Our research aims to engineer synthetic plant neo-chromosomes using the moss Physcomitrium patens as a genetically tractable and scalable model system. By constructing chromosomes from first principles, we seek to understand how complex genome functions—such as gene regulation, robustness, and inheritance—are encoded at the chromosomal level, and how they can be re-designed using synthetic biology.

Synthetic plant chromosomes offer a unique opportunity to move beyond single-gene engineering toward large-scale genome design. To enable this, we apply core synthetic biology principles—including abstraction, standardization, and modularity—to chromosome engineering. We combine plant transformation with synthetic genomics workflows in Saccharomyces cerevisiae and Escherichia coli, allowing large DNA constructs to be assembled, refactored, and mobilized into P. patens, an organism distinguished by its high rate of homologous recombination and haploid life cycle.

A central focus of the group is the construction and functional testing of chromosome components, including centromeres, telomeres, and large non-coding DNA segments. By transferring and adapting concepts from mammalian synthetic genomics—where human artificial chromosomes are an established technology—we aim to develop plant-specific design rules for stable, heritable synthetic chromosomes. This work addresses fundamental gaps in our understanding of chromosome biology in plants and establishes a foundation for programmable genome architectures.

Building on this framework, our current research explores how complex regulatory networks—such as the circadian clock—behave when relocated from their native genomic context to a synthetic chromosome. By treating the circadian system as a biological metrology tool, we investigate questions of modularity, robustness, and genome embedding that are difficult to address using conventional genetics (see below)

By developing and refining methods for plant synthetic chromosome construction, our work contributes to plant genomics, synthetic biology, and evolutionary biology, while opening new avenues for future applications in biotechnology, sustainable production, and long-term genome engineering.

John Templeton Foundation Grant ID 63576

Title: “Bottling Time: Reconstructing a Moss’s Inner Clock Through Synthetic Genomics”
Funder: John Templeton Foundation
Duration: 2026–2028

Summary
This project explores how biological time is encoded, maintained, and remains robust at the genomic level by constructing a synthetic neochromosome carrying the circadian clock of the moss Physcomitrium patens. Rather than studying individual clock genes in their native genomic context, the project relocates and rewires the clock as a modular, engineered system, enabling direct tests of clock autonomy, robustness, and genomic embedding.

By combining plant synthetic genomics, large-scale DNA assembly, centromere and telomere engineering, and absolute circadian quantification, this work treats the circadian clock as a biological metrology instrument—a precise, internal reference to measure genome function, stability, and evolvability. The project establishes a new experimental framework to study how complex regulatory networks behave when removed from their native chromosomal context and re-implemented in a synthetic neochromosome with higher degrees of freedom.

This grant leverage on our synthetic plant artificial chromosomes as a foundational technology for future applications in synthetic biology, genome engineering, and robust biological design.