BrassicaEDB: A Gene Expression Database for Brassica Crops.

Haoyu Chao,Hualei Huang,Kai Zhang,Xiaodong Li,Kun Lu,Wei Sun,Chaoyu Luo,Yue Niu,Yonghai Fan,Yingfei Ruan,Tian Li,Cunmin Qu,Jiana Li

doi:10.3390/ijms21165831

Abstract

The genus Brassica contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including “eFP”, “Treatment”, “Coexpression”, and “SRA Project” modules based on gene expression profiles and “Gene Feature”, “qPCR Primer”, and “BLAST” modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

Highlights

With the availability and low cost of next-generation sequencing (NGS) technologies, genome-wide omics datasets are currently being generated at higher frequencies than ever before
We presented a cartoon to illustrate 103 rapeseed ZS11 plant tissues in Figure 2, and the detailed information for each tissue was descried in Materials and Methods
Using rapeseed genome v.4.1 as a reference, 101,040 genes were used to calculate the fragments per kilobase million (FPKM) in each sample

Summary

Introduction

With the availability and low cost of next-generation sequencing (NGS) technologies, genome-wide omics datasets are currently being generated at higher frequencies than ever before. These resources have rapidly expanded our knowledge of functional genomics in both animals and plants [1]. Other Brassica pangenome databases were hosted in the Brassica Genome (http://www.brassicagenome.net/) [4]. These databases provide us with high-quality reference genomes and pangenomes, which greatly enable us to identify gene function with more accuracy and convenience

Methods

Results

Conclusion