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Open AccessArticle

BrassicaEDB: A Gene Expression Database for Brassica Crops

by Haoyu Chao 1,2,†, Tian Li 3,4,†, Chaoyu Luo 1,†, Hualei Huang 5, Yingfei Ruan 3,4, Xiaodong Li 1,6, Yue Niu 1,6, Yonghai Fan 1,6, Wei Sun 1,6, Kai Zhang 1,6, Jiana Li 1,6, Cunmin Qu 1,6 and Kun Lu 1,6,*
1
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
2
Institute of Innovation & Entrepreneurship, Southwest University, Beibei, Chongqing 400715, China
3
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
4
Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
5
Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
6
Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to the work.
Int. J. Mol. Sci. 2020, 21(16), 5831; https://doi.org/10.3390/ijms21165831
Received: 11 July 2020 / Revised: 4 August 2020 / Accepted: 11 August 2020 / Published: 13 August 2020
(This article belongs to the Section Molecular Genetics and Genomics)
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. View Full-Text
Keywords: BrassicaEDB; Brassica napus; gene expression profile; RNA-Seq BrassicaEDB; Brassica napus; gene expression profile; RNA-Seq
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Chao, H.; Li, T.; Luo, C.; Huang, H.; Ruan, Y.; Li, X.; Niu, Y.; Fan, Y.; Sun, W.; Zhang, K.; Li, J.; Qu, C.; Lu, K. BrassicaEDB: A Gene Expression Database for Brassica Crops. Int. J. Mol. Sci. 2020, 21, 5831.

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