2022
11 Nov
2022
2022
★ Founding document
Primary source
CEPLAS Seed Fund submitted — "Plant Synthetic Genomics" named
Application submitted to the CEPLAS Steering Committee. Title: "Laying the foundations for plant synthetic genomics by creating a Plant Artificial Chromosome in Physcomitrium patens." Three work packages: (1) tool validation in moss, (2) characterisation of chromosomal elements required for artificial chromosome construction, (3) neochromosome assembly, delivery and functional characterisation. Budget: €23,602. This is the earliest verifiable use of "Plant Synthetic Genomics" as a named, funded research programme.
📄 Primary source documents
CEPLAS Seed Fund Application
The three work packages of this €23,602 application anticipate the exact core technical challenges that the £62.4M ARIA Synthetic Plants programme (September 2024) would later organise a national consortium to address — 22 months later.
25 Nov
2022
2022
★ Award
Institutional record
CEPLAS Seed Fund awarded by steering committee
The CEPLAS Steering Committee awards the seed fund at its scheduled meeting. Plant Synthetic Genomics becomes an institutionally funded research programme at HHU Düsseldorf. This is the founding date of the field as an active, resourced research programme.
📄 Primary source
CEPLAS Steering Committee Award Decision
2023 — 2024
2023
–
2024
–
2024
Platform build
Ongoing
Two years of platform development — assembly platform, integration system, chromosome engineering strategy
Assembly methodology: RepTiles developed as a community-standard assembly platform for plant synthetic genomics. Direct synthesis without Gibson assembly. Iterative integration system for progressive large-DNA insertion into the plant genome developed and validated.
Chromosome engineering strategy: Original approaches for both centromere formation and telomere stabilisation on synthetic DNA developed — both unpublished and currently under development.
Chromosome engineering strategy: Original approaches for both centromere formation and telomere stabilisation on synthetic DNA developed — both unpublished and currently under development.
3 Sep
2024
2024
Grant application
Primary source · Not awarded
Volkswagen Stiftung — Pioneering Research Exploration
Pre-proposal submitted with co-applicant Dr André Marques (MPI Plant Breeding Research, Department of Chromosome Biology, Cologne). Application No. S144719. Title: "Engineering of Programmable Neocentromeres for Higher Eukaryotes." Budget: €1,299,400 over 48 months. Programme: Pioneering Research Exploration ("Unknowns Unknowns"). The holocentric chromosome angle — Marques' expertise — provides the evolutionary comparison for centromere specification requirements across eukaryotic diversity. Application not awarded. Submitted 3 September 2024 — the same day ARIA opened its Synthetic Plants call.
📄 Primary source
VW Stiftung Application No. S144719
Submitted the same month ARIA opened its Synthetic Plants call. Establishes a timestamp: this problem was being formally articulated and developed in Düsseldorf before ARIA opened its call.
4 Sep
2024
2024
Field validation
External — UK Government
ARIA opens Synthetic Plants call — £62.4M
UK Advanced Research and Invention Agency opens first call for the Synthetic Plants programme. 22 months after the CEPLAS seed fund founding. Nine teams funded: six chloroplast, one nuclear chromosome (James + Cai, Manchester; John Innes Centre; Earlham Institute — £8.5M using yeast/Gibson assembly in potato). Three socioethical teams including University of Edinburgh (£1.8M for "responsible innovation for plant synthetic genomics").
The ARIA programme uses the phrase "plant synthetic genomics" in its TA2 socioethical brief — the same phrase coined in the November 2022 CEPLAS seed fund application.
The ARIA programme uses the phrase "plant synthetic genomics" in its TA2 socioethical brief — the same phrase coined in the November 2022 CEPLAS seed fund application.
🔗 External sources
ARIA Synthetic Plants Programme
aria.org.uk →
2025
2025
JTF
proposal
JTF
proposal
★ Competitive selection
Primary source · Email record
JTF invites full proposal — "Bottling Time"
Email from Emanuela Sani, Program Officer Life Science, John Templeton Foundation, sending additional Life Science proposal guidelines and confirming invitation to submit a full proposal for the "Bottling Time" grant. JTF operates a two-stage process: pre-proposal screening followed by invitation-only full proposals. Being invited to the full proposal stage is a competitive selection event — the majority of pre-proposals do not advance. This email documents that JTF's Life Science programme assessed the clock modularity hypothesis as sufficiently compelling to invite full development.
