The regulation of plant-nematode parasitism

Lead Research Organisation: University of Cambridge
Department Name: Plant Sciences

Abstract

Summary: The regulation of plant-nematode parasitism.

Plant-parasitic nematodes are a persistent threat to global food security. The most economically important species have the ability to transform plant cells into permanent and dedicated feeding sites. Plants and parasitic nematodes are locked in an "evolutionary arms race". At the front-line, are the parasite "effectors": molecules secreted into the host plant during infection. Plant-parasitic nematodes use hundreds of effectors to manipulate their host. Often individual effectors target a specific function in the host. The scientific community has focused on trying to understand and block these effector functions.

A vulnerability of this approach is that for thousands of years plants have been deploying resistance genes to recognise effectors, and mount an immune response. This means that the parasites are under a strong evolutionary selection pressure to counteract this, developing a number of mechanisms to evade or negate effector recognition (sequence diversity, partitioning effectors in regions of the genome that mutate rapidly, functional redundancy, etc.). Practically, this means that targeting individual effectors to control the parasite is rarely highly successful, and unlikely to be robust. What we need is a series of new targets that have not been the focus of this kind of evolutionary selection pressure.

This proposal is designed to deliver new targets by shifting the focus away from individual effectors to "high-level" functions: how is parasitism regulated? The idea is that if we can disrupt the process of parasitism regulation we can disrupt the functions of many effectors at the same time. Two recent breakthroughs in our understanding of parasitism regulation suggest that now is the right time to initiate this shift in focus.

In 2016 I identified a regulatory genetic signature of nematode effectors. This signature unifies hundreds of otherwise unrelated effectors. This implies there is some nematode regulatory machinery that recognises this signature, and in so doing orchestrates this aspect of parasitism. I predict that if we could disrupt this "master-regulator", it would in turn disrupt hundreds of associated effectors. In a recent effort I have identified a candidate for such a regulator.

The second breakthrough is the discovery that nematodes do not synthesise all effectors at the same time, suggesting that they may be delivered in waves that indicate a complex "parasitism programme" during infection. This sequential programme of effector production suggests that there will be a series of additional regulators that are activated at specific time-points. Disrupting any of these is likely to be severely detrimental to the parasite. Importantly, the plant immune system is "blind" to these master regulators. This means that they are unlikely to be protected by the same mechanisms that make targeting effectors so difficult. Together, this suggests that parasitism master regulators will be an attractive set of targets for control. In this proposal I will identify, validate, and disrupt these master-regulators.

The fact that parasitic nematodes predictably execute a "parasitism programme" also gives us some insights into how they transform plant tissues. It suggests that the regulation of feeding site formation in the host is probably a multi stage process, and has the same or a very similar number of stages. This is a new insight into how this tissue is formed and presents an opportunity to understand the fundamental biology that underpins this process. In this proposal I will develop a system to measure changes in the host gene regulation and link these changes to progression through the nematode parasitism programme, ultimately building the foundation to understand this phenomenon.

Technical Summary

The most economically important plant-parasitic nematode species have the ability to cause existing plant cells to re-differentiate into a novel tissue that acts as a feeding site. How this is regulated, in the nematode and in the host, is one of the great unanswered questions in the field. This proposal is designed to identify, characterise, and disrupt the regulators of parasitism. The main objectives are designed to address the following hypotheses:

Hypothesis 1: The spatio-temporal regulation of the nematode "Parasitism Programme" is controlled by a suite of non-coding DNA motifs and corresponding putative master-regulator transcription factors.
Using a combination of whole gland cell RNA sequencing and bioinformatic predictions, I will identify promoter elements that define various aspects of the nematode "parasitism programme". Cognate transcription factors of these promoter elements will be identified by Yeast-1-Hybrid and Co-immunoprecipitation, to provide a series of high-value targets for control.

Hypothesis 2: The regulation of feeding site development in the host is a complex, multi-stage process.
I will deploy second- and third-generation sequencing technologies to determine the temporally-resolved changes in host gene regulation that are directly linked to progression through the nematode "parasitism programme". This will provide a platform for future exploration of novel tissue re-differentiation in plants.

Hypothesis 3: Disrupting the processes of parasitism regulation in the parasite or the host will be detrimental to infection.
I will disrupt the processes of parasitism regulation in the nematode and in the host to validate the roles of regulatory proteins/processes during parasitism, and demonstrate their utility as a set of putative targets for the control of plant-parasitic nematodes.

This proposal will significantly advance our understanding of a process that is academically fascinating and has global agronomic importance.

