Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China.
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
J Integr Plant Biol. 2021 Aug;63(8):1422-1436. doi: 10.1111/jipb.13112. Epub 2021 Jun 18.
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.
忍冬（Lonicera japonica Thunb.）是一种传统的中国草药，已经被用于治疗人类疾病数千年。最近，忍冬的基因组已经被解码，为研究基因功能提供了有价值的信息。然而，目前还没有一个用于忍冬基因功能分析和挖掘的综合数据库。因此，我们构建了 LjaFGD（www.gzybioinformatics.cn/LjaFGD 和 bioinformatics.cau.edu.cn/LjaFGD），这是一个用于分析和比较忍冬基因功能的数据库。我们基于 77 个 RNA-seq 样本构建了一个基因共表达网络，然后通过与公共数据库中的蛋白质序列比对来注释忍冬的基因。我们还引入了几个用于基因功能分析的工具，包括 Blast、基序分析、基因集富集分析、热图分析和 JBrowse。我们的共表达网络表明，MYB 和 WRKY 转录因子家族基因与在忍冬中生物合成绿原酸和木樨草素的关键酶基因共表达。我们以类黄酮合酶 1（LjFLS1）为例，展示了我们数据库的可靠性和适用性。LjaFGD 及其各种相关工具将为研究人员提供一个可访问的平台，用于检索忍冬基因的功能信息，以进一步进行生物学发现。
