Phytobricks: Standard DNA parts for plants
With wide support from the international plant science community, we have established a common genetic syntax for exchange of DNA parts for plants, extensible to all eukaryotes (Patron et al. 2015). This common syntax for plant DNA parts is at the core of RFC 106, posted at OpenWetWare, and accepted as an official standard for DNA parts in the iGEM synthetic biology competition.
The Phytobrick standard is a consolidated and consistent standard for Type IIS restriction endonuclease based assembly of DNA parts to make synthetic genes. It is based on the widely used "Golden-Gate"-type standard, and allows highly efficient assembly of multiple standard parts into genes without the need to isolate DNA fragments. A range of existing techniques such as Gibson assembly, MoClo and Golden Braid can be used for higher order multiple-gene assemblies, however we have developed a simple and flexible protocol for assembly of plant vectors, the Loop Assembly technique.
The Phytobrick standard is general, and applicable to all plants, and other eukaryotes. For work with the model plant Marchantia polymorpha, we have produced MarpoDB, which is “genecentric” database for MarpoDB describes and presents the Marchantia genome from an engineer’s perspective, rather than a geneticist’s. The database handles the Marchantia genome as a collection of parts. This is highly useful for automatically mining new parts, and managing part description, and part characterisation. We think that this break from standard genome database architecture is essential for tackling the refactoring of synthetic plant genomes. MarpoDB also provides a useful container for gene expression data, and we plan to integrate cellular features via Plant Ontology terms.