Projects Offered

1 PhD project offered in the IPP winter call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background

How does a single cell generates an entire plant? Modern technologies can reveal what individual cells are doing, but usually cannot tell us where each cell came from. This project aims to address this challenge by creating a synthetic genetic recorder that traces cell lineages during development. We will use the fast-growing flowering plant Lemna aequinoctialis (duckweed) as an experimental system. Its simple body plan, rapid clonal reproduction, and established genome-engineering tools provide a unique opportunity to reconstruct the development of an entire organism across multiple generations.

PhD Project: Decoding cell lineages in a miniature flowering plant

The PhD student will develop a synthetic DNA-barcode system in which programmable mutations accumulate as cells divide. These molecular records will be read by sequencing and used to reconstruct cell ancestry.

We will use this system to address fundamental questions:

- How many founder cells generate a new plant?
- Do long-lived stem-cell lineages persist across generations?
- When and how do different tissues acquire distinct developmental histories?
- How are reproductive lineages specified from vegetative lineages? 

The project combines synthetic biology, genome editing, molecular genetics, and computational lineage reconstruction. It therefore offers an opportunity to both develop a new molecular technology and use it to address fundamental questions in developmental biology.

Students with backgrounds in molecular biology, genetics, genome engineering, developmental biology, or computational biology are particularly encouraged to apply. Previous experience with plants is not required.

If you are interested in this project, please select Xu as your group preference in the IPP application platform.

Publications relevant to this project

Siadjeu C, Chakraborty A & Xu S (2026) Duckweeds as a model for minimal floral development. Trends in Genetics 42: 555–564.Link

Liu Y, Wang Y, Xu S, Tang X, Zhao J, Yu C, He G, Xu H, Wang S, Tang Y, Fu C, Ma Y & Zhou G (2019) Efficient genetic transformation and CRISPR/Cas9-mediated genome editing in Lemna aequinoctialis. Plant Biotechnology Journal 17: 2143–2152. Link

Xia FN, Liu K, Wang J, Liu Z, Li A, Hu Z, Li JF & He X (2026) Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching. Nat. Plants 12, 880–896Link