About the Project
Academic supervisor: Professor Vincent Savolainen, Imperial College London
Co-supervisor: Dr Natasha De Vere, Head of Science, National Botanical Garden of Wales
Building on a two decade-long evolutionary research on Lord Howe Island (LHI), we propose to use this emerging model system to disentangle the genomic underpinning of sympatric, with relevance to understanding stress tolerance in plants. Uniquely, we have identified a pair of closely related palm species that have evolved on the minute LHI by adapting to different soil types (Nature 441:210. 2006). One of the species, Howea forsteriana, evolved on calcareous soils deposited by the sea one million years ago, which lead to extreme water, salt and metal stresses whilst affecting flowering phenologies. We examined the role of gene expression and coding sequence in ecological divergence in Howea. Using transcriptome data, we found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. We have also completed a draft assembly of the genome of H. forsteriana. The resulting assembly comprises 3,980 genomic scaffolds with 127x coverage, but which remain relatively fragmented (N50 = 37,986; total length 3.4 Gb).
(1) The student will complete the genome of H. forsteriana using PacBio long reads to link scaffolds and improve the assembly. Then, he/she will conduct comparative genomic analyses with other palms species (coconut palm, fan palm, date palm, oil palm) to look at the underlying genomics and identify the genes involved with the evolution of stress tolerance in palms, taking advantage of Howea’s differences. Noteworthy also that palms have conquered all tropical habitats and evolved multiple times in dry (deserts) and wet (rainforests) habitats, and are thus ideal to look at the evolution of drought tolerance, an acute problem for agriculture following global climate change.
(2) The student will then conduct genome-editing experiments to validate the ‘stress tolerance genes’ identified above, i.e. look for phenotype differences in stress experiments after genomes have been edited to the drought tolerant genes found in H. forsteriana. This will initially be done in model plants but transformation in palms will also be attempted. Genome editing using the CRISPR-Cas9 system in now well established in model plants, including in perennial trees, The student will use CRISPR-Cas9 to edit orthologous genes in rice or Arabidopsis, but also attempt to edit the genomes of the oil palm (which has already been successfully transformed). This research is highly interdisciplinary and will help identify genes of interest for agriculture (oil palm, coconuts, crops) and horticulture, thereby contributing to food security. Note also that Howea forsteriana is the world’s most commonly traded indoor plant.
We expect the student to learn advanced quantitative, molecular biology and fieldwork skills, and publish his/her work in high-impact journals. The project is mainly based at Silwood Park, Imperial College London. The student should have a good Masters degree (already obtained or expecting Distinction), and would be able start in October 2018. Funding is available for a 3.5-year PhD.
Deadline: 8 January 2018
To apply, please send a full CV, letter of motivation and names of two referees to [Email Address Removed]. You can also email me for further information
Research council eligibility applies (UK residency)