In silico Comparative Expression Analyses of Transposable Elements in the PACMAD Clade of Grasses with a Special Focus on Sugarcane
Project Status: Under Development
This project is being developed at the Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), in Piracicaba, Brazil. It is supervised by Dr. Diego M. Riaño-Pachón and co-supervised by Dr. Renato A. Corrêa dos Santos.
Grasses possess remarkable adaptations that enable them to thrive under stresses related to water availability, temperature, and salinity. The PACMAD clade of the Poaceae family plays a significant role in global food production and biofuel supply. Studying C4 crops like sugarcane, maize, and sorghum presents challenges, including polyploidy and complex genomic structures. While model species such as Setaria viridis and Sorghum bicolor offer advantages for genetic studies, the role of transposable elements (TEs) in stress response mechanisms across closely related species remains underexplored.
This project focuses on analyzing the expression patterns of transposable elements (TEs) in response to stress conditions, emphasizing sugarcane (Saccharum spp.) in comparison with other PACMAD species: Setaria viridis, Zea mays (maize), and Sorghum bicolor. By leveraging publicly available transcriptomic data, we aim to:
- Uniform annotation of transposable elements across target genomes.
- Uniform TE classification across target genomes.
- PanTE comparative analysis.
- RNA-Seq selection and processing.
- Comparative transcriptomic analysis of TEs in stress response mechanisms.
- Integration of TE data into CoNekT Grasses.
- Inference of inter-species co-expression networks between TEs and protein-coding genes.
For inquiries about this project, please contact:
Andreza M. da Cunha (andreza.cunha@usp.br)