LjaFGD:Lonicera japonica functional genomics database

• 作者: Qiaoqiao Xiao Zhongqiu Li Mengmeng Qu Wenying Xu Zhen Su Jiaotong Yang
• 来源期刊: 植物学报（英文版）
• 年，卷（期）: 2021,（8）
• 所属期刊栏目: New Resources
• 页码范围: 1422-1436
• 页数: 15页
• 语种: 英文

摘要

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 val-uable information for research into gene func-tion. However, no comprehensive database for gene functional analysis and mining is avail-able 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 sam-ples, 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 anal-ysis, 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 re-searchers with an accessible platform for re-trieving functional information on L. japonica genes to further biological discovery.