J Integr Plant Biol. ›› 2021, Vol. 63 ›› Issue (8): 1422-1436.DOI: 10.1111/jipb.13112

Special Issue: Development Biotechnology

• New Resources • Previous Articles     Next Articles

LjaFGD: Lonicera japonica functional genomics database

Qiaoqiao Xiao1, Zhongqiu Li2, Mengmeng Qu3, Wenying Xu2, Zhen Su2* and Jiaotong Yang1*   

  1. 1 Guizhou University of Traditional Chinese Medicine, Guizhou 550025, China
    2 State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
    3 Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of PLA, Beijing 100039, China

    *Correspondences: Zhen Su (zhensu@cau.edu.cn); Jiaotong Yang (y_jiaotong@163.com, Dr. Yang is fully responsible for the distributions of all materials associated with this article)
  • Received:2021-01-31 Accepted:2021-05-09 Online:2021-05-13 Published:2021-08-01

Abstract: Lonicera japonica Thunb., a traditional Chinese herb, has been used for treating human diseases for thousands of years. Recently, the genome of L. japonica has been decoded, providing valuable information for research into gene function. However, no comprehensive database for gene functional analysis and mining is available for L. japonica. We therefore constructed LjaFGD (www.gzybioinformatics.cn/LjaFGD and bioinformatics.cau.edu.cn/LjaFGD), a database for analyzing and comparing gene function in L. japonica. We constructed a gene co-expression network based on 77 RNA-seq samples, and then annotated genes of L. japonica by alignment against protein sequences from public databases. We also introduced several tools for gene functional analysis, including Blast, motif analysis, gene set enrichment analysis, heatmap analysis, and JBrowse. Our co-expression network revealed that MYB and WRKY transcription factor family genes were co-expressed with genes encoding key enzymes in the biosynthesis of chlorogenic acid and luteolin in L. japonica. We used flavonol synthase 1 (LjFLS1) as an example to show the reliability and applicability of our database. LjaFGD and its various associated tools will provide researchers with an accessible platform for retrieving functional information on L. japonica genes to further biological discovery.

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