Transcriptome assembly. Studying the evolution of Tracheophyta organs through gene expression

Today, algae and plants are highly diverse and form the basis of the food chain in many habitats. The water-to-land transition of plants (plant terrestrialization) occurred ~500 million years ago and the initially morphologically primitive land plants had to evolve complex organs, lifestyles, and specialized metabolites to adapt to an array of new challenges, such as drought, desiccation, and the lack of inorganic nutrients. These molecular adaptations were mediated by the appearance of new genes and the co-option of existing genes to new biological pathways. Understanding these molecular adaptations would be of tremendous interest, as we would better understand how plant organs evolved and adapted to the different environments, which then allow us to better tailor plant crops to our needs. However, the majority of current studies show two significant limitations. Firstly, they focus on studying genomes, which often cannot reveal when and where the different genes are active, and which genes work together. Secondly, in comparison to flowering plants, the non-flowering plants are largely understudied and pose a significant knowledge gap. To address these gaps, and to take advantage of the tremendous biodiversity in Singapore, we will generate 100 gene expression atlases for non-flowering plants and use this data to identify genes and gene expression patterns, which will form a basis for kingdom-wide comparative studies. By including the publicly available gene expression data of >200 plant species, we will compare the organ transcriptomes, biological pathways and specialized metabolism biosynthetic pathways of ~400 plant species. This will tell us which genes are important for the function of plant organs and which pathways appeared or were lost as plants became more complex. Furthermore, by building and comparing gene co-expression networks across the plant kingdom, we will gain a tremendous understanding of gene function in the plant kingdom.