Functional Genomics of Aphid Adaptation to Plant Species
Lead Research Organisation:
John Innes Centre
Department Name: Cell and Develop Biology
Abstract
1. The Background: The green peach aphid (GPA) Myzus persicae, an agronomically important pest worldwide, can colonize over 400 different plant species from more than 50 plant families and holds the world record of insecticide resistance mechanisms, showing resistance to at least 70 different synthetic compounds. Moreover, GPA is remarkably plastic such that one clone consisting of genetically identical females can survive and reproduce on a wide range of plant species. This is in contrast to majority of other aphid species, including the pea aphid (Acyrthosiphon pisum), which has adapted to one or a few related plant species within one plant family.
2. The Big Questions: What are the genetic control mechanisms that underlie the phenotypic plasticity of GPA? Is this plasticity related to GPA ability to evolve insecticide resistance to at least 70 different synthetic compounds in the last 60 years, i.e. an "evolutionary blink-of-an-eye"?
3. The Hypotheses: We hypothesize that the phenotypic plasticity of GPA is due to its (1) genomic adaptations in the form of the expansion of certain multigene families that are important for virulence, in combination with (2) epigenetic regulation affecting gene expression levels of gene family members. Depending on exposure to plant hosts and pesticides, certain members within gene families are differentially up or down-regulated, providing the parasite with a versatile "genetic toolbox".
4. The Supportive Data: The Hogenhout lab has developed research tools for GPA clone "O", which has predominated in the UK, causing damage to diverse crops in recent years. We maintain this clone as genetically identical females that can survive and reproduce on diverse plant species, including for example Chinese cabbage and tobacco plants, which produce different defense compounds that are toxic to aphids. The GPA clone O whole genome sequence is currently being assembled and annotated using gene expression data. We have evidence that members of specific gene families, such as cathepsins and cuticular proteins, play a role in the phenotypic adaptation of GPA to plant species. We are also interested in cytochrome 450 monooxygenases (P450s), which are detoxification enzymes of organic substances such as phytochemicals and pesticides. Finally, we have developed the plant-mediated RNA interference (RNAi) technology enabling studies of the effect of the knock down of specific GPA genes on GPA survival and reproduction on various plant species.
5. The Objectives:
In the first objective we will advance the construction of a physical genomic map, identify coding sequences and conduct evolutionary analysis of gene family members of GPA clone O.
In the second objective we will assess which genes are differentially regulated in GPA clone O reared on different plant species and exposed to various pesticides. We will also sequence the genomes of additional GPA clones that are susceptible and resistant to pesticides and determine if differentially expressed genes are subject to high mutation frequencies.
In the third objective we use plant-mediated RNAi to knock down the expression of specific genes to assess their effect on the ability of GPA to survive on different plant species and upon insecticide exposure. We will assess if DNA methylation is involved in GPA phenotypic plasticity.
6. The Implications: At completion of this project we will have gained a better understanding of how GPA adapts to multiple plant species and if this relates to mechanisms involved in the development of insecticide resistance of GPA. We will also have elucidated the level of genomic variation amongst GPA clones susceptible and resistant to pesticides. This research is fundamentally important to our overall understanding of how insect adapt to their environments. Ultimately, this could have practical implications for the increasing problem of the evolution of insecticide resistance in crop-pest control.
2. The Big Questions: What are the genetic control mechanisms that underlie the phenotypic plasticity of GPA? Is this plasticity related to GPA ability to evolve insecticide resistance to at least 70 different synthetic compounds in the last 60 years, i.e. an "evolutionary blink-of-an-eye"?
3. The Hypotheses: We hypothesize that the phenotypic plasticity of GPA is due to its (1) genomic adaptations in the form of the expansion of certain multigene families that are important for virulence, in combination with (2) epigenetic regulation affecting gene expression levels of gene family members. Depending on exposure to plant hosts and pesticides, certain members within gene families are differentially up or down-regulated, providing the parasite with a versatile "genetic toolbox".