📄 Primary source
Email: Emanuela Sani → Uriel Urquiza-García
JTF Life Science grants are peer-reviewed by external scientists. Full proposal invitation reflects the pre-proposal passed scientific credibility review. The programme officer personally engaged confirms the grant was being actively managed — not just processed.
2025
KTS
KTS
Application · Not awarded
Primary source · KTS
Klaus Tschira Stiftung — GreenBITs: Synthetic Epigenomics in P. patens
Application to Klaus Tschira Stiftung. Title: "GreenBITs: Programmable Epigenetic Pre-patterning and Loading of Large DNA in the Moss Physcomitrium patens." PI: Uriel Urquiza-García. Budget: €492,546 over 36 months (June 2026 – May 2029). Not awarded.
Four work packages: WP1 — Write, integrate, read: in vitro enzymatic methylation on synthetic DNA, persistence monitored across clonal and sexual propagation. WP2 — Programmable typesetting and design rules: epi-BITs on random DNA and synthetic promoters, ML design rules. WP3 — Centromere formation: tests whether pre-programmed chromatin state on synthetic DNA influences chromosome identity establishment. WP4 — EpiCAD: open-source software and standards for biodesign automation of methylation states.
Future vision: Epigenetic Design & Deployment Platform — computational design tools, a foundry for enzymatic epigenetic writing at chromosome scale, and a parts registry annotated with epigenetic response data.
Four work packages: WP1 — Write, integrate, read: in vitro enzymatic methylation on synthetic DNA, persistence monitored across clonal and sexual propagation. WP2 — Programmable typesetting and design rules: epi-BITs on random DNA and synthetic promoters, ML design rules. WP3 — Centromere formation: tests whether pre-programmed chromatin state on synthetic DNA influences chromosome identity establishment. WP4 — EpiCAD: open-source software and standards for biodesign automation of methylation states.
Future vision: Epigenetic Design & Deployment Platform — computational design tools, a foundry for enzymatic epigenetic writing at chromosome scale, and a parts registry annotated with epigenetic response data.
📄 Primary source · Proposed reviewers
KTS Application — GreenBITs
Why this matters regardless of outcome: GreenBITs identifies synthetic epigenomics as the next layer of the plant synthetic chromosome programme — asking not just whether DNA can be inserted but whether its chromatin state can be pre-programmed before entry into the cell. WP3 addresses a key question: does the chromatin state of synthetic DNA influence chromosome identity establishment? This layer of the programme is not addressed by other current approaches in plant synthetic genomics. The proposed reviewers represent leading specialists in the relevant fields.
2 Mar
2025
2025
Preprint
bioRxiv · Under review
RepTiles — Golden Braid assembly for plant synthetic genomics
Petrova V, Andrejic D, Finkenrath T, Grewer J, Zurbriggen MD & Urquiza-García U. bioRxiv (February 2025). RepTiles: a system for generating synthetic random DNA for plant synthetic genomics from community-standard parts (published in preprint). Web application for automated hierarchical assembly design. Demonstrates large random DNA assembly and stable integration in P. patens. First published methodology paper for plant synthetic chromosome assembly from community-standard parts.
🔗 Published preprint
Gearing up Golden Braid assembly for plant synthetic genomics with RepTiles
doi.org/10.1101/2025.02.28.640145 →
2026
2 Apr
2025
2025
Publication
Peer-reviewed
Molecular Systems Biology 2025 — absolute clock protein quantification
Urquiza-García U, Molina N, Halliday KJ & Millar AJ. Molecular Systems Biology (2025). First absolute quantification of transcription factor proteins in any plant system. NanoLUC translational fusions, ODE models in absolute units, sequence-to-affinity pipeline. Provides the quantitative readout infrastructure embedded into the JTF experimental logic — the measurement system built before the experiment it was designed to read.
