Thinking of doing a PhD at the interface of Molecular & Evolutionary Biology?

The Research Training Group 2526 "Gene Regulation in Evolution“ (GenEvo), which is funded by the DFG (German Research Foundation), is offering projects on all levels of organismic complexity, from changes in genes and proteins to the evolution of symbiotic and parasitic behavior. As a GenEvo PhD student, you will join a community of passionate scientists who are applying a broad spectrum of methods on model and non-model organisms.

PhD project:

In the PhD Programme “Gene Regulation in Evolution”, Peter Baumann, Meret Huber, and Shuqing Xu offer the following PhD project: Epimutation rates in an asexually reproducing lizard

Background:

DNA methylation is a major epigenetic mark in both plants and animals. Yet, even within species, there is substantial variation which genomic sites are methylated. In plants, part of this intraspecific variation in DNA methylation is due to the accumulation of epimutations, i.e. the inheritance of spontaneous changes in the methylome across generations. Whether epimutations accumulate across generations not only in plants but also in animals is unclear.

Animals are hypothesized to not accumulate epimutations because in some animals, in particular mammals, the methylome is reset during gametogenesis and embryogenesis. However, resetting of the methylomes seems to be less complete in other animal lineages: for instance, methylome resetting seems to be absent or incomplete in Cnidaria and insects, and only present maternally in zebrafish. While maternal resetting of the methylome in vertebrates may prevent the accumulation of epimutations across generations, this hypothesis has not been tested to date.

The best way to assess whether epimutations accumulate across generations is through mutation accumulation experiments, ideally in a clonally reproducing or self-fertilizing species. In mutation accumulation lines, the offspring from a single ancestor are grown for many generations in the absence of selection, after which the methylomes of the last generations are compared. However, mutation accumulation experiments are rarely done in vertebrates, as most vertebrates have long generation times, reproduce sexually and do not self-fertilize.  

We have established several species of lizards in the genus Aspidoscelis as model for an asexually reproducing vertebrates. We have sequenced and assembled high-quality, chromosome-level reference genomes and maintained lineages for up to 15 generations. This resource provides a unique opportunity to assess epimutation rates in an asexually reproducing vertebrate.

PhD project description:

In this project, the student will assess epimutation rates in the clonally reproducing lizard species A. neomexicanus. You will address the following three key questions: i) Do epimutations accumulate across asexual generations in a lizard? ii) Are these epimutations independent of genetic mutations? iii) Do these epimutations alter gene expression?

To assess whether epimutations accumulate across asexual generations, we will sequence the methylome of mutation accumulation lineages of A. neomexicanus using whole-genome bisulfite and nanopore sequencing, and subsequently compare the methylomes of the terminal generations. To assess whether these epimutations are independent of DNA sequence variation, we will additionally assess underlying mutations using nanopore sequencing data, and subsequently confirm the mutations using Sanger sequencing. This will also provide insights into mutation rates in asexually reproducing vertebrates. Next, we will assess gene expression by transcriptome sequencing, and test whether epimutations at promoter regions are associated with altered gene expression. Taken together, this project will reveal whether vertebrates can accumulate epimutations across generations, and whether these may alter gene expression. 

What we offer:

• Exciting, interdisciplinary projects in a vividly international environment, with English as our working language
• Advanced training in scientific techniques and professional skills
• Access to state-of-the-art Core Facilities and their technical expertise
• 14 funded PhD positions (employment contract)
• A lively community of34 PhD students supported by 28 Principal Investigators
• Collaboration with the International PhD Programme (IPP) at IMB with more than 200 PhD students from 40 different countries

Within the programme the Faculty of Biology of Mainz University (JGU) and the Institute of Molecular Biology (IMB) collaborate — both modern research institutions located on the bustling campus of Mainz University in Germany. With a population of 210,000, of which about 40,000 are students, the city of Mainz is charming and open-minded and within easy reach of cosmopolitan Frankfurt and its international airport, the Rhine valley region with its castles, vineyards, and nature reserves, and the equally picturesque cities of Wiesbaden and Heidelberg.

Requirements:

Are you an ambitious, young scientist looking to push the boundaries of research while interacting with colleagues from multiple disciplines and cultures? Then joining GenEvo is your opportunity to give your scientific career a flying start!

All you need is:

• Master or equivalent
• Motivation to contribute to the forefront of science in molecular and evolutionary biology
• Interactive personality & good command of English
• 2 letters of reference

The deadline for applications is 15 July 2024. Interviews will take place on 9-10 September 2024. Starting date will be 1 January 2025.

For more details on the projects offered and how to apply via our online form, please visit https://www.genevo-rtg.de/application