Planned Impact

The beneficiaries of my proposal are detailed in the relevant sections of the JeS form and the pathways to impact. To summarise, my proposal has substantial potential to impact the academic, societal, and industrial sectors. A series of measures are detailed to realise that impact over the course of the fellowship, and these timescales are detailed in the diagrammatic work plan.

Academic impact:
The major academic impact of the proposal will come from delivering the outcome of the pan-kingdom linked transcriptome to end-users in an accessible format. By permanently incorporating these data into the A. thaliana community resources (e.g. ePlant), the unusual biology of the nematode feeding site will be viewed by approximately 60,000 plant scientists per month. There is probably no better way to consistently highlight plant-nematode interaction to such a broad audience, and for such a long time.

Societal impact:
Informing the public, and training the next generation of scientists, is our responsibility. During the fellowship, I will continue to train young plant scientists to address the major global issue of food security. The combination of engagement infrastructures at the University of Dundee and the James Hutton Institute will help appropriately deliver the messages of the outcomes to a broad spectrum of audiences.

Industrial impact:
Although a challenging aim, the long-term goal of the research is to develop approaches with the potential to increase agricultural stability by combatting plant-parasitic nematodes. The combination of the Drug Discovery Unit at the University of Dundee, the Commercialisation arm of the James Hutton Institute, and the promising link established with a major AgChem company, indicate a number of potential routes to realise industrial impact in the UK and globally.

Publications

10 25 50
 
Title Additional file 3 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description In situ hybridization assays using the corresponding sense DIG-labeled probes (control) for 30 candidate effector genes detected within the esophageal glands of Pratylenchus penetrans. Details regarding each gene annotation and description are presented in the same order as sorted in Table 1. Bars = 20 µm. (TIFF 5250 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2020 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_of_A_new_esophageal_gland_tran...
 
Title Additional file 3 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description In situ hybridization assays using the corresponding sense DIG-labeled probes (control) for 30 candidate effector genes detected within the esophageal glands of Pratylenchus penetrans. Details regarding each gene annotation and description are presented in the same order as sorted in Table 1. Bars = 20 µm. (TIFF 5250 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2020 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_of_A_new_esophageal_gland_tran...
 
Title Additional file 4 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description In situ hybridization assays using the corresponding sense DIG-labeled probes (control) for transcripts encoding: (a) ShK domain-like protein, and (b) a 14-3-3 protein. Bars = 20 µm. (TIFF 656 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2020 
URL https://springernature.figshare.com/articles/figure/Additional_file_4_of_A_new_esophageal_gland_tran...
 
Title Additional file 4 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description In situ hybridization assays using the corresponding sense DIG-labeled probes (control) for transcripts encoding: (a) ShK domain-like protein, and (b) a 14-3-3 protein. Bars = 20 µm. (TIFF 656 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2020 
URL https://springernature.figshare.com/articles/figure/Additional_file_4_of_A_new_esophageal_gland_tran...
 
Description Preparation of/input to various reports on Genome editing to DEFRA consultation.
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description A new dimension to nematode infection phenotyping using low-cost imaging and AI-powered trait analysis
Amount £11,858 (GBP)
Funding ID BB/S506710/1 
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 12/2021 
End 03/2022
 
Description An mRNA vaccine-like approach to overcome genetic intractability
Amount £173,144 (GBP)
Funding ID RPG-2023-001 
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2023 
End 02/2026
 
Description BBSRC DTP Cambridge
Amount £60,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 09/2019 
End 10/2023
 
Description BBSRC responsive mode standard grant
Amount £542,162 (GBP)
Funding ID BB/S006397/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 10/2022
 
Description British Society of Plant Pathology MSc/MRes Bursary for Ko Itsuhiro
Amount £4,000 (GBP)
Organisation The British Society of Plant Pathology 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2020 
End 08/2021
 
Description Effector biogenesis: an unexplored, and yet critically important, part of plant-nematode interactions
Amount € 1,486,990 (EUR)
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 12/2022 
End 12/2027
 
Description Potato PCN Resistance: Cloning effective resistances against potato cyst nematodes
Amount £234,739 (GBP)
Funding ID BB/X006352/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2023 
End 01/2026
 
Description Potato PCN Resistance: Cloning effective resistances against potato cyst nematodes
Amount £1,200,000 (GBP)
Funding ID BB/X009068/1 
Organisation James Hutton Institute 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2023 
End 04/2026
 
Description Prevalence and distribution of the single greatest threat to crop production in the tropics: the root knot nematode Meloidogyne incognita
Amount £23,666 (GBP)
Funding ID G118282 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2023 
End 03/2023
 
Description Proof-of-principle gene editing in plantparasites
Amount $10,000 (USD)
Organisation Genewiz 
Sector Private
Country Germany
Start 04/2019 
End 12/2019
 
