Synthetic genomics is an emerging field of synthetic biology that aims to create novel genomes or modify existing ones. It has been successfully applied to viral, bacterial, and yeast genomes, but the complexity of multicellular eukaryotes poses significant challenges. In this article, we review the current state of plant synthetic genomics and propose a new bottom-up approach using the model moss Physcomitrium patens.
Why Moss?
Mosses are ancient land plants that have retained many features of their aquatic ancestors. They have a simple body plan, a haploid-dominant life cycle, and a high capacity for homologous recombination. These characteristics make them ideal candidates for genome synthesis and engineering. Moreover, mosses have a relatively small genome size (around 500 Mb), low transposon content (around 10%), and high gene density (around 1 gene per 5 kb). They also have efficient methods for DNA delivery and regeneration, allowing for large-scale genome manipulation.
What is the Bottom-Up Approach?
The bottom-up approach to genome synthesis involves assembling DNA fragments into larger units, such as genes, operons, pathways, or chromosomes. This allows for precise control over the sequence, structure, and function of the synthetic genome. The bottom-up approach has been successfully used to create viral, bacterial, and yeast genomes, but it has not been applied to multicellular eukaryotes yet. We propose to use the model moss Physcomitrium patens as a start for this approach, as it has many advantages for genome synthesis and engineering.
What are the Challenges and Opportunities?
The main challenges of plant synthetic genomics are related to genome assembly, chromosome engineering, plant transformation, and regeneration. These challenges are exacerbated by the large genome size, high transposon content, complex epigenetic regulation, and low efficiency of DNA delivery and regeneration in seed plants. However, these challenges also offer opportunities for innovation and discovery. For example, genome assembly can be facilitated by using novel methods such as nanopore sequencing or CRISPR-based editing. Chromosome engineering can be enhanced by creating synthetic centromeres or telomeres, or by using chromosome fusion or fission techniques. Plant transformation and regeneration can be improved by optimizing tissue culture conditions or by using alternative methods such as protoplasts or microspores.
What are the Applications and Implications?
Plant synthetic genomics has many potential applications in biotechnology, agriculture, medicine, and basic research. For example, it can be used to create novel traits or pathways in crops, such as drought tolerance or vitamin production. It can also be used to study fundamental questions in plant biology, such as gene regulation or evolution. Moreover, plant synthetic genomics can provide insights into the origin and diversity of life on Earth, as plants are among the oldest and most diverse groups of organisms.
Conclusion
Plant synthetic genomics is a promising field that offers new possibilities for engineering biology. Using the model moss Physcomitrium patens as a start, we propose a new bottom-up approach to genome synthesis in multicellular plants. This approach can overcome some of the technical hurdles and pave the way for future applications in more complex seed plants.