Development of a central data repository and visualisation framework for Fusarium transcriptomic data

Abstract

Background: Contamination of grain crops by mycotoxins is a serious threat to food security, affecting up to 40% of cereals worldwide. One of the main contaminants are members of the Fusarium family, which produce trichothecene mycotoxins. Trichothecene biosynthesis is influenced by climatic conditions, and this interaction is essential to study to understand how mycotoxin production will change in the future under more extreme climate change. Transcriptomic studies display gene expression under different conditions, and many datasets are publicly available. However, existing repositories specifically holding fungal transcriptomic data can be tricky to navigate and lack clear annotation of experimental conditions, limiting their effectiveness for exploratory analysis. Results: To address this issue, the Fungal Transcriptomic Database (FTD) was developed as a Fusarium specific repository to hold gene expression data. It was populated with differential expression data from five studies, covering four Fusarium species and four experimental conditions. The FTD provided clear visualisation of data through interactive tables and graphs, including volcano plots and heatmaps. The rapid and accurate recreation of a heatmap showing differential expression of trichothecene genes was used as a benchmark to validate the functionality and efficiency of the repository. Conclusions: The FTD provides a straightforward and interactive tool for exploring and re-analysing fungal transcriptomic datasets. Its modular design supports efficient integration of new features, ensuring the repository remains compatible with emerging technologies and scientific advancements. By highlighting experimental metadata alongside interactive gene expression visualisations, the FTD facilitates data interpretation and reveals new insights regarding Fusarium behaviour. These capabilities provide a deeper understanding of mycotoxin production, enabling accurate predictions regarding trichothecene biosynthesis under future climatic conditions.