Resistance: DNA methylation and the evolution of pesticide-resistance genes in aphids
Lead Research Organisation:
John Innes Centre
Department Name: Crop Genetics
Abstract
Most insect species are specialist parasites that have adapted to colonize one or a few closely related plant species. Circa 10% of all insect herbivores are generalist ("polyphagous"), and these are often the most noxious pests, having evolved resistance to many pesticides. Generalist insects are prone to such "pesticide-breaking" because by being exposed to a wide range of hosts, they have already evolved resistance to many different plant chemicals. Worryingly, many of these phytochemicals have been used to derive pesticides, and this makes such generalist insects pre-adapted to pesticide-breaking.
The green peach aphid (GPA) Myzus persicae can colonize over 400 different plant species, and it has evolved resistance or tolerance to 71 chemicals in 50 years. GPA has become a model to understand how "pesticide-breaking" has evolved. In a former BBSRC funded project, we discovered the molecular mechanism underpinning the insect's remarkable adaptive potential; DNA methylation by two genes (DNMT3A and 3B) enables GPA to adjust to diverse plant species and overcome pesticide toxicity without genetic modification. Genetically identical clones can adjust to a new host plant and show pesticide resistance within hours or days after exposure, and furthermore, their (genetically identical) offspring becomes increasingly well-adjusted. We have shown that the expression of detoxification genes is controlled by DNA methylation (which is an epigenetic process). We also showed that when DNMT3A/B methylation is knocked-down, that the aphids can no longer adjust. We also know that different genes are being up- or down-regulated by DNMT3A/B methylation depending on the host plant or pesticide being encountered.
Building on this knowledge, our new proposal has two principal objectives:
1) Identify and describe the entire gene networks affected by de novo DNA methylation mediated by DNMT3A/B. This is important because these are the genes that enable the aphid to detect and respond to the pesticide, and hence, this will help the development of pesticides against novel insect targets. Our Project Partner Syngenta, and others, will thus be helped in their development of such pesticides.
2) Understand the evolutionary forces that generate and shape the DNA variation underpinning the genetic variation in these "resistance genes" in the DNMT3A/B pathway. This is important because the 50 years of pesticide usage will have left a decipherable signature in the genome of the aphids (and other pest insects). By studying this signature, we can optimise pest insect control strategies.
The hypotheses are:
1) GPA possesses genes that help the insect to detect the novel host plant / pesticides, which instigates DNMT3A/B upregulation.
2) The DNMT3A/B methylated genes enable the insect to detoxify these chemicals.
3) Generalist aphids (e.g., GPA) display a larger change in DNMT3A/B expression levels upon host switch and pesticide exposure than specialist aphids (such as the cabbage aphid Brevicoryne brassicae, and the English grain aphid Sitobion avenae).
4) Co-regulatory networks affected by DNMT3A/B are more extensive for generalist than specialist aphids.
5) Generalist insect pests (including herbivores, animal and human insect pests) show genome streamlining, lineage-specific gene families and gene duplication that is distinctive from specialist pest insects.
6) The historic use of pesticide treatment will have impacted the 5 evolutionary forces (mutation, recombination, gene flow, genetic drift and natural selection), which has shaped the genomic variation in GPA in populations across the world.
In collaboration with our Project Partner Syngenta, we have designed three exciting experiments that test these hypotheses. We believe the knowledge generated by this research is likely to uncover new targets for insect control, and will help to optimise species-specific insect control strategies, and hence secure sustainable agriculture.
The green peach aphid (GPA) Myzus persicae can colonize over 400 different plant species, and it has evolved resistance or tolerance to 71 chemicals in 50 years. GPA has become a model to understand how "pesticide-breaking" has evolved. In a former BBSRC funded project, we discovered the molecular mechanism underpinning the insect's remarkable adaptive potential; DNA methylation by two genes (DNMT3A and 3B) enables GPA to adjust to diverse plant species and overcome pesticide toxicity without genetic modification. Genetically identical clones can adjust to a new host plant and show pesticide resistance within hours or days after exposure, and furthermore, their (genetically identical) offspring becomes increasingly well-adjusted. We have shown that the expression of detoxification genes is controlled by DNA methylation (which is an epigenetic process). We also showed that when DNMT3A/B methylation is knocked-down, that the aphids can no longer adjust. We also know that different genes are being up- or down-regulated by DNMT3A/B methylation depending on the host plant or pesticide being encountered.
Building on this knowledge, our new proposal has two principal objectives:
1) Identify and describe the entire gene networks affected by de novo DNA methylation mediated by DNMT3A/B. This is important because these are the genes that enable the aphid to detect and respond to the pesticide, and hence, this will help the development of pesticides against novel insect targets. Our Project Partner Syngenta, and others, will thus be helped in their development of such pesticides.
2) Understand the evolutionary forces that generate and shape the DNA variation underpinning the genetic variation in these "resistance genes" in the DNMT3A/B pathway. This is important because the 50 years of pesticide usage will have left a decipherable signature in the genome of the aphids (and other pest insects). By studying this signature, we can optimise pest insect control strategies.
