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of California, Davis |
Department | Department of Entomology and Nematology |
Country | United States |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Cambridge |
Department | Gurdon Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Ghent |
Country | Belgium |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Illinois |
Country | United States |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Leeds |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | University of Warwick |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Transformation of Plant Parasitic Nematodes Consortium |
Organisation | Wageningen University & Research |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | Organisation of first workshop. Acquired seed corn funding. Lead of consortium. |
Collaborator Contribution | Attending workshop, developing and implementing strategies. |
Impact | None yet |
Start Year | 2016 |
Description | Address to agronomists on potato cyst nematodes - youtube broadcast |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Invited to address a group of several hundred agronomists on the importance of monitoring potato cyst nematodes in their fields. Talk was live streamed, and permanently hosted, on youtube for increased engagement with third partied after the event. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.youtube.com/watch?v=OMCWA21Y1rM |
Description | BBC Radio interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Spoke about the open cambridge festival "through the laboratory keyhole" event taking place, where we made films about what it is like to work in a lab and our research more generally. Purpose was to promote the event, our research, and new research centre. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bbc.co.uk/sounds/play/p09szcgl |
Description | Media engagement for Genome biology publication - and subsequent spotlight article |
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 | Public/other audiences |
Results and Impact | Press release around the completion of the G. rostochiensis genome consortium publication (see partnertships and collaboration section). Implications highlighted by various national and international media outlets. http://www.soci.org/news/horticulture/potato-parasite-toolkit-sebastian-eves-van-der-akker http://www.thenational.scot/news/14903470.Scientists_prepare_to_use_DNA_of_potato_killing_worm_against_it_to_save_crops_worth_billions/ https://potatonewstoday.com/2016/06/14/scientists-prepare-to-use-dna-of-pcn-against-it-to-save-crops/ http://www.farmassist.com/Alerts/AlertDetail.aspx?alertId=199041&AlertType=64&AlertTypeName=GPN%20News&type=FA_AGNEWSALL http://merid.org/en/Content/News_Services/Food_Security_and_AgBiotech_News/Articles/2016/Jun/16/potato.aspx |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.dundee.ac.uk/news/2016/potato-parasites-toolkit-revealed.php |
Description | Open Cambridge: Through the Laboratory Keyhole |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | On Thursday 16th October our 'Through the Laboratory Keyhole' on-line event took place, as part of the Open Cambridge Festival. Viewers were treated to a privileged behind-the-scenes peek at four research projects in the Department of Plant Sciences. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.globalfood.cam.ac.uk/news/event-report-through-laboratory-keyhole |
Description | Plant Power Day - University of Dundee Botanical Gardens |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Worked with local artist Rhoda Ellis (https://rhodaellis.wordpress.com/) to provide an exhibition for plant power day (http://www.hutton.ac.uk/events/plant-power-day-2016) involving felting different flower forms. Designed to increase awareness of how form follows function in nature. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.hutton.ac.uk/events/plant-power-day-2016 |
Description | Press release for Award of Peter Massalski Prize |
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 | Public/other audiences |
Results and Impact | Press release around the award of the Peter Massalski prize for research excellence. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.pressreader.com/uk/the-courier-advertiser-dundee-edition/20160514/282604557067617 |
Description | Press release for Transformation workshop |
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 | Professional Practitioners |
Results and Impact | Press release following the transformation workshop. Since have had numerous requests for other to be involved in the consortium. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.lifesci.dundee.ac.uk/news/2016/sep/19/dundee-investigator-leads-expert-discussion-transfo... |
Description | Street Food public engagement |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | As part of the Dundee Science Festival, the School of Life Sciences houses a fabulous indoor Street for perfect pairings of scientists and food makers. The event, "Street Food" aimed to explore links between science and food. Plant Scientists from the University of Dundee and the James Hutton Institute exhibited some of our work on potato resistance genes, and soft fruit production. The event consisted of a raft of food stalls and live science demonstrations. |
Year(s) Of Engagement Activity | 2017 |
Description | media interest (metagenetics study) |
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 | Publication was picked up by 11 media outlets, both national and international, with a potential audience of 7,571,958 Media response sparked further enquiries, including press representatives associated with Syngenta for the potato review. |
Year(s) Of Engagement Activity | 2015 |