Guide RNA design in non-model organisms

Full Project Title

Bioinformatic resources for single guide RNA design in non-model organisms

Project Summary

Insect vectors of pathogens affecting human health and agricultural pests will demand new strategies of targeted biological control that are both more environmentally friendly and more effective. In Australia alone, invasive species control costs over $3 billion a year, with agriculture required to bear the majority of this cost. The opportunities for and utility of biocontrol technologies such as gene-drives is rapidly developing in terms of controlling mosquito-borne disease, elimination of invasive species and the advancement of One Health initiatives. Moving such technologies from laboratory cage experiments through regulatory approval will likely require the identification of sgRNA targets unique to discrete populations, allowing gene-drives to be confined within specific genetic and geographic boundaries. To help researchers satisfy regulatory requirements, this project aims to provide a bioinformatic resource to mine genomes for sgRNA targets that are unique to populations with genetic and geographic boundaries, while also allowing identification of off-target issues such as cross-species movement. This is important work in terms of moving any gene-drive control technology forward. The tool being developed in this project would not only provide a vital and exciting contribution to our research question in controlling malaria mosquitoes but also to the development of population specific gene drives for non-model systems more broadly.

Potential Outcomes

This project will deliver novel bioinformatic resources for identification of genetic and geographic sgRNA targets in non-model species, with clear utility extending across a broad range of other species. Development of this bioinformatic pipeline will facilitate the population genomic analysis of individuals, outlining population structure and population genetic parameters. It will then identify sgRNA target options that could be utilised both within and between genetic/geographic populations and evaluate the risk of gene-drive movement into related off-target species.

This pipeline will deliver an important resource for work beyond this single project. It will be of utility to researchers from UQ and beyond, for other potential vector-control and public health outcomes, as well as for research using non-model systems more broadly such as invasive pest species.