The hypotheses are:
1) GPA possesses genes that help the insect to detect the novel host plant / pesticides, which instigates DNMT3A/B upregulation.
2) The DNMT3A/B methylated genes enable the insect to detoxify these chemicals.
3) Generalist aphids (e.g., GPA) display a larger change in DNMT3A/B expression levels upon host switch and pesticide exposure than specialist aphids (such as the cabbage aphid Brevicoryne brassicae, and the English grain aphid Sitobion avenae).
4) Co-regulatory networks affected by DNMT3A/B are more extensive for generalist than specialist aphids.
5) Generalist insect pests (including herbivores, animal and human insect pests) show genome streamlining, lineage-specific gene families and gene duplication that is distinctive from specialist pest insects.
6) The historic use of pesticide treatment will have impacted the 5 evolutionary forces (mutation, recombination, gene flow, genetic drift and natural selection), which has shaped the genomic variation in GPA in populations across the world.
In collaboration with our Project Partner Syngenta, we have designed three exciting experiments that test these hypotheses. We believe the knowledge generated by this research is likely to uncover new targets for insect control, and will help to optimise species-specific insect control strategies, and hence secure sustainable agriculture.
Technical Summary
The green peach aphid (GPA) Myzus persicae has evolved resistance to 71 chemicals in 50 years, and it has become a model to study the evolution of "pesticide-breaking". In a former BBSRC project, we discovered that DNA methylation by two genes (DNMT3A and 3B) enables GPA to up- and down-regulate genes associated with resistance. In this proposal, we aim study the entire gene networks affected by de novo DNA methylation mediated by DNMT3A and 3B. We also analyse the evolutionary forces that generate and shape the DNA variation underpinning the existing genetic adaptations in an agricultural setting.
Aim 1 is to characterize the genes that depend on DNMT3A/B for differential expression (DE) upon GPA host change (Aim 1.1) and pesticide treatment (Aim 1.2). We will isolate and sequence RNA from aphids with and without host transfer / insecticide exposure to identified DE genes. We will then conduct gene-specific bisulphite sequence of DE genes to examine the link between gene body methylation and DE (Aim 1.3).
Aim 2 investigates how pesticide treatment and DNMT3A/B affect gene expression of two specialist aphid species. We will test how the knock down of DNMT3A/B affects GPA and two specialist aphid species to adjust to new plant hosts and pesticides. We will also identify the genes that depend on DNMT3A/B regulation in specialist and generalist aphids.
Aim 3 elucidates the evolution of genes in the DNMT3A/B pathway involved in response to plant host change and pesticides in GPA, and other (generalist and specialist) pest insects. Aim 3.1 examines the level of genome streamlining, the number of lineage-specific genes in multigene families, and number tandem-duplications of detoxifying genes, testing the hypothesis that these features are associated to rapid pesticide-breaking. Aim 3.2 will identify genes and genomic areas in GPA that are under positive selection across world populations with known history of insecticide usage (in collaboration with Syngenta).
Aim 1 is to characterize the genes that depend on DNMT3A/B for differential expression (DE) upon GPA host change (Aim 1.1) and pesticide treatment (Aim 1.2). We will isolate and sequence RNA from aphids with and without host transfer / insecticide exposure to identified DE genes. We will then conduct gene-specific bisulphite sequence of DE genes to examine the link between gene body methylation and DE (Aim 1.3).
Aim 2 investigates how pesticide treatment and DNMT3A/B affect gene expression of two specialist aphid species. We will test how the knock down of DNMT3A/B affects GPA and two specialist aphid species to adjust to new plant hosts and pesticides. We will also identify the genes that depend on DNMT3A/B regulation in specialist and generalist aphids.
Aim 3 elucidates the evolution of genes in the DNMT3A/B pathway involved in response to plant host change and pesticides in GPA, and other (generalist and specialist) pest insects. Aim 3.1 examines the level of genome streamlining, the number of lineage-specific genes in multigene families, and number tandem-duplications of detoxifying genes, testing the hypothesis that these features are associated to rapid pesticide-breaking. Aim 3.2 will identify genes and genomic areas in GPA that are under positive selection across world populations with known history of insecticide usage (in collaboration with Syngenta).
Planned Impact
This proposal is for the BBSRC highlight call 'Understanding the challenge of resistance in agriculture' in which the green peach aphid (GPA, Myzus persicae) is specifically mentioned. This proposal responds to all aims in the call. Here we detail who will benefit from our proposed research and explain how, focusing on the specific aims from the BBSRC highlight call:
1. "Using new scientific approaches to address practical problems for agriculture or resistance to pesticides." and "Focusing on the molecular mechanisms of resistance, its evolutionary drivers and the ecological processes involved in the emergence and spread." - Our previous BBSRC grant (BB/L002108/1: "Functional Genomics of Aphid Adaptation to Plant Species") identified DNMT3A/B as an important molecular mechanism controlling the regulation of genes that enable GPA to parasitise new host plants and overcome pesticide toxicity. Building on this breakthrough, we now wish to dissect the entire gene pathway enabling GPA to detect and adapt to pesticides.
Beneficiaries: We believe this will help industry, such as our project partner Syngenta, to identifying new potential targets for pesticide development. In turn, this will aid agriculture and food security.
