The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA‐seq samples

Abstract

SUMMARYSoybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA‐seq data in public databases and the computational challenges of processing raw RNA‐seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA‐seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript‐ and gene‐level transcript abundance matrices for 5481 publicly available RNA‐seq samples. New features in our database include the availability of transcript‐level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias‐corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high‐quality and easily accessible gene expression data.

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

“…About 3.5% (83) of the soybean oil candidate genes showed seed specific expression (Supplementary Table 9). In order to have a more conservative estimate, we retrieved the tissue specificity metrics from a broader and more heterogeneous set of samples available at the Soybean Expression Atlas (Almeida-Silva, Pedrosa-Silva, and Venancio 2023). These 83 genes were enriched in protein domains such as GDSL lipase/esterase and MADS-box TFs (Figure 3, Supplementary Table 11).…”

“…Expression of oil candidate genes with preferential expression in seeds. Tissue specificity metrics were obtained from the Soybean Expression Atlas (Almeida-Silva, Pedrosa-Silva, and Venancio 2023). Annotations were retrieved from Phytozome (V13) and Soybase.org.…”

“…We conducted a meticulous selection of RNA-Seq samples from the Soybean Expression Atlas (https://soyatlas.venanciogroup.uenf.br/) (Almeida-Silva, Pedrosa-Silva, and Venancio 2023). To ensure the selection of relevant samples, a filtering process was carried out using the following criteria to exclude samples that originated from: 1) indeterminate plant parts (e.g.…”