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The genomic basis of obligate ant/plant symbioses


   School of Biosciences

  Dr Guillaume Chomiki  Wednesday, December 15, 2021  Funded PhD Project (UK Students Only)

Sheffield United Kingdom Bioinformatics Evolution Genetics Molecular Biology

About the Project

I am seeking a highly motivated PhD student to join this exciting project on the genomics of mutualism dependence using ant/plant symbioses as model systems. The scope of the project can be modified in function of the students interests and skills. Students with –or eager to acquire– bioinformatics skills are especially encouraged to apply.

Background Mutualisms –cooperation between species– are ubiquitous and linked to major transitions in the history of life, such as the evolution of eukaryotes or the conquest of the land by plants. They have allowed the diversification of new lineages, permitted species to access otherwise inaccessible resources and radically modified Earth’s geochemical cycles. Yet, understanding the origins and evolutionary trajectories of mutualistic dependences remains a major challenge. How symbiotic mutualisms impact genomes is poorly known besides microbial endosymbioses.

This project proposes to test how mutualistic dependence influences the evolution interaction-related genes in the largest ant/plant symbiotic system. The study system involves epiphytic plants offering lodging and sometimes food to ants in return for extra nutrients and sometimes defence against herbivores. The most specialized species are farmed by ants – the first true insect agriculture outside fungiculture by attine ants, termites and beetles (Chomicki and Renner 2016 Nature Plants; Chomicki et al. 2020 PNAS). This system, the Hydnophytinae clade in the coffee plant family (Rubiaceae) is uniquely replicated: obligate dependence and breakdown of the mutualism occurred recurrently over the group’s evolutionary history (Chomicki et al. 2017 PNAS).

In this project, you will employ phylogenomics to build a strong phylogenetic tree for the Hydnophytinae ant plants (~105 species), using comparative genomics, and transcriptome at hands, you will identify mutualistic genes in the plant partners and trace their evolutionary history across the entire clade. This will allow you to test a number of hypotheses regarding how mutualism impact genome evolution.

Methodology This project will use (i) PacBio and Illumina sequencing together with HiC scaffolding and transcriptomics to generate reference genomes; (ii) whole genome-based phylogenomics to build a strong phylogenetic tree and datasets for comparative genomics; (iii) Selection tests implemented in a comparative framework to test competing hypotheses of molecular evolution.

Timetable of Activities Year 1: Generate all sequence data, becoming familiar with the systematics of the group. Year 2: Generate species phylogeny, and phylogenies for key gene families, assemble whole genome data. Year 3: Finish genomic analyses and write up thesis.

Timeliness & Novelty The proposed PhD project is timely and novel for several reasons: (1) the advent of genomics with both sequencing methods and computational tools now allow genome assembly for non-model, wild species; (2) the Hydnophytinae are a promising system to study evolution and ecology of mutualism; (3) the comparative genomics of mutualisms is an emerging, highly promising research field.

As a result, I anticipate that this PhD will result in several high-profile publications.

Student Training The student will receive training in (1) molecular methods for next-generation sequencing; (2) phylogenomics; (3) genomic analyses (genome assembly, gene selection test, genome-wide gene selection).

*If you are interested, please contact Dr. Guillaume Chomicki () with your CV attached*

Science Graduate School

As a PhD student in one of the science departments at the University of Sheffield, you’ll be part of the Science Graduate School. You’ll get access to training opportunities designed to support your career development by helping you gain professional skills that are essential in all areas of science. You’ll be able to learn how to recognise good research and research behaviour, improve your communication abilities and experience the breadth of technologies that are used in academia, industry and many related careers. Visit http://www.sheffield.ac.uk/sgs to learn more.


Funding Notes

This is a fully-funded 3-year project for UK students only or UK permanent residents.
Entry Requirements
First class or upper second 2(i) in a relevant subject. To formally apply for a PhD, you must complete the University’s application form using the following link:
View Website
*All applicants should ensure that both references are uploaded onto their application as a decision will be unable to be made without this information.*
*If you are interested, please contact Dr. Guillaume Chomicki () with your CV attached*

References

https://scholar.google.com/citations?user=wRlUuY0AAAAJ&hl=en

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