2. "Promoting collaboration between researchers with existing interests in resistance and others with wider relevant expertise in underpinning science." - The proposal involves researchers interested in molecular aspects of plant-insect interactions (Hogenhout. JIC), genomics / bioinformatics (Swarbreck. EI), and evolution (Van Oosterhout, UEA), and Syngenta, Jealott's Hill (Firth and colleagues). The integration of functional genetics and genomics with evolutionary theory enhances the proposed research project. We will be using population genetic theory to understand the processes that occur during the evolution of insecticide resistance in the field, resequencing the genomes of ~100 GPA individuals exposed to pesticides across the globe.
Beneficiaries: The research is of direct relevance to Syngenta, who have committed to support this proposal with a >10% contribution, and others. Besides this financial contribution, the project will benefit significantly from the knowledge of Syngenta about the previous usage of pesticides in locations that will be sampled for GPA to resequence. We believe that the knowledge generated will improve pest insect control strategies, promoting more sustainable usage of pesticides in agriculture, thereby helping long-term food security.
3. "Stimulating innovative research to understand resistance and inform interventions for enhancing effectiveness of existing products and optimizing the use of new ones" - The neonicotinoid TMX has been particularly effective at control of GPA for many years, but "pesticide breaking" appears to be an evolutionary inevitability, especially for generalist pests such as GPA. By using a comparative phylogenomic approach, this proposal investigates how GPA and a wide range of other pest insects have evolved resistance to pesticides in the agricultural setting.
Beneficiaries: The proposed research will aid Syngenta as well as other strategic research projects of the Hogenhout lab, such as the identification of plant resistance to GPA (funded by BBSRC-LINK and iCASE projects with the sugar beet seed breeding company SESVanderHave), development of control methods for the notorious insect pest, the tobacco whitefly Bemisia tabaci (iCASE project with Oxitec), and establishing global networks on vector-borne diseases (funded by the UK-US partnership award and GCRF network with East Africa).
4. "Raising the profile amongst the broader research community of the impact of resistance on agriculture and the scientific challenges it presents." - Here, we plan to engage to broader research community and the public by setting up the OpenINSECTVector website and engaging with the general public in a Citizen Science (see Pathways to Impact).
1. "Using new scientific approaches to address practical problems for agriculture or resistance to pesticides." and "Focusing on the molecular mechanisms of resistance, its evolutionary drivers and the ecological processes involved in the emergence and spread." - Our previous BBSRC grant (BB/L002108/1: "Functional Genomics of Aphid Adaptation to Plant Species") identified DNMT3A/B as an important molecular mechanism controlling the regulation of genes that enable GPA to parasitise new host plants and overcome pesticide toxicity. Building on this breakthrough, we now wish to dissect the entire gene pathway enabling GPA to detect and adapt to pesticides.
Beneficiaries: We believe this will help industry, such as our project partner Syngenta, to identifying new potential targets for pesticide development. In turn, this will aid agriculture and food security.
2. "Promoting collaboration between researchers with existing interests in resistance and others with wider relevant expertise in underpinning science." - The proposal involves researchers interested in molecular aspects of plant-insect interactions (Hogenhout. JIC), genomics / bioinformatics (Swarbreck. EI), and evolution (Van Oosterhout, UEA), and Syngenta, Jealott's Hill (Firth and colleagues). The integration of functional genetics and genomics with evolutionary theory enhances the proposed research project. We will be using population genetic theory to understand the processes that occur during the evolution of insecticide resistance in the field, resequencing the genomes of ~100 GPA individuals exposed to pesticides across the globe.
Beneficiaries: The research is of direct relevance to Syngenta, who have committed to support this proposal with a >10% contribution, and others. Besides this financial contribution, the project will benefit significantly from the knowledge of Syngenta about the previous usage of pesticides in locations that will be sampled for GPA to resequence. We believe that the knowledge generated will improve pest insect control strategies, promoting more sustainable usage of pesticides in agriculture, thereby helping long-term food security.
3. "Stimulating innovative research to understand resistance and inform interventions for enhancing effectiveness of existing products and optimizing the use of new ones" - The neonicotinoid TMX has been particularly effective at control of GPA for many years, but "pesticide breaking" appears to be an evolutionary inevitability, especially for generalist pests such as GPA. By using a comparative phylogenomic approach, this proposal investigates how GPA and a wide range of other pest insects have evolved resistance to pesticides in the agricultural setting.
Beneficiaries: The proposed research will aid Syngenta as well as other strategic research projects of the Hogenhout lab, such as the identification of plant resistance to GPA (funded by BBSRC-LINK and iCASE projects with the sugar beet seed breeding company SESVanderHave), development of control methods for the notorious insect pest, the tobacco whitefly Bemisia tabaci (iCASE project with Oxitec), and establishing global networks on vector-borne diseases (funded by the UK-US partnership award and GCRF network with East Africa).
4. "Raising the profile amongst the broader research community of the impact of resistance on agriculture and the scientific challenges it presents." - Here, we plan to engage to broader research community and the public by setting up the OpenINSECTVector website and engaging with the general public in a Citizen Science (see Pathways to Impact).