4. The Supportive Data: The Hogenhout lab has developed research tools for GPA clone "O", which has predominated in the UK, causing damage to diverse crops in recent years. We maintain this clone as genetically identical females that can survive and reproduce on diverse plant species, including for example Chinese cabbage and tobacco plants, which produce different defense compounds that are toxic to aphids. The GPA clone O whole genome sequence is currently being assembled and annotated using gene expression data. We have evidence that members of specific gene families, such as cathepsins and cuticular proteins, play a role in the phenotypic adaptation of GPA to plant species. We are also interested in cytochrome 450 monooxygenases (P450s), which are detoxification enzymes of organic substances such as phytochemicals and pesticides. Finally, we have developed the plant-mediated RNA interference (RNAi) technology enabling studies of the effect of the knock down of specific GPA genes on GPA survival and reproduction on various plant species.
5. The Objectives:
In the first objective we will advance the construction of a physical genomic map, identify coding sequences and conduct evolutionary analysis of gene family members of GPA clone O.
In the second objective we will assess which genes are differentially regulated in GPA clone O reared on different plant species and exposed to various pesticides. We will also sequence the genomes of additional GPA clones that are susceptible and resistant to pesticides and determine if differentially expressed genes are subject to high mutation frequencies.
In the third objective we use plant-mediated RNAi to knock down the expression of specific genes to assess their effect on the ability of GPA to survive on different plant species and upon insecticide exposure. We will assess if DNA methylation is involved in GPA phenotypic plasticity.
6. The Implications: At completion of this project we will have gained a better understanding of how GPA adapts to multiple plant species and if this relates to mechanisms involved in the development of insecticide resistance of GPA. We will also have elucidated the level of genomic variation amongst GPA clones susceptible and resistant to pesticides. This research is fundamentally important to our overall understanding of how insect adapt to their environments. Ultimately, this could have practical implications for the increasing problem of the evolution of insecticide resistance in crop-pest control.
Technical Summary
The green peach aphid (GPA) Myzus persicae is an agronomically important pest worldwide. This aphid colonizes over 400 different plant species from more than 50 plant families and has developed resistance to all insecticides that are currently in use. Remarkably, a single GPA clone (consisting of genetically identical individuals) can colonize diverse plant species of several plant families, whilst the specialist pea aphid Acyrthosiphon pisum (for which the genome sequence is available) consists of genetically distinct races each of which colonizes different plant species of the family Fabaceae (or Leguminosae).
The objective of this project is to identify mechanisms that have given GPA its impressive phenotypic plasticity.
We will test the hypothesis that some gene families have adaptively expanded, offering GPA better protection to phytochemicals and insecticides. Given that genetically identical clones can exploit distinct host plants, we hypothesize that epigenetic regulation affects gene expression levels, and that certain gene members within these gene families are differentially up or down-regulated depending on exposure to host species and insecticides.
This project tests an exiting new idea that adaptive gene duplication and expansion of certain gene families has provided GPA with a versatile "genetic toolbox" allowing for a phenotypically plastic response through epigenetic regulation, thereby equipping this parasite with a vast evolutionary potential that could threaten future food security. We will use state-of-the-art genomics tools to compare aphid genomes and assess gene expression and DNA methylation profiles of GPA reared on diverse plant species and exposed to insecticides with different chemistries. We will then knock down the expression of specific GPA genes to study their effect on GPA adaptation to plants and insecticides.
This project includes a translational component that will be taken forward in collaboration with Syngenta.
The objective of this project is to identify mechanisms that have given GPA its impressive phenotypic plasticity.
We will test the hypothesis that some gene families have adaptively expanded, offering GPA better protection to phytochemicals and insecticides. Given that genetically identical clones can exploit distinct host plants, we hypothesize that epigenetic regulation affects gene expression levels, and that certain gene members within these gene families are differentially up or down-regulated depending on exposure to host species and insecticides.
