*Part of [[Our research]] · Pillar 3 of 3 (Testbed 2) · See also [[Gene function prediction]] · [[Stress resilience]]* **Pathways and networks across plants — Testbed 2.** Most of our knowledge on plant gene function comes from a single dicotyledonous weed, *Arabidopsis thaliana*. To understand how plant traits evolve — and to make any [[Gene function prediction]] generalise beyond a handful of model species — we need a kingdom-wide view. Evolution of regulatory circuits is the second **biological testbed** of the lab. ![[three_pillars.png|700]] Our core idea is that **gene expression provides a quantitative readout of regulatory circuit activity**, allowing us to pinpoint when pathways are conserved, duplicated, or rewired during evolution. We have shown that major developmental innovations can arise through **co-option of existing genes** into new expression contexts, and that key programmes such as **diurnal regulation are conserved across more than a [billion years](https://pubmed.ncbi.nlm.nih.gov/30760717/)**. Dense atlases in strategically placed lineages — *Selaginella*, ferns, gymnosperms — illuminate the emergence of vasculature, roots, secondary metabolism and cell-wall innovations. ### Three threads 1. **Cross-species expression & gene regulatory network atlases.** We build and curate kingdom-wide atlases across algae, bryophytes, lycophytes, ferns, gymnosperms and flowering plants. Much of the data comes from species nobody else is sequencing: we lead sampling campaigns that dissect and flash-freeze plants on-site and build atlases from scratch with [LSTrAP-denovo](https://github.com/pengkenlim/LSTrAP-denovo/) for species without reference genomes. 2. **Genes and pathways behind key traits.** Comparative transcriptomics identifies the genes underlying organogenesis, reproduction, vascular tissue, diurnal rhythms, and secondary cell walls. For example, the transcriptional programme of lignocellulose biosynthesis is [conserved across vascular plants](https://pubmed.ncbi.nlm.nih.gov/31988262/), ferns harbour **divergent secondary cell-wall innovations** ([Ali et al., Nat Plants 2025](https://www.nature.com/articles/s41477-025-01978-y)), and a recent cross-species effort dissects the **regulatory logic of pollen formation and function** in flowering plants ([Mutwil, Moon, Koh et al., bioRxiv 2026](https://www.biorxiv.org/content/10.64898/2026.02.15.705993)). 3. **Compare and model network evolution.** Beyond cataloguing, we develop **network alignment and deep-learning embedding approaches** to compare regulatory networks across species — quantifying when modules are created, duplicated, lost, or rewired. Our most recent method, **ORBIT** (*Orthogonal Rotation for Biological Inter-species Transfer*; [Wissenberg, Lee & Mutwil, bioRxiv 2026](https://www.biorxiv.org/content/10.64898/2026.05.04.722193)), aligns gene-expression spaces across species so that knowledge can be **transferred** from data-rich to data-poor organisms. We are also building methods to identify **entirely new types of proteins** in earlier-diverging plant lineages, where many agriculturally-important traits (stress resilience, photosynthesis) appear to be encoded by proteins of unknown function. ![[Pasted image 20240823223031.png|600]] *Kingdom-wide gene expression atlases reveal how organs and biological pathways have evolved over deep time.* ![[sampling.png|600]] *Generating our own data in the field — here, processing a fern in the Singapore Botanical Garden.* ### Representative papers 1. *ORBIT: Orthogonal Rotation for Biological Inter-species Transfer.* Wissenberg P, Lee JM, Mutwil M. [bioRxiv, 2026](https://www.biorxiv.org/content/10.64898/2026.05.04.722193). A new method to align gene-expression spaces across species and transfer functional knowledge. 2. *Unravelling the processes controlling pollen formation and functions with cross-species comparative analysis.* Mutwil M, Moon J, Koh E, et al. [bioRxiv, 2026](https://www.biorxiv.org/content/10.64898/2026.02.15.705993). Cross-species dissection of the regulatory programmes underpinning pollen biology. 3. *Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls.* Ali Z, Tan QW, Lim PK, et al. [Nat Plants, 2025](https://www.nature.com/articles/s41477-025-01978-y). 2. *Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.* Julca I, et al. [Nat Plants, 2021](https://pubmed.ncbi.nlm.nih.gov/34253868/). 3. *Expression Atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism, and roots.* Ferrari C, et al. [Plant Cell, 2020](https://pubmed.ncbi.nlm.nih.gov/31988262/). 4. *Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.* Ferrari C, et al. [Nat Commun, 2019](https://pubmed.ncbi.nlm.nih.gov/30760717/). 5. *Beyond Genomics: Studying Evolution with Gene Coexpression Networks.* Ruprecht C, et al. [Trends Plant Sci, 2017](https://pubmed.ncbi.nlm.nih.gov/28126286/). 6. *Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.* Ruprecht C, et al. [Plant J, 2017](https://pubmed.ncbi.nlm.nih.gov/28161902/). 7. *FamNet: A framework to identify multiplied modules driving pathway expansion in plants.* Ruprecht C, et al. [Plant Physiol, 2016](https://pubmed.ncbi.nlm.nih.gov/26754669/). 8. *Elucidating gene function and function evolution through comparison of co-expression networks of plants.* Hansen BO, et al. [Front Plant Sci, 2014](https://pubmed.ncbi.nlm.nih.gov/25191328/).