Our research combines experimental approaches (plant physiology, genetics, molecular biology) with computational methods (gene function prediction, omics, machine learning, big data, and database/tool development) to study three interlinked topics: plant evolution, specialized metabolism, and stress acclimation.
Plant evolution: 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 that plant organs evolve by the cooption of existing genes and that diurnal gene expression can be conserved across more than a billion years. 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.
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Specialized metabolism: The plant kingdom contains an amazing assortment of specialized metabolites (a conservative estimate is >200.000), and thus plants are still a largely untapped source of high-value compounds. Specialized metabolites are the active molecules in medicinal plants used in traditional Chinese medicine (TCM) and Ayurveda, but also many modern plant-based medicines (e.g, taxol, vinblastine, vincristine, aspirin, artemisinin, and morphine). One of the major hurdles in the plant bioprospecting process is that the specialized metabolites responsible for the activities of interest and their biosynthetic pathways are largely unknown. Knowing the enzymes in a metabolic pathway is a prerequisite for efficient, large-scale production and improvement of these metabolites for use in medicine and industry. To reveal these pathways, we are currently exploring different approaches based on gene expression and co-expression network analyses to various local plants showing anti-cancer and anti-bacterial activities.
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Plant evolution x 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. 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.
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Stress acclimation: Abiotic stress is the primary factor shaping the biosphere and our food supply, but we still do not understand how algae and land plants acclimatize to stresses. This knowledge is needed to engineer our crops to be more resilient to adverse conditions. Therefore, to better understand the various coping strategies, we study how plants acclimatize to various abiotic stresses (e.g., cold, heat, drought, high light/salinity, micro- and macro-nutrient deficiency) with experimental approaches. To apply these stresses, we use an environmental growth chamber that allows modulating the temperature (0-60C), light (0-2000umol), humidity (20-100RH), and day length. We apply these stresses to various algae and land plants, either alone or in combination (e.g., heat+darkness, heat+high light), to study how these stresses interact (e.g., are certain sublethal stresses lethal when combined? If yes, why?). To better understand how plants respond to these stresses, we use transcriptomics to reveal the responsive genes and pathways. Currently, we are studying stress responses of several crops and a model bryophyte Marchantia polymorpha, but we aim to expand our studies to more species, including algae.
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Stress acclimation x specialized metabolism: Plants use specialized metabolism to survive adverse conditions (e.g., flavonols protect plants from harmful UV radiation), and the specialized metabolism can highly responsive to different growth conditions. For example, just by increasing the light intensity, we can increase the anti-cancer activity of our plants by 5-fold. Thus, abiotic stresses can be used to modulate the levels of specialized metabolites and activity of their biosynthetic pathways, and present a good system to study the underlying regulatory networks.
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