Organisations
- John Innes Centre (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Syngenta International AG (Collaboration)
- Chinese Academy of Sciences (Collaboration)
- INTERNATIONAL INSTITUTE OF TROPICAL AGRICULTURE (Collaboration)
- International Centre of Insect Physiology and Ecology (ICIPE) (Collaboration)
- East Malling Research (United Kingdom) (Collaboration)
- Syngenta (United Kingdom) (Project Partner)
Publications
Biello R
(2021)
A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae).
in Molecular ecology resources
Chen Y
(2020)
An aphid RNA transcript migrates systemically within plants and is a virulence factor
in Proceedings of the National Academy of Sciences
Guo H
(2020)
An Aphid-Secreted Salivary Protease Activates Plant Defense in Phloem.
in Current biology : CB
Mathers T
(2018)
Sex-specific changes in the aphid DNA methylation landscape
Mathers TC
(2019)
Sex-specific changes in the aphid DNA methylation landscape.
in Molecular ecology
Mathers TC
(2020)
Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts.
in G3 (Bethesda, Md.)
Mathers TC
(2021)
Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome.
in Molecular biology and evolution
Mugford S
(2020)
High quality DNA extraction from very small individual insects v1
| Description | Obj 1. Elucidate and compare genes involved in GPA responses to host change and pesticides: We generated a chromosome-level assembly of M. persicae clone O. This involved the optimization of high molecular weight DNA extraction methods - the protocol for this was published (dx.doi.org/10.17504/protocols.io.bhftj3nn). We discovered a large new aphid gene family, the Ya family, which encodes candidate long non-coding (lnc) RNAs that regulate aphid-plant interactions. We annotated the Ya genes and other genes that encode lncRNAs in the newly generated chromosome-level assembly of M. persicae clone O. This was not straightforward, because genome annotation pipelines are generally optimized for protein-coding genes. Hence, we developed new tools to annotate the lncRNAs. The annotation of the lncRNAs was done on a high-quality chromosome-level assembly of the GPA genome that together with additional RNA-seq data enabled the separation of lncRNA repeats into single genes. We discovered that the Ya family comprise several tandemly repeated gene clusters located on different aphid chromosomes and that are highly responsive to GPA plant host changes. Moreover, the green peach aphid Myzus persicae deposits some of the Ya lncRNAs, including Ya1, into plants. The Ya1 lncRNA transcript was shown to migrate away from aphid feeding sites to distal leaves. Finally, via RNAi-mediated knockdown of Ya genes in aphids and transgenic plant lines that stably express the gene for Ya1, we were able to show that Ya genes are M. persicae virulence factors. The work was published in a high-profile journal (Chen, Singh et al., 2020. Proc. Natl. Acad. Sci) with first co-authorships of the two postdoctoral researchers who conducted the experiments on the Grant. We generated RNA-seq and whole-genome bisulphite data of adjusted M. persicae colonies on 9 divergent plant species and at several time points during the adjustment phase of this aphid on 3 divergent plant species. We made progress with studying temporal M. persicae transcriptome changes upon transfer to divergent plant species. So far, these data show that the changes are phased with early and late responsive genes and that the Ya genes belong to the early group. Analyses of how Ya genes may affect aphid response to plant host change are ongoing. Obj. 2: Comparative genome and transcriptome analyses of GPA, B. brassicae and S. avenae We sequenced the genomes of B. brassicae and S. avenae to completion. Annotation of these genomes is ongoing. Comparative genome analyses will commence as soon as the annotations are finished. We discovered that Ya genes are present in all aphid species for which genome sequence data are available, whereas no obvious homologs were detected in other hemipteran species, such as whiteflies (Chen, Singh et al., 2020. Proc. Natl. Acad. Sci). Phylogenetic analyses of the Ya genes showed evidence of fast evolution that include recombination between Ya genes. Nonetheless, a small region that corresponds to a 38-amino acid is conserved among the Ya genes - this region may be translated into a peptide. We didn't find clear homologs of M. persicae Ya1 in the other aphid species. Investigations in how far Ya1 function is unique compared to other Ya transcripts are ongoing. Obj. 3: Study the evolution of genes that respond to host change and pesticides in specialist and generalist insect species and identify genes under selection in GPA field populations We re-sequenced the genomes of ± 100 M. persicae individuals collected from field plots across Europe and in several other countries. This involved optimization of sample collection and DNA isolation methods, and both methods were published as protocols (dx.doi.org/10.17504/protocols.io.bg6wjzfe and dx.doi.org/10.17504/protocols.io.bgxnjxme). The dataset is being analysed for population structure analyses, copy number and single nucleotide polymorphism variations, selective sweeps and genes subjected to purifying versus diversifying selection. We established SapFeedersHub that enables the downloading of aphid genome sequence data and annotations generated within this grant. |