🔗 Published record
Abundant clock proteins point to missing molecular regulation in the plant circadian clock
doi.org/10.1038/s44320-025-00086-5 →
31 Jul
2025
2025
Institutional funding
Awarded
HHU Strategic Research Fund — Plant Synthetic Genomics
Heinrich Heine University Strategic Research Fund awarded to the Plant Synthetic Genomics programme. Presentation to SFF committee (Beirat): 21 July 2025. Rektorat decision (718. Sitzung): 31 July 2025. Award notification: 8 August 2025. Third independent institutional body to fund the programme alongside CEPLAS (2022) and JTF (2025–26).
16 Oct
2025
2025
★ Major grant awarded
Primary source · Awarded
John Templeton Foundation — "Bottling Time" — awarded
Grant ID 63576. Title: "Bottling Time: Reconstructing a Moss's Inner Clock Through Synthetic Genomics." Hypothesis: The circadian clock is a modular and genetically portable system whose function does not depend on its native genomic architecture or chromosomal context. Four work packages addressing: clock gene quantification in P. patens, stepwise clock relocation to a synthetic locus, synthetic chromosome formation and excision, and episomal clock reconstitution as an independent test. JTF does not fund incremental science — award signals external, independent judgment that the question is genuinely foundational. This grant unifies the Edinburgh clock quantification lineage and the Düsseldorf synthetic chromosome lineage into a single programme.
📄 Primary sources
JTF Grant ID 63576 — Award
HHU Rektorat Congratulatory Letter — Zuwendungsbescheid F-2025/2948
Apr
2026
2026
Active experiment
In progress
42 kb three-fragment knock-in — ~50 colonies in antibiotic selection
42 kb synthetic chromosome body assembled directly in P. patens without yeast intermediary — a technical distinction from yeast-based assembly approaches used by other groups. Fluorescent marker colonies confirmed in antibiotic selection. Sequencing confirmation of correct integration imminent. Manuscript in preparation.
The Manchester synPAC consortium (£8.5M) uses yeast assembly to build synthetic chromosomes for transfer to potato. This experiment was assembled directly in moss without yeast intermediary — a technically distinct approach from yeast-based assembly.
2026
In preparation
in preparation
New funding cycles in preparation — European-level competitive grants
Applications for new funding cycles are being prepared in coordination with the HHU grants office and CEPLAS. The programme's track record includes three independent funding sources since November 2022, the RepTiles preprint, 16 supervised students, and external recognition including the CSHL Asia faculty invitation. Key elements of the track record:
Founding date: CEPLAS seed fund November 2022. ARIA call opened September 2024.
Independent funding: CEPLAS + JTF + HHU SFF — three sources, three independent assessments.
External recognition: CSHL Asia faculty invitation, JTF competitive selection, HHU institutional ratification.
Technical approach: No Gibson assembly, no yeast intermediary, community-standard parts throughout. Original chromosome engineering strategies for centromere formation and telomere stabilisation — both unpublished.
Biological question: Clock modularity hypothesis predating platform by a decade — the question that made the platform necessary.
Founding date: CEPLAS seed fund November 2022. ARIA call opened September 2024.
Independent funding: CEPLAS + JTF + HHU SFF — three sources, three independent assessments.
External recognition: CSHL Asia faculty invitation, JTF competitive selection, HHU institutional ratification.
Technical approach: No Gibson assembly, no yeast intermediary, community-standard parts throughout. Original chromosome engineering strategies for centromere formation and telomere stabilisation — both unpublished.
Biological question: Clock modularity hypothesis predating platform by a decade — the question that made the platform necessary.
The synthetic chromosome body paper, once published, will transform the application from a vision with preliminary data to a vision with a demonstrated platform — the single most important near-term milestone for the next funding phase.
2026
–
2027
–
2027
Upcoming
In preparation
Manuscript in preparation + European-level funding in preparation
Manuscript in preparation: First major plant synthetic genomics paper as corresponding author. 42 kb assembly without yeast intermediary. Will establish the assembly platform in the peer-reviewed record.
