Most of our knowledge on gene function in plants is derived from a dicotyledonous weed, the model plant *Arabidopsis thaliana*. We want to expand our understanding of how plant traits evolve by combining genomic and transcriptomic analyses of algae, bryophytes, vascular plants, ferns, gymnosperms, and flowering plants. We are particularly interested in using gene expression to gain a better insight into how genes and pathways evolve. For example, [we showed](https://www.nature.com/articles/s41477-021-00958-2) that plant organs evolve by the cooption of existing genes and that diurnal gene expression can be conserved across more than a [billion years](https://pubmed.ncbi.nlm.nih.gov/30760717/). ![[Pasted image 20240823223031.png|600]] *We are generating gene expression atlases of diverse representatives from the plant kingdom to study gene expression and function, and the evolution of organs and biological pathways* However, this is just the tip of the iceberg, and to better understand the evolution of plant organs, tissues, and other traits, we are currently tapping into local biodiversity to construct and analyze genomes and gene expression atlases of neglected representatives of Archaeplastida. To this end, we are leadins several sampling projects around the world, where we build gene expression atlases of neglected plants, which can then be used to reveal biological pathways. ![[sampling.png|600]] *We are generating our own data by dissecting and flash-freezing the plants of interest on the spot. Here, the team is processing a fern found in Singapore Botanical Garden.* Plant evolution + [[Specialized metabolism]]: Since plants have evolved specialized metabolism to interact with their environment, we are interested in understanding how the numbers, types, and complexity of the underlying metabolic pathways have changed during plant evolution. To address these questions, we use genomics, transcriptomics, metabolomics, activity profiling, and machine learning approaches to propose the identity of the metabolic pathways and to compare these pathways across species. For example, we showed that the transcriptional program involved in the biosynthesis of lignocellulose is likely [conserved in all vascular plants]([http://www.plantcell.org/content/32/4/853.abstract](https://pubmed.ncbi.nlm.nih.gov/31988262/)). To further pursue this topic, we are looking into elucidating metabolic pathways of ferns and gymnosperms with anti-bacterial and anti-cancer activities. Fortunately, we have access to hundreds of medicinal plants the Yunnan Garden, the NTU Community Herb Garden, and several gardens outside of NTU, such as the fantastic [Singapore Evolution Garden](https://www.nparks.gov.sg/sbg/our-gardens/nassim-entrance/evolution-garden). Representative papers on plant evolution from our group: 1. [Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.](https://pubmed.ncbi.nlm.nih.gov/36813788/)Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Nat Commun (IF: 14.92; **Q1**). 2023 Feb 22;14(1):986. doi: 10.1038/s41467-023-36517-w 2. [Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.](https://pubmed.ncbi.nlm.nih.gov/34253868/)Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. Nat Plants (IF: 13.26; **Q1**). 2021 Aug;7(8):1143-1159. doi: 10.1038/s41477-021-00958-2 3. [Expression Atlas of _Selaginella moellendorffii_ Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots.](https://pubmed.ncbi.nlm.nih.gov/31988262/)Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M Plant Cell (IF: 11.28; **Q1**). 2020 Apr;32(4):853-870. doi: 10.1105/tpc.19.00780 4. [Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants.](https://pubmed.ncbi.nlm.nih.gov/31602652/) Ferrari C, Mutwil M.New Phytol (IF: 10.15; **Q1**). 2020 Feb;225(4):1562-1577. doi: 10.1111/nph.16257 5. [Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.](https://pubmed.ncbi.nlm.nih.gov/30760717/)Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. Nat Commun (IF: 14.92; **Q1**). 2019 Feb 13;10(1):737. doi: 10.1038/s41467-019-08703-2 6. [Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.](https://pubmed.ncbi.nlm.nih.gov/28161902/)Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M. Plant J (IF: 6.42; **Q1**). 2017 May;90(3):447-465. doi: 10.1111/tpj.13502 7. [Beyond Genomics: Studying Evolution with Gene Coexpression Networks.](https://pubmed.ncbi.nlm.nih.gov/28126286/)Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M Trends Plant Sci (IF: 18.31; **Q1**). 2017 Apr;22(4):298-307. doi: 10.1016/j.tplants.2016.12.011 8. [FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.](https://pubmed.ncbi.nlm.nih.gov/26754669/)Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S,  Mutwil M. Plant Physiol (IF: 8.34; **Q1**). 2016 Mar;170(3):1878-94. doi: 10.1104/pp.15.01281 9. [Elucidating gene function and function evolution through comparison of co-expression networks of plants.](https://pubmed.ncbi.nlm.nih.gov/25191328/)Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M. Front Plant Sci (IF: 5.75; **Q1**). 2014 Aug 19;5:394. doi: 10.3389/fpls.2014.00394