EORNA, a barley gene and transcript abundance database.

Area of Science:

• Plant Genomics
• Transcriptomics
• Bioinformatics

Background:

• Accurate quantification of gene and transcript abundances is crucial for understanding plant biology.
• Existing barley transcript datasets lack comprehensive, easily accessible expression data.
• High-throughput RNA sequencing (RNA-seq) generates large volumes of gene expression data.

Purpose of the Study:

• To develop a comprehensive Barley Expression Database (EORNA) using a high-quality barley gene reference transcript dataset (BaRTv1.0).
• To create a visualization tool for comparative gene and transcript abundance analysis.
• To facilitate the exploration of cultivar, tissue, and condition-specific gene expression patterns in barley.

Main Methods:

• Quantification of gene and transcript abundances from 22 RNA-seq experiments (843 samples) using the BaRTv1.0 dataset.
• Development of the Barley Expression Database (EORNA) to store and visualize abundance data.
• Implementation of search functionalities including BaRT/HORVU gene names and BLAST for sequence identification.

Main Results:

• The Barley Expression Database (EORNA) provides gene and transcript models and abundance data (transcripts per million - TPM).
• Visualization tool allows on-demand comparative analysis of gene and transcript abundances across all samples.
• Analysis revealed cultivar, tissue, and condition-specific gene expression and alternative splicing events.

Conclusions:

• EORNA serves as a valuable resource for barley researchers, enabling detailed investigation of gene expression.
• The database facilitates the study of alternative splicing and transcript abundance variation.
• TPM values are readily extractable for statistical analysis and meta-analyses of RNA-seq data.