This project tests an exiting new idea that adaptive gene duplication and expansion of certain gene families has provided GPA with a versatile "genetic toolbox" allowing for a phenotypically plastic response through epigenetic regulation, thereby equipping this parasite with a vast evolutionary potential that could threaten future food security. We will use state-of-the-art genomics tools to compare aphid genomes and assess gene expression and DNA methylation profiles of GPA reared on diverse plant species and exposed to insecticides with different chemistries. We will then knock down the expression of specific GPA genes to study their effect on GPA adaptation to plants and insecticides.
This project includes a translational component that will be taken forward in collaboration with Syngenta.
Planned Impact
The green peach aphid (GPA) Myzus persicae is one of the most notorious plant pests worldwide for various reasons. First, this insect transmits more than 100 different plant viruses, which can cause dramatic yield losses in crops. One example is Turnip yellows virus (TuYV), which is thought to reduce yield of oilseed rape by up to 30% in the UK. Secondly, GPA can colonize over 400 different plant species, including important crops such as oilseed rape, beet, tomato and potato, and wild plant species, which may serve as sources of the plant viruses. As well, GPA has developed resistance to over 70 different synthetic compounds. This, coupled with changes in the regulatory landscape on pesticide usage, has resulted in the neonicotinoids class of pesticides being one of few left that successfully controls these insects. In addition, climate change has contributed to the insect pest emerging several weeks earlier in annual crop growing seasons, exacerbating crop losses and affecting in particular the temperate regions in Europe, including the UK. Finally, intensification and globalization of agriculture has contributed to new introductions of insect pests (including insecticide-resistant GPA clones) and vectored viruses into production fields worldwide. The research described in this proposal will use state-of-the-art technologies and novel approaches to increase the likelihood of making fundamental discoveries that will underpin the development of new strategies to control this notorious pest in the future. Therefore, this project addresses two of the BBSRC key priorities - 'Living with Environmental Change' and 'Crop Science'.
This project could inform industry and strategic research programs that focus on the identification of new pest control methods on four accounts. First, genome sequence information of various clones and RNAi technology will identify GPA genes involved in insecticide resistance. This information can be used for the generation of markers for the detection of insecticide-resistant GPA in the field. Furthermore, the described research enables assessment of the role of GPA genes in GPA-plant interactions, which could inform plant-breeding strategies for increasing plant resistance to GPA and other aphids. As well, this project may identify targets in GPA for aphid control e.g. new targets for biochemical control or control via in planta RNAi. Finally, it will elucidate the role of epigenetic regulation in GPA development and phenotypic plasticity leading possibly to novel control targets of GPA.
Syngenta has acknowledged the strategic importance of this research by supporting this proposal as an Industrial Partnership Award (IPA). A good working relationship between PI Hogenhout and Syngenta colleagues at Jealott's Hill has already led to the sharing of information and the establishment of new protocols at Syngenta.
Intellectual property (IP) will be managed by the Plant Bioscience Limited (PBL), which is an independent technology management company specializing in plant, food and microbial science based that manages IP at the Norwich Research Park.
The proposed research will aid other strategic research projects of the Hogenhout lab, such as understanding the mechanisms involved in GPA transmission of viruses, including TuYV (funded by a CASE studentship), and whole-genomics approaches to understand the interactions of whiteflies, which are sister species of aphids, with plants (funded by the Gates foundation).
We will communicate science to the general public. The three team leaders will host Nuffield scholars and we will, in coordination with Dr. Ian Bedford (Manager of the Insectary at JIC), organize plant pest and disease clinics. As well, we will participate in 'Science Camps' for high school students, converse achievements relevant for press releases and general public engagement (JIC Press Office) and join in knowledge exchange and commercialization (KEC) activities at the JIC.
