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Evolutionary genomics and functional testing of novel genes in lineages of pest insect species

Principal Supervisor: Dr Kristen Panfilio, School of Life Sciences

Co-supervisor: Dr Andre Pires da Silva, School of Life Sciences

PhD project title: Evolutionary genomics and functional testing of novel genes in lineages of pest insect species

University of Registration: University of Warwick

Project outline:

Invasive insect pest species are a growing problem that severely impacts agriculture and crop plants. The UK Plant Health Risk Register currently recognizes nearly 1000 specific pests, with beetles (Coleoptera) and bugs (Hemiptera) among those recognized as high profile pests and those with rapidly changing statuses. Combatting these pests in a species-specific way is crucial to limit the use of general chemical pesticides that can harm the environment or beneficial species such as honey bees. Moreover, understanding the genomes and gene expression profiles of invasive pests will clarify the mechanisms behind their robust development and adaptive feeding ecologies that take advantage of local food sources.

This project focuses on unique genes in the Heteroptera, or “true” bugs, including the brown marmorated stink bug (Halyomorpha halys), an invasive pest that is able to feed on a wide array of plant species and plant tissue types. For example, we recently identified lateral gene transfer events from bacteria that have conferred cell wall degradation capacity within the common ancestor of H. halysand the lab research model Oncopeltus fasciatus, the milkweed bug, where positive selection has led to copy number expansion of this gene in both species [1]. Our recent comparative genomic and transcriptomic datasets have also identified novel, Heteroptera-specific genes that are implicated in embryogenesis as essential factors. This project will combine computational and wet bench experimental approaches, building on our recent work in sequencing the genomes and transcriptomes of pest species [e.g., 2, 3], constructing comparative databases of species’ metabolic repertoires [based on 4], and reverse-genetics functional testing (RNAi) in representative lab insect models [5, 6]. Comparative approaches incorporating data from >100 insect species with sequenced genomes will ground the evaluation and testing of target genes’ expression and function.

References:

  1. Panfilio, K.A., Vargas Jentzsch, I.M., Benoit, J.B., Erezyilmaz, D., Suzuki, Y., Colella, S., Robertson, H.M., Poelchau, M.F., Waterhouse, R.M., Ioannidis, P., et al. (2017). Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. bioRxiv 201731, doi: 10.1101/201731.
  2. Benoit, J.B., Adelman, Z.N., Reinhardt, K., Dolan, A., Poelchau, M., Jennings, E.C., Szuter, E.M., Hagan, R.W., Gujar, H., Shukla, J., et al. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat. Commun. 7, 10165.
  3. McKenna, D.D., Scully, E.D., Pauchet, Y., Hoover, K., Kirsch, R., Geib, S.M., Mitchell, R.F., Waterhouse, R.M., Ahn, S.-J., Arsala, D., et al. (2016). Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface. Genome Biol. 17, 227.
  4. Baa-Puyoulet, P., Parisot, N., Febvay, G., Huerta-Cepas, J., Vellozo, A.F., Gabaldón, T., Calevro, F., Charles, H., and Colella, S. (2016). ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. Database (Oxford) pii, baw081.
  5. Horn, T., and Panfilio, K.A. (2016). Novel functions for Dorsocrossin epithelial morphogenesis in the beetle Tribolium castaneum. Development 143, 3002-3011.
  6. Panfilio, K.A., Liu, P.Z., Akam, M., and Kaufman, T.C. (2006). Oncopeltus fasciatuszenis essential for serosal tissue function in katatrepsis. Dev. Biol. 292, 226-243.

BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

  • Transcriptomics
  • in vivogene expression
  • comparative genomics
  • RNA interference (RNAi)

Contact: Dr Kristen Panfilio, University of Warwick