New funding cycles in preparation: The programme is actively preparing applications for competitive funding at the European level, coordinated with the HHU grants office and CEPLAS. Three independent funding sources since November 2022. The synthetic chromosome body paper, once published, will strengthen the track record for the next funding phase.
New funding cycles in preparation: The programme is actively preparing applications for competitive funding at the European level, coordinated with the HHU grants office and CEPLAS. Three independent funding sources since November 2022. The synthetic chromosome body paper, once published, will strengthen the track record for the next funding phase.
26 Jul
2026
2026
External recognition
Faculty invitation
Cold Spring Harbor Asia Synthetic Biology Course — invited faculty
Invited as faculty (not participant) to the CSHL Asia Synthetic Biology Course, Suzhou, 26 July – 9 August 2026. Organised by Junbiao Dai and Daniel Schindler. CSHL courses are highly curated; faculty slots at CSHL courses are extended to researchers whose work is considered relevant to the field. This invitation preceded the major publications from the programme.
Competitive landscape — plant synthetic genomics, nuclear chromosomes · April 2026
SynMoss · Dai Group · Shenzhen/Beijing
Nat Plants Jan 2024. Replaced 155 kb of chr18 short arm with redesigned synthetic sequence in P. patens — 55.8% reduction. Yeast TAR assembly. GenoDesigner platform. Goal: synthesise entire P. patens genome within 10 years. Recoding paradigm (Sc2.0). Not a neochromosome — rewrites existing chromosome, does not create one. No published strategy for de novo chromosome identity. Biological question vague: "explore the potential of creating artificial genomes for various applications." 10-year horizon with no specific falsifiable hypothesis.
Cambridge team · ARIA £6.6M · Jun 2025
"From Prototype to Production." Nuclear synthetic chromosome technology in crops. Potato focus (tetraploid, low HDR, months per cycle). Framing implies transfer from non-plant prototype — not ground-up plant synthetic genomics. Three-year ARIA Phase One deadline in wrong chassis. No biological question stated. Crop improvement framing only. Potato biology makes the experiment fundamentally harder than P. patens.
James + Cai · Manchester / JIC / Earlham · ARIA £8.5M (Jun 2025)
synPACs — yeast (Gibson) assembly → transfer to potato. Potato tetraploidy and low HDR efficiency mean each integration cycle takes months. Three-year ARIA mandate incompatible with the iteration speed the experiment requires. No published strategy for chromosome identity establishment. No community-standard foundation.
ARIA chloroplast teams ×6
Six teams across UK and international institutions working on synthetic plastid genomes in crop plants. Plastid genome — small, prokaryotic-like, fundamentally different problem from nuclear chromosome engineering. Not competitors in this space.
Urquiza-García · HHU Düsseldorf / CEPLAS · Founded 25 Nov 2022
De novo synthetic neochromosome in P. patens — a chromosome that never existed before. Community-standard assembly throughout, no Gibson assembly, no yeast intermediary, no recoding. Original chromosome engineering strategies for centromere formation and telomere stabilisation — unpublished. Clock modularity hypothesis — specific, falsifiable biological question predating platform by a decade. Founded November 2022. SynMoss published January 2024. ARIA call opened September 2024. Cambridge and Manchester awards June 2025. P. patens native HDR enables rapid iteration — weeks not months. 16 students trained across two pillars. 7 theses covering every essential chromosome component. 42 kb knock-in in selection April 2026 — direct in-plant synthetic assembly without yeast intermediary.
Evidentiary conclusion
The primary source documents in this record establish that Plant Synthetic Genomics as a named, funded research programme was initiated at HHU Düsseldorf on 25 November 2022 — before the UK Synthetic Plants programme (£62.4M) was announced. Three grants have been awarded by independent sources: CEPLAS (2022), HHU Strategic Research Fund (2025), and the John Templeton Foundation (2025–26). Two further applications — VW Stiftung (€1.3M) and Klaus Tschira Stiftung (€492K, GreenBITs) — were submitted but not awarded. They serve as dated records that these research directions were being formally developed and submitted for competitive review before the broader field had organised around them.