Purpose

The difference in the biology of plants unveils a need for new standards. We decided to write a Request for Comments (RFC) to unite the plant SynBio community by defining a common language for plant synthetic biology, extensible to all other Eukaryotes. Its syntax is based on the Golden Gate System¹ cloning method which uses TypeIIS restriction enzymes; variations, such as GB2.0² and MoClo³, are already being used across the field. This RFC brings together their common features and sets a consensus across the plant field for construct assembly and part repositories.

Marchantia polymorpha, a primitive liverwort, is being established as a new model organism for plant Synthetic Biology⁴; Contrary to historical model species, the choice of M. polymorpha has preceded its establishment. This is an opportunity to set standards in a coherent and united way paving the way for faster and more efficient sharing of information and parts.

The fewer the rules defining a standard, the more widely that standard is adopted. The introduction of this new chassis with its novel tool kit is the occasion to allow more flexibility in the Registry⁵, opening it to wider usage and contributions.

Thank you to the UEA and Valencia iGEM teams for their collaborations.

Table of Contents

BBF RFC 105: Standardized Plant Syntax
1. Purpose
2. Relation to other BBF RFCs
3. Copyright Notice
4. A Common Type IIs Grammar for Eukaryotic transcriptional units
i. Introduction to the Golden Gate Standards
ii. Part Standards
iii. Common Vector for Level 0 Parts
iv. Domestication Protocol of Level 0 Parts
5. Golden Gate Assembly Rules
6. Multigenic constructs
a. GoldenBraid assembly
b. MoClo assembly
7. Unified features of binary vector for agrobacterium-mediated delivery
a. Introduction to Agrobacterium-mediated delivery
b. Standard Features for Agrobacterium-mediated delivery backbones
8. Applications
a. Library construction
b. Expression Cassettes
9. Marchantia polymorpha, a model organism
i. Introduction to the new chassis
ii. Marchantia OpenParts Library and Codon optimization
iii. Marchantia Agoro-mediated Transformation protocol and T-plasmid specification
10. Nicotiana benthamiana and Arabidopsis thaliana: model dicotyledenous plants
i. Description of the chassis
ii. GoldenGate parts and codon-optimisation for model dicotyledenous plants
iii. Agrobacterium-mediated Transformation protocol
11. Additional Resources and Information
12. Authors’ Contact Information
13. References