| Exploitation Route | The three protocols mentioned above have been widely used, also for other projects, such as BRIGIT (BB/S016325/1) and CALIBER (BB/T010851/1). Metrics of the high molecular weight extraction method publication dx.doi.org/10.17504/protocols.io.bhftj3nn shows regular usage since 12 July '20 (835 views and 263 exports). For the sample collection protocol (dx.doi.org/10.17504/protocols.io.bgxnjxme) this was 2,131 views and 234 exports, and for the DNA extraction from single insects protocol (dx.doi.org/10.17504/protocols.io.bg6wjzfe) 657 views and 313 exports. The Chen et al publication in the Proc. Natl. Acad. Sci received an Altmetric attention score of 150, which is in the top 5% of all research outputs (97th percentile compared to outputs of the same age and 87th percentile compared to outputs of the same age and source). Data were shared with our industrial collaborator in regular meetings and email exchanges - the latter included several versions of the Chen et al. manuscript before publication. Two postdoctoral researchers hired on this project obtained prestigious positions elsewhere. One leads currently their own research group at one of the best agricultural universities in China. The other has obtained an excellent research position at Sanger. We managed to recruit two talented postdoctoral researchers (despite Covid lockdown) to continue the proposed work. |
| Sectors | Agriculture, Food and Drink,Chemicals,Education,Environment |
| URL | http://sapfeederhub.jic.ac.uk/ |
| Description | Three protocols developed and published in this project are used for other projects, such as BRIGIT (BB/S016325/1) and CALIBER (BB/T010851/1). Metrics of the high molecular weight extraction method publication dx.doi.org/10.17504/protocols.io.bhftj3nn shows regular usage since 12 July '20 (835 views and 263 exports). For the sample collection protocol (dx.doi.org/10.17504/protocols.io.bgxnjxme) this was 2131 views and 234 exports, and for the DNA extraction from single insects protocol (dx.doi.org/10.17504/protocols.io.bg6wjzfe) 657 views and 313 exports. The Chen et al publication in the Proc. Natl. Acad. Sci received an Altmetric attention score of 144, which is in the top 5% of all research outputs (97th percentile compared to outputs of the same age and 87th percentile compared to outputs of the same age and source). Data were shared with our industrial collaborator in regular meetings and email exchanges - the latter included several versions of the Chen et al. manuscript before publication. Two postdoctoral researchers hired on this project obtained prestigious positions elsewhere. One leads currently their own research group at one of the best agricultural universities in China. The other has obtained an excellent research position at Sanger. We managed to recruit two talented postdoctoral researchers (despite Covid lockdown) to continue the proposed work. Data generated in this project led to additional funding, including BRIGIT (BB/S016325/1) and CALIBER (BB/T010851/1) and an iCASE studentship co-funded by Syngenta that is also a collaboration with the Liverpool School of Tropical Medicine. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Education,Environment,Retail,Transport |
| Impact Types | Societal,Economic |
| Description | Project Leader of BRIGIT, a UK-wide consortium to mitigate the risks of Xylella fastidiosa outbreaks in the UK |
| Geographic Reach | Europe |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The BRIGIT consortium includes people from various layers of government, charities, research institutes and industry. The writing of the BRIGIT proposal and activities within BRIGIT so far increased the knowledge of the consortium members about the Xylella pathosystem and how Xylella fastidiosa may spread in the UK and harm the environment. This is likely to influence future regulations to maximize protection of the UK environment. |
| URL | https://www.jic.ac.uk/brigit/ |
| Description | All Aphid Effectors on DEK |
| Amount | £689,277 (GBP) |
| Funding ID | BB/V008544/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2021 |
| End | 03/2024 |
| Description | BRIGIT - A consortium for enhancing UK surveillance and response to Xylella fastidiosa |
| Amount | £5,000,000 (GBP) |
| Funding ID | BB/S016325/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 03/2021 |
| Description | Benign infections or damaging epidemics: the influence of biology, the environment and agricultural practice on vector-borne phytobacteria |
| Amount | £1,868,603 (GBP) |
| Funding ID | BB/T010851/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 08/2023 |
| Description | Cash contribution to IPA grant |
| Amount | £131,700 (GBP) |
| Organisation | Syngenta International AG |
| Sector | Private |
| Country | Switzerland |
| Start | 04/2018 |
| End | 03/2021 |
| Title | BS-seq analyses on aphids |
| Description | We optimized bisulphite sequencing of aphids, including library construction, sequencing and data analyses. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Providing a useful method and strategy to the research community. |
| Title | Genome assembly |
| Description | Developed strategies to improve the assembly of aphid genomes that includes the identification and removal of contigs derived from microbial organisms that are abundantly present in aphids. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Assisted colleagues in the US with improving genome assembly of the soybean aphid. |
| Title | Nanopore for aphids |
| Description | We optimized DNA isolation methods for nanopore sequencing of aphid genomes. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We are able to improve aphid genome assemblies. |
| Title | A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausman) (Hemiptera: Aphididae) |
| Description | Eriosoma lanigerum v1.0 frozen release Genome assembly: Eriosoma_lanigerum.v1.0.scaffolds.fa.gz BRAKER2 gene models: Eriosoma_lanigerum.v1.0.scaffolds.gff BRAKER2 protein sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.cds.fa Buchnera aphidicola scaffolds: Buchnera_aphidicola.scaffolds.fa Aphid orthogroups OrthoFinder run files (see for details https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf): OrthoFinder_run.tar.gz |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | The dataset had 194 views and 120 downloads (10 Mar 2022). |
| URL | https://zenodo.org/record/3797131 |
| Title | Aphidinae comparative genomics resource |