Description Proof-of-principle gene editing in plantparasites
Amount $7,500 (USD)
Organisation Synthego Inc 
Sector Private
Country United States
Start 03/2019 
End 04/2020
 
Description Royal Society of Biology Plant-health Summer Studentship
Amount £2,500 (GBP)
Organisation Royal Society of Biology (RSB) 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 08/2019
 
Description Royal Society of Biology Plant-health Summer Studentship
Amount £2,500 (GBP)
Organisation Royal Society of Biology (RSB) 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2021 
End 08/2021
 
Description The Rank Prize Fund
Amount £20,000 (GBP)
Organisation Rank Prize Funds 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2018 
End 12/2020
 
Description The genetics of environmental sex determination
Amount £200,000 (GBP)
Funding ID APP3600 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2024 
End 01/2025
 
Description Wellcome/Newton Institutional Strategic Support Fund
Amount £60,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 03/2019 
End 04/2021
 
Title Low-cost phenotyping 
Description Low-cost phenotyping for plant-nematode infections. 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? Yes  
Impact None to date 
URL https://doi.org/10.1186/s13007-022-00963-2
 
Title Sperling prep in situ hybridisation 
Description Multiplex in situ hybridisation to parasitic nematodes 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? Yes  
Impact Increased recognition of our work. 
URL https://plantmethods.biomedcentral.com/articles/10.1186/s13007-023-01112-z#
 
Title Transient expression in plant-parasitic nematodes. 
Description We develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security. 
 
Title Additional file 1 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description Summary of BLAST hit analyses of the top 230 most abundant transcripts of Pratylenchus penetrans encoding putative secreted proteins (FPKM > 8) originated from the esophageal gland cells library. BLAST analyses were performed against the non-redundant GenBank database. Transcript abundance was determined as Fragments Per Kilobase of Transcript per Million mapped reads (FPKM) values. (XLSX 30 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_A_new_esophageal_gland_tra...
 
Title Additional file 1 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description Summary of BLAST hit analyses of the top 230 most abundant transcripts of Pratylenchus penetrans encoding putative secreted proteins (FPKM > 8) originated from the esophageal gland cells library. BLAST analyses were performed against the non-redundant GenBank database. Transcript abundance was determined as Fragments Per Kilobase of Transcript per Million mapped reads (FPKM) values. (XLSX 30 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_A_new_esophageal_gland_tra...
 
Title Additional file 2 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of transcripts encoding putative effector proteins with FPKM values below the established cut-off (FPKM 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_2_of_A_new_esophageal_gland_tra...
 
Title Additional file 2 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of transcripts encoding putative effector proteins with FPKM values below the established cut-off (FPKM 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_2_of_A_new_esophageal_gland_tra...
 
Title Additional file 2: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S1. MEME motifs annotated with BLAST annotations to NR. Annotated MEME motifs from effector motif-finding. (TXT 1 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_2_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 2: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S1. MEME motifs annotated with BLAST annotations to NR. Annotated MEME motifs from effector motif-finding. (TXT 1 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_2_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 3: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S2. All horizontal gene transfer events. All putative horizontal gene transfer events above an alien index of zero. (XLSX 398 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_3_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 3: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S2. All horizontal gene transfer events. All putative horizontal gene transfer events above an alien index of zero. (XLSX 398 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_3_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 4: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S3. Horizontal gene transfer events novel to H. glycines. Horizontal gene transfer events not previously reported in other plant parasitic nematodes. (XLSX 19 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_4_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 4: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Data S3. Horizontal gene transfer events novel to H. glycines. Horizontal gene transfer events not previously reported in other plant parasitic nematodes. (XLSX 19 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_4_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 5 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of promoter sequences extracted for 30 genes with gland cell localization in Pratylenchus penetrans. The 600 nt of the upstream region of the start codon was queried for the presence of the CAA[AG|T|C]TG[T|G] C motif previously found associated with gland cell expression of other candidate effectors of P. penetrans. (XLSX 17 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_of_A_new_esophageal_gland_tra...
 
Title Additional file 5 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of promoter sequences extracted for 30 genes with gland cell localization in Pratylenchus penetrans. The 600 nt of the upstream region of the start codon was queried for the presence of the CAA[AG|T|C]TG[T|G] C motif previously found associated with gland cell expression of other candidate effectors of P. penetrans. (XLSX 17 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_of_A_new_esophageal_gland_tra...
 
