Applications of the Soybean Expression Atlas in Genomics and Transcriptomics Research.

Area of Science:

• Genomics and transcriptomics
• Plant biology and agriculture
• Bioinformatics and data science

Background:

• Genomics research, particularly in crops like soybean (Glycine max), benefits from gene expression data.
• RNA sequencing (RNA-Seq) is crucial for understanding gene function and complex traits.
• Processing raw RNA-Seq data is computationally intensive and requires specialized expertise.

Purpose of the Study:

• To introduce the Soybean Expression Atlas (SEA) as a user-friendly resource for accessing and analyzing soybean gene expression data.
• To simplify the process of exploring transcript- and gene-level abundance data from numerous RNA-Seq samples.
• To demonstrate the utility of SEA in facilitating research on soybean's metabolic pathways, environmental responses, and pathogen interactions.

Main Methods:

• Development of the Soybean Expression Atlas (SEA) with a user-friendly interface.
• Integration of 5481 RNA-Seq samples for transcript- and gene-level abundance data.
• Implementation of tools for data visualization (Global Expression Viewer) and gene list generation (Search Gene List).

Main Results:

• SEA provides easy access to processed RNA-Seq data for soybean.
• The platform facilitates exploration of gene expression profiles across various tissues and experimental conditions.
• SEA has been instrumental in studies of soybean oil biosynthesis, nodulation, environmental responses, and pathogen interactions.

Conclusions:

• The Soybean Expression Atlas (SEA) significantly lowers the barrier to entry for soybean gene expression analysis.
• SEA supports diverse research applications, from fundamental biology to applied agricultural challenges, including pathogen resistance.
• The SEA model serves as a foundation for similar initiatives in other plant species.