School of Biological and Chemical Sciences

To determine if global N and P availability explains why most plant genomes are small, despite a huge range in angiosperm genome sizes

  • Supervisors: Professor Andrew Leitch, Dr Ilia Leitch (Royal Botanic Gardens, Kew)
  • Deadline: 31st January 2019
  • Funding: QMUL (UK/EU and International)

Project description

Angiosperms (flowering plants) not only have the largest range in genome size (GS) for any comparable eukaryotic group, varying c. 2,400-fold, but they also include the largest genome so far recorded (Paris japonica) in any organism. Given this range, it is surprising that the distribution of GS is strongly skewed towards small genomes, with the modal and mean values being just 0.6 Gb/1C and 6.7 Gb/1C respectively. 

One of the key missing knowledge gaps of genomic diversity is to understand why the distribution of genome sizes is strongly skewed towards small genomes. This proposal addresses this gap by testing the hypothesis that “the limited availability of environmental Nitrogen (N) and Phosphate (P) across most global ecosystems provides a selection pressure across the whole genome, impacting GS”. Nitrogen and/or P almost always limit the growth of terrestrial plants, yet are essential to build DNA and RNA, which are amongst the most N and P demanding molecules of the cell (being ~15% N and ~ 9% P by mass). Given this, it is surprising that there is such a range in GS. Certainly, it is predicted that building and maintaining a cell will become increasingly expensive, in terms of N and P, as GS increases (e.g. via polyploidy), and this is likely to lead to trade-offs in N and P allocation between the genome (whose N and P requirements must first be satiated) and other cellular processes (e.g. transcription and photosynthesis) needed for growth and survival. Such trade-offs are likely to become acute in species with large genomes, particularly in environments that are limiting in N and/or P, as commonly occurs across the globe 

You will be integrated into a thriving group, and, depending on your interests, we will tailor your research to focus on related global challenges in ecology, and/or agriculture. Opportunities exist to develop your skills in bioinformatics, data mining, spatial analysis, field and/or lab experiments. In data mining we can use GS reconstructions over time-calibrated phylogenies to explore the effects of GS, studying, for example: (i) Ancestral polyploidy events, predicted from genome and transcriptome assemblies. These polyploid events provide a point in time where we know GS must have undergone a step-wise increase in size, and (ii) Shifts in character states relating to: (a) N- and P–use efficiency (e.g. C3/C4 photosynthesis, mature leaf N and P, leaf lifespan, efficiency of resorbing from senescing leaves), (b) Environmental N and P availability (e.g. using indicator values for species’ ecological preferences to nutrient levels in soils and associations with mycorrhiza), (c) Ecological preference (e.g. for low nutrient acid bogs), and (d) Life-forms (e.g. geophyte, parasites, annuals, perennials. Using bioinformatics, we can analyse transcriptomic data (e.g. 1kp on line data), and compare patterns of gene expression in species with high N and P use-efficiency but differing in genome size, or plants we grow under nutrient limitation. In field-work, we can integrate our research into internationally established fertilizer experiments (e.g. the Nutrient Network), to explore the effect of GS on species establishment, depending on N and P availability. In laboratory experiments we can explore how interactions between GS and nutrient limitation impact physiological processes involved in photosynthesis, transcription and growth. 

Outcome: You will become expert in cutting edge methods to generate a deep understanding of interaction between GS and N and P availability. You will address the question WHY angiosperm genomes are surprisingly small given the incidence of polyploidy in their ancestries. Your work will be tailored towards publishing in high profile papers in good journals and invitations to give lectures at prestigious venues. 

The work promises to develop new approaches to demonstrate selection pressures that are acting across the genome, generating fundamental new understanding in genomics and the role of the genome size itself as a unit of heredity. You will develop skills in team-work, integrating your work and understanding with other team members so that you can share in each others success.

Funding

The studentship will cover tuition fees and provide an annual tax-free maintenance allowance for 3 years at the Research Council rate (£16,777 in 2018/19).

Eligibility and applying

You will need to have a relevant BSc (2:1 or higher, with an A (or its equivalent in your project), or ideally an MSc (in progress or with a Distinction). If you are interested in bioinformatics components of this project, you will need some experience in bioinformatics or coding. Applicants from outside the UK are required to provide evidence of their proficiency in English language skills. Please see our entry requirements page for further details.

Informal enquiries can be made by emails to Professor Andrew Leitch (a.r.leitch@qmul.ac.uk). Formal applications should be submitted online by the stated deadline.

Apply Online

References

  1. Becher et al. 2014. Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome. The Plant Journal 80: 823–833. 
  2. Dodsworth et al. 2015. Is post-polyploidization diploidization the key to the evolutionary success of angiosperms? Botanical Journal of the Linnean Society. 180: 1–5. 
  3. Dodsworth et al. 2015. Genome size diversity in angiosperms and its influence on gene space. Current Opinion in Genetics & Development 35: 73–78. 
  4. Guignard et al. 2017. Impacts of nitrogen and phosphorus: from genomes to natural ecosystems and agriculture. Frontiers in Ecology and Evolution 5: 70 
  5. Guignard et al. 2016. Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation. New Phytologist 210: 1195-1206 
  6. Hidalgo et al. 2017. Is there an upper limit to genome size? Trends in Plant Science 22: 567–573. 
  7. Kelly et al. 2015. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytologist 208: 596–607. 
  8. Leitch et al. 2014. Impact of genomic diversity in river ecosystems. Trends in Plant Science 19(6): 361-366. 
  9. Greilhuber and Leitch 2012. Genome size and the phenotype. In: Plant Genome Diversity Volume 2. 323–344. 
  10. Lomax et al. 2014. Reconstructing relative genome size of vascular plants through geological time. New Phytologist 201: 636–644. 
  11. Pellicer et al. 2018. Genome size diversity and its impact on the evolution of land plants. Genes 9: 88 
  12. Suda et al. 2015. The hidden side of plant invasions: the role of genome size. New Phytologist 205: 994–1007. 
  13. Leitch AR and Leitch IJ. 2012. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytologist 194(3): 629-646.