This project could inform industry and strategic research programs that focus on the identification of new pest control methods on four accounts. First, genome sequence information of various clones and RNAi technology will identify GPA genes involved in insecticide resistance. This information can be used for the generation of markers for the detection of insecticide-resistant GPA in the field. Furthermore, the described research enables assessment of the role of GPA genes in GPA-plant interactions, which could inform plant-breeding strategies for increasing plant resistance to GPA and other aphids. As well, this project may identify targets in GPA for aphid control e.g. new targets for biochemical control or control via in planta RNAi. Finally, it will elucidate the role of epigenetic regulation in GPA development and phenotypic plasticity leading possibly to novel control targets of GPA.
Syngenta has acknowledged the strategic importance of this research by supporting this proposal as an Industrial Partnership Award (IPA). A good working relationship between PI Hogenhout and Syngenta colleagues at Jealott's Hill has already led to the sharing of information and the establishment of new protocols at Syngenta.
Intellectual property (IP) will be managed by the Plant Bioscience Limited (PBL), which is an independent technology management company specializing in plant, food and microbial science based that manages IP at the Norwich Research Park.
The proposed research will aid other strategic research projects of the Hogenhout lab, such as understanding the mechanisms involved in GPA transmission of viruses, including TuYV (funded by a CASE studentship), and whole-genomics approaches to understand the interactions of whiteflies, which are sister species of aphids, with plants (funded by the Gates foundation).
We will communicate science to the general public. The three team leaders will host Nuffield scholars and we will, in coordination with Dr. Ian Bedford (Manager of the Insectary at JIC), organize plant pest and disease clinics. As well, we will participate in 'Science Camps' for high school students, converse achievements relevant for press releases and general public engagement (JIC Press Office) and join in knowledge exchange and commercialization (KEC) activities at the JIC.
Publications
Mathers T
(2018)
Sex-specific changes in the aphid DNA methylation landscape
Mathers TC
(2017)
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.
in Genome biology
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
Mathers TC
(2019)
Sex-specific changes in the aphid DNA methylation landscape.
in Molecular ecology
| Title | Video Abstract for Genome Biology publication |
| Description | Genome Biology created a video abstract to explain the science described in the Genome Biology to students. The video shows animation of an aphid changing plant hosts with a narrator who explains what happens in the aphid upon the host change. The video was posted on YouTube. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2017 |
| Impact | So far the video had 488 views on YouTube, and 9 viewers liked the video and none disliked the video. The video has likely increased the amount of attention the Genome Biology article received by different media (current Altmetric attention score of the paper is 110). |
| URL | https://www.youtube.com/watch?v=EKy_SuaFKMk |
| Description | We achieved the objectives of the proposal. As part of objective 1, we sequenced and annotated the genomes of two Myzus persicae clones (clone G006 and clone O). This was a consortium project that involved scientists from UK, USA, France and Spain. The UK team provided leadership in the completion of the work and writing of the publication. Genome assemblies and annotations of M. persicae clones O and G006 were frozen and made available to the scientific community via AphidBase (http://www.aphidbase.com/Myzus-DB). A manuscript reporting the M. persicae clones G006 and O genome sequences was published (Mathers et al., 2017. Genome Biol). As part of objective 2, we analyzed the transcriptome data of the aphids on Brassica rapa (orginal host), Arabidopsis thaliana and Nicotiana benthamiana and identified M. persicae gene families that are co-regulated and adjust their gene expression levels depending on the plant species. We found that aphids adjust the expression of these genes within a few hours upon host transfer. Similar genes have also been reported to be differentially regulated in M. persicae exposed to pesticides. The work is included in the Mathers et al. 2017 publication. As part of objective 3, we found that RNA interference (RNAi)-mediated knock down of multiple members of the cathepsin B (cathB) family affects M. persicae performance on A. thaliana, but not on N. benthamiana, consistent with the CathB genes being upregulated on A. thaliana relatively to N. benthamiana. Therefore, CathB are candidate virulence proteins. This work