| Description | Here we provide early access to 18 new genome assemblies, including 8 assembled to chromosome-scale, for aphids from the subfamily Aphidinae. For consistency and to aid comparative analysis, all genomes have been annotated using the same repeat masking and RNA-seq-based gene prediction pipeline. Using this pipeline we also provide new annotations for three previously published genome assemblies. The genome assemblies and annotations are made freely available without restriction, we only request that this Zenodo resource is cited when using the data. Raw sequence data upload to NCBI is underway and full details of all accessions will be given in an updated version of this resource. Manuscripts are in preparation describing the individual genome assemblies in detail and larger comparative genome analyses and we will update this resource with additional citation information as papers are published. Full details of all genome assemblies and annotations included in this release are given in the attached "Data_Description.pdf" document. Aphid species included in this release (bold type = chromosome-scale assembly): Aphis fabae Aphis glycines (updated annotation) Aphis gossypii Aphis thalictri Aphis rumicis Brachycaudus cardui Brachycaudus helichrysi Brachycaudus klugkisti Brevicoryne brassicae Diuraphis noxia Macrosiphum albifrons Metopolophium dirhodum Myzus cerasi (updated annotation) Myzus ligustri Myzus lythri Myzus varians Pentalonia nigronervosa (updated annotation) Phorodon humuli Rhopalosiphum padi Sitobion avenae Sitobion miscanthi |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | The resource has 797 views and the dataset was downloaded 520 times (as of 10 Mar 2022). |
| URL | https://zenodo.org/record/5908005 |
| Title | Developed and launched SapFeederHub |
| Description | Database that provides access via an Ensemble platform to genome sequences and annotations of insect species of the order Hemiptera, including aphids, leafhoppers, planthoppers and froghoppers/spittle bugs. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Colleagues can download sequence data and annotations of economically important insect pests, including for instance the Xylella insect vector Philaenus spumarius. Data can be used for population structure analyses and GWAS to study genomic regions involved in insect phenotypes or host preference. |
| URL | http://sapfeederhub.jic.ac.uk/index.html |
| Title | Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts |
| Description | Pentalonia nigronervosa v1 frozen release Genome assembly: Pentalonia_nigronervosa.v1.scaffolds.fa.gz BRAKER2 gene models: Pentalonia_nigronervosa.v1.scaffolds.gff BRAKER2 protein sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.cds.fa InterProScan functional annotation: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.interproscan.tsv Pentalonia nigronervosa v1 mitochondrial genome: Pentalonia_nigronervosa.v1.mt_genome.fa Buchnera aphidicola (BPn) scaffolds: Buchnera_aphidicola_BPn.scaffolds.fa Wolbachia (WolPenNig) scaffolds: Wolbachia_WolPenNig.scaffolds.fa Myzus cerasi v1.2 frozen release Genome assembly: Myzus_cerasi.v1.2.scaffolds.fa BRAKER2 gene models: Myzus_cerasi.v1.2.scaffolds.gff BRAKER2 protein sequences: Myzus_cerasi.v1.2.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_cerasi.v1.2.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Myzus_cerasi.v1.2.scaffolds.gff.cds.fa Aphid orthogroups and species tree Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv Single copy conserved orthogroups used for species tree: Orthogroups_for_concatenated_alignment.txt Species tree alignment: SpeciesTreeAlignment.fa Rooted species tree: SpeciesTree_rooted.nwk Bash script to run k-mer based assembly deduplication pipeline File: disco_filter_dups.v1.1.sh This script will parse a discovar de novo assembly and remove scaffolds likely to be haplotigs based on their k-mer content and a self alignment of the assembly (see manuscript for details). The input discovar assembly needs to have white space in scaffold IDs replaced with "_" before running. Illumina reads should be unzipped before running. Usage: sh disco_filter_dups.sh |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | This dataset had 178 views and 266 downloads (10 Mar 2022) |
| URL | https://zenodo.org/record/3765644 |
| Title | Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome |
| Description | Myzus persicae clone O v2 frozen release Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3 List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the M. persicae de novo repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out RepeatMasker transposable element annotation using the M. persicae de novo repeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Acyrthosiphon pisum clone JIC1 v1 frozen release Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the A. pisum de novo repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out RepeatMasker transposable element annotation using the A. pisum de novo repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Rhodnius prolixus DNA zoo chromosome-scale genome assembly annotation R. prolixus chromosome-scale genome assembly was obtained here: https://www.dnazoo.org/assemblies/Rhodnius_prolixus. Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa Triatoma rubrofasciata chromosome-scale genome assembly annotation T. rubrofasciata chromosome-scale genome assembly was obtained here: http://dx.doi.org/10.5524/100614 Genome assembly: zhuichun_assembly.fasta BRAKER2 gene models: zhuichun_assembly.braker2.gff BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa Hemiptera orthogroups and species tree OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details: Species included, taxon IDs and data source: Mcer = Myzus cerasi v1.1 (https://bipaa.genouest.org/sp/myzus_cerasi/) MperO = Myzus persicae clone O v2 (This study) Dnox = Diuraphis noxia Thorpe et. al. gene predictions (https://bipaa.genouest.org/sp/diuraphis_noxia/) Apis = Acyrthosiphon pisum JIC1 v1 (This study) Pnig = Pentalonia nigronervosa (This study) Rmai = Rhopalosiphum maidis v0.1 (http://gigadb.org/dataset/100572) Rpad = Rhopalosiphum padi v1.0 (https://bipaa.genouest.org/sp/rhopalosiphum_padi/) Agly = Aphis glycines biotype 4 v2.1 (https://zenodo.org/record/3453468#.XnpL5JOgLRY) BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi) Trub = Triatoma rubrofasciata (This study) Rpro = Rhodnius prolixus (This study) Ofas = Oncopeltus fasciatus OGS v1.0 (https://i5k.nal.usda.gov/Oncopeltus_fasciatus) Sfuc = Sogatella furcifera v1 (http://dx.doi.org/10.5524/100255) Nlug = Nilaparvata lugens (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42) Files: Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt Species tree alignment: SpeciesTreeAlignment.fa r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex r8s time calibrated species tree: r8s_tree.nwk |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/3712088 |
