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Comparative genomics of insects and their microbiomes to explain feeding ecology dynamics

Primary Supervisor: Dr Kristen Panfilio, School of Life Sciences

Secondary supervisor: Andre Pires da Silva, School of Life Sciences

PhD project title: Comparative genomics of insects and their microbiomes to explain feeding ecology dynamics

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 over 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. Analyses between closely related insects will elucidate the genomic and physiological basis for invasive potential and species-specific targeting for management practices.

    An insect’s habitat range is in part determined by its feeding ecology and ability to make use of diverse plant species and tissue types. In turn, metabolic and digestive capacities are determined by the interplay of the insect and its gut microbiome, a complex microbial community that is itself dynamic and dependent on the insect’s development, food sources, and environment.

    This project focuses on true bugs of the major infraorder Pentatomomorpha. Our in-lab species, the milkweed bug Oncopeltus fasciatus, has a rich history as a tractable research model since the mid-20th century. Its resources include genomic, transcriptomic, and metabolic pathway databases, coupled with the intriguing biology of being a specialist feeder that recently underwent a successful dietary switch in the lab to a new food source within the last 60 years. It also possesses an anatomically “cryptic” microbiome and multiple digestive enzymes that were acquired by lateral gene transfer from bacteria. In comparison, several species of closely related stink bugs are invasive generalist feeders, heavily exploiting certain LGT acquisitions and with unknown additional mechanisms of invasiveness. How do these closely related specialist and generalist feeders compare? This project offers the opportunity to work with genomic and metagenomic data across these species, embedded within an international collaborative network on comparative insect genomics (i5K, Ag100Pest). Furthermore, experimental studies of gut and microbiome development in the milkweed bug across the life cycle (embryos, nymphs, adults) provides the opportunity to integrate a range of cutting-edge sequencing and functional genetic approaches. Our major goal is to reveal the dietary basis of plant-feeing insects’ ecological niche requirements and invasive potential.

    Suggested reading:

    1. Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, et al: Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019, 20:64.
    2. Reding K, Pick L: High Efficiency CRISPR/Cas9 mutagenesis of the white gene in the milkweed bug Oncopeltus fasciatus. Genetics 2020, 215:1027-1037.
    3. Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni HV, et al: Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics 2020, 21:227.
    4. Hernandez J, Pick L, Reding K: Oncopeltus-like gene expression patterns in Murgantia histrionica, a new hemipteran model system, suggest ancient regulatory network divergence. EvoDevo 2020, 11:9.
    5. Matsuura Y, Kikuchi Y, Miura T, Fukatsu T: Ultrabithorax is essential for bacteriocyte development. Proc Natl Acad Sci U S A 2015, 112:9376-9381.

    BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science & Understanding the Rules of Life: Industrial Biotechnology: Microbiology

    Techniques that will be undertaken during the project:

    • Transcriptomics

    • in vivo gene expression

    • Comparative (meta)genomics

    • RNA interference (RNAi)

    • Dietary and metabolic experimentation and phenotyping

    • High-resolution microscopy imaging

    Contact: Dr Kristen Panfilio, University of Warwick