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NERC GW4+ DTP PhD project: Mobile DNA and their epigenetic regulation across plant genome size diversity


   Department of Life Sciences

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  Dr Hans-Wilhelm Nützmann  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP) for entry in October 2023. The GW4+ DTP consists of the Great Western Four alliance of the Universities of Bath, Bristol and Exeter and Cardiff University plus five prestigious Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology & Hydrology, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad multi-disciplinary training, designed to produce tomorrow’s leaders in earth and environmental science.

Supervisory Team:

Lead Supervisor: Dr Hans-Wilhelm Nuetzmann, University of Bath, Department of Life Sciences 

Co-Supervisor: Dr Ilia Leitch, Royal Botanic Gardens, Kew, Department of Trait Diversity and Function 

Co-Supervisor: Dr Alexandros Bousios, University of Sussex, School of Life Sciences 

Co-Supervisor: Prof Andrew Leitch, Queen Mary, University of London, School of Biological and Chemical Sciences

Project Background 

Genome size, which refers to the total amount of DNA in the nucleus of a cell, varies over 64,000-fold across eukaryotes and yet most lineages are characterized by narrow ranges of small genome size (e.g. the genome sizes of mammals, birds and reptiles range only 4-6-fold). In contrast, plants show the largest range for any comparable group with genome sizes ranging 2,400-fold. Thus, while some plants have 50x less DNA per cell compared with our own genome, others have genomes that are 50x bigger. Indeed, if unravelled, the DNA from just one cell of the plant species with the largest genome (Paris japonica, 148 Gbp) of any eukaryote would stretch 100m! 

Studies have shown that the majority of this immense genome size diversity arises from the balance between (i) the amplification of repetitive DNA sequences, especially transposable elements, leading to genome size increase, and (ii) recombination activity which leads to the elimination of DNA and hence genome downsizing. Recently, it was suggested that the dynamics of repeat turnover in the genome may be influenced by genome size itself, such that species with large and very large genomes have slower turnover of repetitive elements compared to species with smaller genomes. Given the importance of repeats in contributing to the generation of genetic diversity of an organism, the study suggested that species with big genomes may be more evolutionarily constrained, and hence less likely to speciate, diversify and adapt to environmental change.   

Despite these novel insights at the genomic level, we still lack a clear understanding of how the epigenetic regulation of repeats varies across the full range of genome sizes encountered - an important but missing link in our understanding of why some plants have such large genomes, and how genome size impacts the generation and persistence of biodiversity and the adaptation to changing environmental conditions. 

Project Aims and Methods 

The overall aims of this project are: 

(1) to unravel the epigenetic mechanisms that determine why some plant species have highly compact and others extremely large genomes, and 

(2) to define how genome size affects the ability of plants to adapt to changing environmental conditions.  

The prospective student will study the distribution of epigenetic silencing pathways and mobile DNA composition in plants across the range of possible genome sizes. Furthermore, the student will investigate the functional impact of genome size diversity on genome evolution in plant populations inhabiting sites with different environmental conditions.  

To address these aims, this project will use state of the art bioinformatic and genomic approaches. It may further apply molecular genetics tools to functionally characterise genomic and epigenomic features of the investigated plant species.  

In this project, the prospective student will actively participate in the design of the project and is encouraged to bring in their own research ideas.  

Candidate requirements 

Prospective students should be curious about genomes and genome size diversity and why these matter in influencing plant evolution and survival. Basic bioinformatic and/or molecular biology skills are beneficial. 

Applicants must have, or expect to receive, a UK Honours degree 1st or 2.1, or international equivalent.

Non-UK applicants must meet the programme’s English language requirement by 01 February 2023 (unless you will be awarded a UK degree or degree conducted in English before your PhD start date).

Project partners  

The project will be based at the Milner Centre for Evolution, University of Bath. The recently opened Centre is a hub for evolutionary research in the UK and houses world leading expertise in evolutionary biology, genomics and bioinformatics. The supervisory team is further based at the Royal Botanic Gardens, Kew, the University of Sussex and Queen Mary University of London. As such, the prospective student will gain access to the vast plant resources of Kew Gardens and expertise across genome biology, plants, mobile DNAs and epigenetics.  

Training 

This project offers training opportunities in bioinformatics, genome biology and molecular genetics.  

Enquiries and Applications:

Informal enquiries are welcomed and should be directed to Dr Hans-Wilhelm Nuetzmann [Email Address Removed]

Formal applications should be made via the University of Bath's online application form for a PhD in Biology

When completing the form, please identify your application as being for the NERC GW4+ DTP studentship competition in Section 3 Finance (question 2) and quote the project title and lead supervisor’s name in the ‘Your research interests’ section. 

More information about applying for a PhD at Bath may be found on our website.

We welcome and encourage student applications from under-represented groups. We value a diverse research environment. If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.

Project keywords: Genetics, Genomics, Evolution, Plant Biology, Molecular Biology, Biodiversity, Environmental Biology, Bioinformatics 


Funding Notes

Candidates may be considered for a NERC GW4+ DTP studentship tenable for 3.5 years. Funding covers tuition fees, a stipend (£17,668 p/a in 2022/23) and a generous allowance for research expenses and travel. Studentships are open to both Home and International students; however, International applicants should note that funding does NOT cover the cost of a student visa, healthcare surcharge and other costs of moving to the UK. In line with guidance from UK Research and Innovation (UKRI), the number of awards available to International candidates will be limited to 30% of the total.

References

Novak et al 2020 Repeat-sequence turnover shifts fundamentally in species with large genomes. Nature Plants.
Hidalgo et al 2017 Is there an upper limit to genome size? Trends in Plant Science.
Niederhuth et al 2016 Widespread natural variation of DNA methylation within angiosperms. Genome Biology.
Takuno et al 2016 Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants.

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