PROJECT
DNA Zoo - Understanding evolution
Characterising, recording and supporting our unique biodiversity
Living on an island continent, Australian biota have evolved in isolation, which has given rise to Australia's unique biodiversity. All three lineages of mammals are found on the continent including monotremes (egg-laying), marsupials (pouched) and eutherians (placental) (Woinarski et al., 2015). Monotremes were the earliest diverging mammalian lineage and it is estimated marsupials and eutherians diverged ~150mya. Marsupials have a unique biology, giving birth to extremely under-developed young and having a complex lactation system. Genomic studies of marsupials are limited compared to eutherians. However, given their phylogenetic position and unusual biological features, genomic studies of marsupials have provided important insights into mammalian evolution, disease and development.
Remarkably, it is approximated that 87% of Australian terrestrial mammals are endemic. However, Australia has one of the highest recent rates of mammalian extinction in the world. Since European settlement over 10% of the 273 endemic terrestrial mammals have become extinct, with particularly high losses of marsupial species. A major driver of the decline of Australian mammals is thought to be the introduction of non-native species (Woinarski et al., 2015).
Project goals:
- Contribute significantly to conservation of ecosystems under rapid environmental change, with unique 3D genomics to complete chromosome-genome assemblies critical for gene regulation studies, the key to understanding all species – plants, animals
- Develop an integrated system for data production and analysis and train scientific leaders with diverse skillsets that blend biology, applied mathematics, computational linear algebra and algorithm design
- Accelerate fundamental research with genomics to meet critical needs of conservation management of biodiversity, as identified by society, government and industry
As part of this project, the successful PhD applicant will:
- Facilitate chromosome level genome assemblies across tree of life
More information can be found at the DNA Zoo website and the following webinar video - DNA Zoo – Facilitating conservation through rapid and open release of high-quality genomes.
Suggested readings
- Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95.
- Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797.
- Durand, Shamim et al. “Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.” Cell Systems 3.1 (2016): 95–98.
- James T. Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdóttir, Jill P. Mesirov, Erez Lieberman Aiden, Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data, Cell Systems, Volume 6, Issue 2, 2018
Research team leader: Associate Professor Parwinder Kaur
I'm currently leading an innovative Translational Genomics research program that aims to translate fundamental science into ready-to-use solutions across the agricultural and medical sectors. My DNA Lab team enables research to span the spectrum of scientific activities beyond the traditional ‘Lab-to-Landscape’ model, using new age technologies such as CRISPR, single-cell and 3D genomics. With DNA Zoo Australia I'm on a mission to provide genomic empowerment to unique Australian biodiversity facilitating conservation efforts for the threatened and endangered species.
Multiple projects are available please contact Parwinder Kaur parwinder.kaur@uwa.edu.au for further details and choosing a specific topic of interest.
Funding and Collaborations
- DNA Zoo is a watershed initiative, leading the world in rapid generation and release of high-quality genomic resources. DNA Zoo Australia at The University of Western Australia is the lead Australian node of a global project, the DNA Zoo consortium. The DNA Zoo consortium was founded as a not-for-profit organization on Nov 2nd, 2018 at Houston, TX, USA, with UWA as the lead Australian node established on 4th June 2019.
- Globally >60 collaborating partners across 9 countries!
- We welcome new collaborations and sharing the platform developed!
Videos
How to Apply
Check criteria
- To be accepted into the Doctor of Philosophy, an applicant must demonstrate they have sufficient background experience in independent supervised research to successfully complete, and provide evidence of English language proficiency
- Requirements specific to this project - Advanced molecular biology OR bioinformatics skills are required
Submit enquiry to research team leader
- Contact the research team leader by submitting an Expression of Interest form via the button below
- After you have discussed your project with the research team leader, contact hdr-science@uwa.edu.au to proceed with your application
Scholarships
- Domestic students
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All domestic students may apply for Research Training Program and University Postgraduate Awards (UPA) scholarships
- International students
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A range of scholarships are available from international organisations and governments. The full list, organised by country, is available on the Future Students website.
In addition, all international students may apply for International Research Training Program scholarships.
- Indigenous students
- Indigenous students are encouraged to apply for Indigenous Postgraduate Research Supplementary Scholarships.
- Forrest Foundation scholarships
- All international and Australian students who wish to study towards the degree of Doctor of Philosophy (PhD) at The University of Western Australia may apply for Forrest Scholarships.