Title Additional file 5: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Table S5. Significance tests for gene expression and snp density (XLSX 15 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_5_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 5: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Table S5. Significance tests for gene expression and snp density (XLSX 15 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_5_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 6 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description BLAST hit analyses of transcripts with gland cell localization against the draft genome of Pratylenchus penetrans. (XLSX 11 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_A_new_esophageal_gland_tra...
 
Title Additional file 6 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description BLAST hit analyses of transcripts with gland cell localization against the draft genome of Pratylenchus penetrans. (XLSX 11 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_A_new_esophageal_gland_tra...
 
Title Additional file 6: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Table S6. Nematode isotypes and selection. Hg-types, selection, and heritage of nematodes using in sequencing. (XLSX 12 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_6_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 6: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes 
Description Table S6. Nematode isotypes and selection. Hg-types, selection, and heritage of nematodes using in sequencing. (XLSX 12 kb) 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_6_of_The_genome_of_the_soybean_cyst_nem...
 
Title Additional file 7 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of primers used in this study. (XLSX 14 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_7_of_A_new_esophageal_gland_tra...
 
Title Additional file 7 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of primers used in this study. (XLSX 14 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_7_of_A_new_esophageal_gland_tra...
 
Title Additional file 8 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of CEGMA genes used in this study. (XLSX 693 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_8_of_A_new_esophageal_gland_tra...
 
Title Additional file 8 of A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans 
Description List of CEGMA genes used in this study. (XLSX 693 kb) 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_8_of_A_new_esophageal_gland_tra...
 
Title Data from: The origin, deployment, and evolution of a plant-parasitic nematode effectorome 
Description Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 659 effector gene loci: 293 "known" high-confidence homologs of plant-parasitic nematode effectors, and 366 "novel" effectors with high gland cell expression. In doing so we define a comprehensive "effectorome" of a plant-parasitic nematode. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.rfj6q57hn
 
Title King's College Cambridge wildflower meadow monitoring data: biodiversity, climate change and society 
Description The biodiversity and climate crises are critical challenges of this century. Wildflower meadows in urban areas could provide important nature-based solutions, addressing the biodiversity and climate crises jointly, and benefitting society in the process. King's College Cambridge (England, UK) established a wildflower meadow over a portion of its iconic Back Lawn in 2019, replacing a fine lawn first laid in 1772. We used biodiversity surveys, Wilcoxon signed rank, and ANOVA models to compare species richness, abundance, and composition of plants, spiders, bugs, bats, and nematodes supported by the meadow, and remaining lawn, over three years. We estimated the climate change impact of meadow vs lawn from maintenance emissions, soil carbon sequestration, and reflectance effect. We surveyed members of the university to quantify the societal benefits of, and attitudes towards, increased meadow planting on the collegiate university estate. In spite of its small size (0.36 ha), the meadow supported approximately three times more plant species, three times more spider and bug species and individuals, and bats were recorded three times more often over the meadow than the remaining lawn. Terrestrial invertebrate biomass was 25 times higher in the meadow compared with the lawn. Fourteen species with conservation designations were recorded on the meadow (six for lawn), alongside meadow specialist species. Reduced maintenance and fertilising associated with meadow reduced emissions by an estimated 1.36 Mg CO2-e per hectare per year compared with lawn. Relative reflectance increased by 25-34% for meadow relative to lawn. Soil carbon stocks did not differ between meadow and lawn. Respondents thought meadows provided greater aesthetic, educational, and mental well-being services than lawns. In open responses, lawns were associated with undesirable elitism and social exclusion (most colleges in Cambridge restrict lawn access to senior members of the college), and respondents proved overwhelmingly in favour of meadow planting in place of lawns on the collegiate university estate. This study demonstrates the substantial benefits of small urban meadows for local biodiversity, cultural ecosystem services, and climate change mitigation, supplied at a lower cost than maintaining conventional lawn. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.kd51c5bbb
 
Title The genome and lifestage-specific transcriptomes of a plant-parasitic nematode 
Description The genome and lifestage-specific transcriptomes of a plant-parasitic nematode Heterodera schachtii 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Accelerating research. 
URL https://doi.org/10.1038/s41467-022-33769-w
 
Title Towards genetic modification of plant-parasitic nematodes: Delivery of macromolecules to male germlines and expression of exogenous mRNA in second stage juveniles 
Description Plant-parasitic nematodes are a current and future threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics. Forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate progress in plant-parasitic nematology, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic "tool kit" in plant-parasitic nematodes. We characterise the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, and, taken together, will expedite the development of genetic modification protocols for sedentary endoparasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.r4xgxd296
 
Description Collaboration on nematode resistant potato - Jonathan Jones, TSL 
Organisation The Sainsbury Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution Testing nematode resistant lines of transgenic potato.
Collaborator Contribution Generation of transgenic lines.
Impact None yet.
Start Year 2020
 
