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Updated: Jun 25, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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OrangeExpDB: an integrative gene expression database for Citrus spp.

Chang Liu1, Tingting Li2, Licao Cui3

  • 1College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.

BMC Genomics
|May 27, 2024
PubMed
Summary

OrangeExpDB provides an accessible platform for citrus researchers to analyze RNA-sequencing data. This database simplifies the identification of genes related to important traits and pathogen resistance in Citrus species.

Keywords:
CitrusDatabaseExpressionOrangeExpDBRNA-sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Citrus is a vital fruit crop, with RNA-sequencing (RNA-seq) data offering insights into gene function, heredity, evolution, and development.
  • Accessing and analyzing public RNA-seq datasets for citrus research is challenging for scientists lacking bioinformatics expertise.

Purpose of the Study:

  • To develop a user-friendly, web-based database for exploring citrus transcriptome data.
  • To facilitate functional genomic analysis and candidate gene identification in Citrus species.

Main Methods:

  • Integrated transcriptome data from various Citrus species (e.g., C. sinensis, C. reticulata) obtained from the NCBI SRA database.
  • Developed a web interface featuring a BLAST tool for browsing, searching, and downloading expression matrices.
  • Enabled gene expression visualization through heatmaps and provided associated sample information.

Main Results:

  • OrangeExpDB offers a centralized repository for diverse citrus transcriptome data.
  • The database allows users to search genes by ID or sequence similarity to retrieve expression data.
  • Expression matrices can be downloaded for further analysis, and data is presented visually via heatmaps.

Conclusions:

  • OrangeExpDB empowers researchers to conduct functional genomic studies on citrus.
  • The platform aids in the identification of candidate genes associated with essential traits or pathogen resistance.
  • OrangeExpDB is accessible online at http://www.orangeexpdb.com/ for public use.