was also included in the Mathers et al., 2017. publication. Three CathB proteins are candidate effectors that may modulate plant processes and are being functionally characterized as part of a new grant that is a collaboration with the Chinese Academy of Sciences (CAS) in Shanghai. We also optimized strategies to sequence the M. persicae DNA methylomes via bisulphite sequencing. We first analyzed DNA methylation in M. persicae sexual morphs, including asexual females and males and found differential methylation of the sex chromosomes of M. persicae. The work is published in Mathers et al., 2018. Biorxiv and is being revised for resubmission to a scientific journal. As per objective 2, we also generated transcriptome and bisulphite data of M. persicae clone O on 9 divergent species of 5 families, including 8 dicots and one monocot. Analyses of the transcriptomes confirmed data published in Mathers et al., 2017. Genome Biol. We are currently conducting further analyses of the transcriptomes and methylomes. Throughout the project we had regular meetings with the project leaders, two postdoctoral researchers and a research assistant of the three Norwich research institutes involved in the project and we also presented regular updates in the form of powerpoint presentations to our colleagues at Syngenta, Jealott's Hill, UK. We successfully applied for a new BBSRC-IPA project that received 10% support from Syngenta and that started in 2018. |
| Exploitation Route | The genome assemblies and annotations of GPA clone O and G006 genomes are available for downloading by the scientific community worldwide. A publication reporting on unique aspects of the GPA genome was published. Scientific findings were communicated to colleagues at Syngenta Ltd in regular meetings. Postdoctoral researchers on the project have shared data generated in this project with colleagues at scientific meetings, including those organized by the European COST program, Kiel, Germany (one talk) and the French-UK Aphid meeting in Paris, France (Nov 2015, 2 talks). PIs, postdocs and research assistants working on the project have presented talks at several (inter)national scientific meetings. |
| Sectors | Agriculture, Food and Drink,Chemicals,Education,Environment |
| URL | http://www.aphidbase.com/Myzus-DB |
| Description | We obtained more knowledge about fundamental processes that enable Myzus persicae to colonize divergent plant species. We also optimized RNA interference (RNAi) methods to knock down gene expression in aphids. The industrial partner of this project, Syngenta, is using this knowledge to develop new control strategies for aphids. This is important given that pesticides, including neonicotionoids that are particularly effective for aphid control, are being taken off the market. Therefore, this project has generated essential information for the future protection of agriculture and food production that are primarily economic and societal impacts. The new control strategies for aphids are likely less detrimental and so this project will also helps to improve the overall environment. The project employed two postdoctoral researchers. One postdoctoral researcher received a prestigious BBSRC Future Leader Fellowship that started in 2018. He used data and experience gained in this proposal to obtain this fellowship. The postdoctoral researcher is currently applying for faculty positions at UK universities. We produced a video abstract for the Mathers et al., 2017 publication. The video communicates our discoveries to a general audience. This video is being used for educational purposes. |
| First Year Of Impact | 2016 |
| Sector | Agriculture, Food and Drink,Education,Environment |
| Impact Types | Societal,Economic |
| 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 | BBSCR Future Leadership Award awarded to TM |
| Amount | £429,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2021 |
| Description | BBSRC IPA |
| Amount | £962,887 (GBP) |
| Funding ID | BB/R009481/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2021 |
| Description | BBSRC-IPA grant |
| Amount | £1,316,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2021 |
| Description | CAS-JIC collaboration |
| Amount | £120,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 03/2020 |
| Description | Cash contribution to IPA grant |
| Amount | £95,000 (GBP) |
| Organisation | Syngenta International AG |
| Sector | Private |
| Country | Switzerland |
| Start | 10/2014 |
| End | 09/2016 |
| Description | Cash contribution to IPA grant |
| Amount | £131,700 (GBP) |
| Organisation | Syngenta International AG |
| Sector | Private |
| Country | Switzerland |
| Start | 04/2018 |
| End | 03/2021 |
| Description | Future Leader Fellowship awarded to Thomas Mathers |
| Amount | £317,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 04/2021 |
| Description | JIC-CAAS collaboration funds |
| Amount | £100,000 (GBP) |