Description Heterodera schachtii genome sequencing consortium 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution Lead on consortium. Sequencing and assembly of genome. Sequencing and analysis of transcriptome
Collaborator Contribution Preparation of samples for transcriptome analysis (Bonn). Genome annotation (others).
Impact None yet
Start Year 2018
 
Description Heterodera schachtii genome sequencing consortium 
Organisation University of Bonn
Country Germany 
Sector Academic/University 
PI Contribution Lead on consortium. Sequencing and assembly of genome. Sequencing and analysis of transcriptome
Collaborator Contribution Preparation of samples for transcriptome analysis (Bonn). Genome annotation (others).
Impact None yet
Start Year 2018
 
Description Heterodera schachtii genome sequencing consortium 
Organisation University of St Andrews
Country United Kingdom 
Sector Academic/University 
PI Contribution Lead on consortium. Sequencing and assembly of genome. Sequencing and analysis of transcriptome
Collaborator Contribution Preparation of samples for transcriptome analysis (Bonn). Genome annotation (others).
Impact None yet
Start Year 2018
 
Description Heterodera schachtii genome sequencing consortium 
Organisation University of Tennessee
Country United States 
Sector Academic/University 
PI Contribution Lead on consortium. Sequencing and assembly of genome. Sequencing and analysis of transcriptome
Collaborator Contribution Preparation of samples for transcriptome analysis (Bonn). Genome annotation (others).
Impact None yet
Start Year 2018
 
Description Heterodera schachtii genome sequencing consortium 
Organisation Wageningen University & Research
Country Netherlands 
Sector Academic/University 
PI Contribution Lead on consortium. Sequencing and assembly of genome. Sequencing and analysis of transcriptome
Collaborator Contribution Preparation of samples for transcriptome analysis (Bonn). Genome annotation (others).
Impact None yet
Start Year 2018
 
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 Article in The Vegetable Farmer on Potato cyst nematodes 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Article in The Vegetable Farmer on Potato cyst nematodes. The Vegetable Farmer has been the vegetable industry's leading magazine for over 30 years. The purpose was to highlight the importance of the problem, and the recent advances made by Uk groups.
Year(s) Of Engagement Activity 2020
 
Description BBC Radio interview 
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 Public/other audiences
Results and Impact Spoke with the "NakedScientists" live on BBC Radio Cambridgeshire, and later broadcast on BBC radio 5, about nematodes and other diseases as part of a program on plants and climate change.
Year(s) Of Engagement Activity 2020
URL https://www.bbc.co.uk/programmes/p08n78c6
 
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 CUPGRA - accelerating potato breeding 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CUPGRA conference
Year(s) Of Engagement Activity 2022
 
Description CUPGRA - the future of potato research at Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CUPGRA 31st annual cambridge potato conference 2020 talk about the future of potato research at Cambridge.
Year(s) Of Engagement Activity 2020
URL https://www.niab.com/services/membership/cupgra
 
Description Fascination of plants 
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 Fascination of plants day at the University of Cambridge Botanical Gardens. 3,409 attendees.
Year(s) Of Engagement Activity 2023
 
Description Interview with Gatsby 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview following the Gatsby plant sciences summer school
Year(s) Of Engagement Activity 2024
URL https://youtu.be/IDjI9iU6L9g
 
Description King's 50th Anniversary Reunion event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact On Saturday 12th August, the Development Office will be holding our annual 50th Anniversary Reunion event where King's alumni who matriculated in 1973 return to the College for a daytime programme of activities and dinner.
Year(s) Of Engagement Activity 2023
 
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 Protecting crops in a challenging future (London, UK) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact In support of the international year of Plant Health - organised an online conference as part of membership of Society of Chemical Industry Horticultural Group.
Year(s) Of Engagement Activity 2020
 
Description Science on Sunday Seminar at the Cambridge Botanical Gardens - online 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public engagement talk at the Cambridge University Botanical gardens "Science on Sundays" Seminar series. Was recorded and made available online due to pandemic. Intended audience is general public. Aim was to increase awareness around plant health.
Year(s) Of Engagement Activity 2020
URL https://www.botanic.cam.ac.uk/whats-on/science-on-sundays-july20/
 
Description UKPlantSciPresents webinar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk on work from the group at the UKPlantSciPresents webinar series (was Garnet).
Year(s) Of Engagement Activity 2020
 
Description University of Cambridge alumni event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Cambridge's annual flagship alumni event, with over 1,000 + alumni (mostly over 50's) returning to Cambridge each year.
Year(s) Of Engagement Activity 2023