| Title | Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome |
| Description | Myzus persicae clone O v2 frozen release Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3 List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the M. persicae de novo repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out RepeatMasker transposable element annotation using the M. persicae de novo repeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Acyrthosiphon pisum clone JIC1 v1 frozen release Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the A. pisum de novo repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out RepeatMasker transposable element annotation using the A. pisum de novo repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Rhodnius prolixus DNA zoo chromosome-scale genome assembly annotation R. prolixus chromosome-scale genome assembly was obtained here: https://www.dnazoo.org/assemblies/Rhodnius_prolixus. Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa Triatoma rubrofasciata chromosome-scale genome assembly annotation T. rubrofasciata chromosome-scale genome assembly was obtained here: http://dx.doi.org/10.5524/100614 Genome assembly: zhuichun_assembly.fasta BRAKER2 gene models: zhuichun_assembly.braker2.gff BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa Hemiptera orthogroups and species tree OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details: Species included, taxon IDs and data source: Mcer = Myzus cerasi v1.1 (https://bipaa.genouest.org/sp/myzus_cerasi/) MperO = Myzus persicae clone O v2 (This study) Dnox = Diuraphis noxia Thorpe et. al. gene predictions (https://bipaa.genouest.org/sp/diuraphis_noxia/) Apis = Acyrthosiphon pisum JIC1 v1 (This study) Pnig = Pentalonia nigronervosa (This study) Rmai = Rhopalosiphum maidis v0.1 (http://gigadb.org/dataset/100572) Rpad = Rhopalosiphum padi v1.0 (https://bipaa.genouest.org/sp/rhopalosiphum_padi/) Agly = Aphis glycines biotype 4 v2.1 (https://zenodo.org/record/3453468#.XnpL5JOgLRY) BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi) Trub = Triatoma rubrofasciata (This study) Rpro = Rhodnius prolixus (This study) Ofas = Oncopeltus fasciatus OGS v1.0 (https://i5k.nal.usda.gov/Oncopeltus_fasciatus) Sfuc = Sogatella furcifera v1 (http://dx.doi.org/10.5524/100255) Nlug = Nilaparvata lugens (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42) Files: Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt Species tree alignment: SpeciesTreeAlignment.fa r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex r8s time calibrated species tree: r8s_tree.nwk |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/3712089 |
| Description | Collaboration with CAS, Bejing |
| Organisation | Chinese Academy of Sciences |
| Department | Beijing Institutes of Life Science Chinese Academy of Sciences |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Contributed scientific knowledge to an experimental system and provided input into the writing of a scientific publication. |
| Collaborator Contribution | Contributed scientific knowledge to an experimental system and provided input into the writing of a scientific publication. |
| Impact | Published a scientific paper in an international peer-reviewed journal. |
| Start Year | 2018 |
| Description | Collaboration with East Malling Research |
| Organisation | East Malling Research |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We are sequencing and annotating the genome of the woolly apple aphid, a serious pest of apple trees |
| Collaborator Contribution | The collaborator provided frozen aphids for genome and RNA sequencing |
| Impact | We will obtain the complete genomes and transcriptomes of the woolly apple aphid, which is in a distinct clade in the aphid phylogenetic tree and useful for comparative genome analyses among aphids. |
| Start Year | 2018 |
| Description | Collaboration with International Institute of Tropical Agriculture (IITA), Kenya |
| Organisation | International Institute of Tropical Agriculture |
| Department | IITA Tanzania |
| Country | Tanzania, United Republic of |
| Sector | Charity/Non Profit |
| PI Contribution | We analyzed and annotated genome sequence data of banana aphid samples and we wrote the majority of the manuscript that was published. |
| Collaborator Contribution | The collaborator provided genome sequence data of Kenyan aphid species. |
| Impact | We published a scientific paper in an international journal. |
| Start Year | 2018 |
| Description | Collaboration with Syngenta on an iCASE studentship |
| Organisation | Syngenta International AG |
| Department | Syngenta Ltd (Bracknell) |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Wrote iCASE studentship. Advertised position for PhD student and hosted and interviewed applicant. |
| Collaborator Contribution | Contributed to the writing of the iCASE studentship |
| Impact | iCASE project that starts Oct '20. |
| Start Year | 2019 |
| Description | Collaboration with University of Oxford |
| Organisation | University of Oxford |
| Department | Department of Plant Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Visited colleagues at University of Oxford to discuss specific project and experimental approaches |
| Collaborator Contribution | Contributed knowledge and resources for new experiments |
| Impact | Progress with achieving research goals by graduate student and postdoctoral researcher in the lab. Making plans for a collaborative research proposal. |
| Start Year | 2019 |