| Organisation | John Innes Centre |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 12/2018 |
| Description | iCASE PhD studentship |
| Amount | £27,800 (GBP) |
| Funding ID | 1805607 |
| Organisation | John Innes Centre |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 09/2020 |
| Description | iCASE PhD studentship |
| Amount | £12,400 (GBP) |
| Organisation | Oxitec Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 10/2015 |
| End | 09/2019 |
| 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 | 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 | 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/3712089 |
| 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 |
| Description | Formal research collaboration with Earlham Institute, Norwich, UK |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our time provides knowledge, resources and materials for the insect-plant interaction research system. |
| Collaborator Contribution | Colleagues team provides knowledge on bioinformatics and genomics, including genome and transcriptome assembly pipelines and genome annotations. |
| Impact | We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We are co-authors on Mathers et al., 2017. Genome Biology, and a paper that is being submitted this month. We assisted postdoctoral researcher Thomas Mathers with the writing of a Future leader fellowship application, which was succesful (starts Apr 2018). |
| Start Year | 2010 |
| Description | Formal research collaboration with Syngenta |
| Organisation | Syngenta International AG |
| Department | Syngenta Ltd (Bracknell) |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provide information about aphid biology and genomics, and mechanisms involved in aphid adjustment to diverse plant species and pesticides. |
| Collaborator Contribution | Contributed 10% cash towards two BBSRC-IPA projects (2014-2017; 2017-2020) and advised on how to conduct pesticide applications. Provided aphid clones for sequencing and analyses. |
| Impact | Made progress with understanding processes involved in aphid adjustments to plants and pesticides. This collaboration resulted in a publication: Mathers, Chen et al., 2017. Genome Biol. 18: 27. As well, the collaboration was renewed with follow-up funding, that is a BBSRC-IPA grant commencing April 2018. Held regular meetings to discuss progress, including visits of my group to Syngenta and collagues of Syngenta to JIC, and Skype and phone conference meetings. |
| Start Year | 2014 |
| Description | Formal research collaboration with University of East Anglia, Norwich, UK |
| Organisation | University of East Anglia |
| Department | School of Environmental Sciences UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Knowledge, resources and materials for the insect-plant interaction research system. |
| Collaborator Contribution | Colleague's team provides knowledge on evolutionary biology and population genetics. |
| Impact | We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We co-authored on publications. We assisted postdoctoral researchers with the writing of a succesful Future Leader Fellowship application. |
| Start Year | 2013 |
| Title | METHODS OF INCREASING BIOTIC STRESS RESISTANCE IN PLANTS |
| Description | The invention relates to methods of increasing biotic stress resistance in a plant as well as plants with increased biotic stress resistance and methods of screening plants for the beneficial phenotype |
| IP Reference | WO2021048272 |
| Protection | Patent application published |
| Year Protection Granted | 2021 |
| Licensed | No |
| Impact | Obtained new knowledge of how to obtain plants, including crops, with increased resistance to aphids and possibly other related sap-sucking insects that transmit a diverse plant pathogens, including a broad range of viruses, phytoplasmas, liberibacters and Xylella fastidiosa. |
| 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 | 3rd Hemipteran-Plant Interactions Symposium, Madrid, Spain, 5th June 2017. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Presented talk with the Title: Sequencing two aphid genera: comparative genomics of Myzus and Brachycaudus to infer the genomic basis of generalism at an International meeting of circa 150 people, resulting in increased awareness and discussion about the genomics of plant pests. |
| Year(s) Of Engagement Activity | 2017 |
| Description | BBC Radio 4 Farming Today interview. Broadcast 14th June 2017. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | TM gave a 5 minute interview discussing the impact of our recent Myzus persicae genome paper on understanding of plant-insect interactions and the biology and evolution of pest species. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.bbc.co.uk/programmes/b08tbf1c |
| Description | BBC Radio Norwich interview. Broadcast 14th September 2017. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Live interview as part of radio Norwich broadcasting day at JIC to promote the open day. Discussed how we are using genomics to understand the evolution of aphid crop pests. |