| Description | Engaged with colleagues at the International Centre of Insect Physiology and Ecology (ICIPE) |
| Organisation | International Centre of Insect Physiology and Ecology (ICIPE) |
| Country | Kenya |
| Sector | Academic/University |
| PI Contribution | Involved colleague at ICIPE in the GCRF-funded project to study Napier grass stunt phytoplasma |
| Collaborator Contribution | Provided plant and insect materials for sequencing |
| Impact | Materials are being processed |
| Start Year | 2018 |
| Title | Annotation of genes encoding long non-coding RNAs in aphid genomes |
| Description | We developed a pipeline to annotate genes for long non-coding RNAs in aphid genomes |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | We have the sequences of aphid candidate long non-coding RNAs |
| Title | Improve aphid genome assembly pipeline |
| Description | We optimized methods to improve aphid genome assemblies using existing software |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | We obtained high quality chomosome level assemblies of aphid genomes |
| Title | Improved aphid genome annotation pipeline |
| Description | We work with the Earlham Institute to optimize annotation of aphid genomes |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | Improved annotation of aphid genomes. |
| Description | Attended Gatsby Plant Science Annual Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Attended the annual meeting on behalf of Gatsby-funded graduate student |
| Year(s) Of Engagement Activity | 2019 |
| Description | Attended Introductory programme for UvA professors |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Participated in an introductory programme for UvA professors. The Executive Board of the University of Amsterdam offers this programme to all newly appointed UvA professors, to facilitate them in their new role in the academic community and as UvA representatives. The programme offered insights and tools that helped strengthen personal effectiveness in daily work situations including extending network within the UvA. It also allows to gain more insight into the role and position of a UvA professor, meet colleagues and exchange experiences plus learn more about Dutch academic leadership codes. Furthermore, organizational and financial aspects of the university will be highlighted as well as current developments within the UvA and the role of academic leadership. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Engagement with Syngenta |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Regular meetings with colleagues at Syngenta, Jealott's Hill, UK, and Switserland and USA to discuss project proposals and research progress on aphids. |
| Year(s) Of Engagement Activity | 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019 |
| Description | Invited research seminar at CAS institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a research seminar at IGDB, Beijing, China on 16 Mar 2018. Research fellow Thomas Mathers in my lab also contributed a talk. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited research seminar at the Max Planck Institute, Cologne, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to give a research seminar at the Max Planck Institute for Plant Breeding, Cologne, Germany. Approximately 50 people, including PhD students, attended. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited research seminar at the annual Life Sciences conference, Beijing, China |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk in a paralell session focused on insect pests at the Life Sciences Conference, Beijing, China, 28-31 Oct '19. |
| Year(s) Of Engagement Activity | 2018 |
| Description | MSc colloquium on epigenetics and adaptive evolution |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | MSc colloquium on the role of epigenetics in adaptive evolution to an audience of MSc students from the UEA and visiting MSc students from the International Masters in Applied Ecology (IMAE) from Europe. |
| Year(s) Of Engagement Activity | 2021,2022 |
| Description | Meeting with industrial partners |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Communicated our research findings to our industrial partners |
| Year(s) Of Engagement Activity | 2021 |
| Description | Participated in conference at Syngenta |
| 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 | Attended Syngenta external collaboration event. Three postdoctoral lab members in my group presented research talks and updates with their project progress. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participated in visit of Syngenta to the Norwich Research Park |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussed progress on current funded projects and possibilities of future projects with colleagues from Syngenta. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participated summerschool, Pwani University, Kenya |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Co-organized a two-day course as part of the two-week AfriPlantSci summerschool for ±25 professionals and students from research institutes and university in Kenya and several other countries in sub-saharan Africa. Two PhD students of my team participated in the organization of the summerschool. Protocols we taught in the course were shared and are being used in current projects of the course participants. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participation in autumn workshop of The Sainsbury Laboratory |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participated in the autumn workshop of The Sainsbury Laboratory. A PhD student in my group gave a talk and received substantial feedback. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Progress meeting with Syngenta collaborators |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Project progress meetings |
| Year(s) Of Engagement Activity | 2020 |
| Description | Visit of Syngenta |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Visited Syngenta to give update on project progress. Three team members presented and engaged with Syngenta colleagues. |
| Year(s) Of Engagement Activity | 2019 |