| Year(s) Of Engagement Activity | 2017 |
| 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 | ICE, Florida, USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented an invited talk at the International Conference of Entomology (ICE), Orlando, Florida, USA. |
| Year(s) Of Engagement Activity | 2016 |
| 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 iDiv, Leipzig, 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 by PhD students to give a research presentation at the Integrative Biodiversity Research Institute (iDiv), Halle-Jena-Leipzig, Germany, 18 Apr 2018. I was hosted by Crispus Mbaluto, PhD student at iDiv. |
| 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 | Lecture on plant pathogens |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This forms part of a lecture series for the MSc course and BSc course in Evolutionary Biology & Conservation Genetics organised and presented by CVO at the UEA. Students showed interest in this area of research. |
| 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 | Meetings with industry (Lucy Firth, Syngenta and colleagues) on 5 Sep 2014, 29 June 2015, 8 Sep, 2015, 22 Feb 2016, 7 Dec 2016 and 31 Jan 2017 |
| 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 | Meetings with industry (Syngenta), which is our project partner, to relay our research findings. Our data generated in BBSRC funded research is important to understand the evolution of insecticide resistance, which has a potential applied impact. |
| Year(s) Of Engagement Activity | 2014,2015,2016,2017 |
| Description | Orlando, USA (Oral Presentation) Aphid-specific expanded gene families are required for Myzus persicae colonisation of diverse plant species |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Communicating primary research findings and data from research |
| Year(s) Of Engagement Activity | 2016 |
| Description | Population Genetics Group Meeting, Bristol, UK, 4th January 2018. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Presented a tad with the title: Evolutionary genomics of host range expansion in the green peach aphid in an international meeting of 250 people, resulting in discussions and further collaborations with researchers in related subject areas. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Research presentation at CAS-JIC Bilateral Workshop, Beijing, China in March 2015. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Amount of people 50-100 from JIC and CAS mostly PIs were updated on the research progress which stimulated discussions. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk about the aphid genome sequence at Effectome meeting VIII, Lauret, France in Sept 2015. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Reporting progress on aphid genome sequence, particular wrt the effectome. Much research is dedicated into understanding the underpinning genetic of host-parasite interactions, and the effector repertoire of plant pests. The talk stimulated discussions. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk about the aphid genome sequence at the ICE, Orlando, Florida, USA in Sept 2016. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Research findings and new data was presented which sparked discussion. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at The Sainsbury Laboratory Council Meeting, Norwich, UK, 10th November 2017. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Study participants or study members |
| Results and Impact | TM presented a talk with the title: Decoding the aphid methylome and an internal meeting, 100 people, sparking debate. |
| Year(s) Of Engagement Activity | 2017 |
| Description | UK-France joint meeting on Aphids. November 5-6, 2015 Paris, France (Oral Presentation). |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The talk entitled "Specific gene families are involved in Myzus persicae response to diverse plant species" at the UK-France joint meeting on Aphids, in Paris, informed the scientific community that we identified a small number of gene families that enable the aphid to adapt to new host plants. |
| Year(s) Of Engagement Activity | 2015 |
| Description | University of Sheffield Department of Animal and Plant Sciences Seminar (invited speaker), Sheffield, UK, 3rd May 2017. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | TM presented a talk with the title: Evolutionary genomics of aphid host range expansion and phenotypic plasticity. This was for a departmental seminar as an invited speaker. Talk resulted in exchange of ideas and discussion. |
| Year(s) Of Engagement Activity | 2017 |
| Description | VBD, Liverpool |
| 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 talk about my lab's recent progress made in aphid-plant interactions research at the UK Vector-Borne Diseases meeting. |
| Year(s) Of Engagement Activity | 2016 |