MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi‐Omics Data

• Published in: Plant, cell and environment Vol. 48; no. 5; pp. 2950 - 2962
• Main Authors: Xu, Chaoqun, Song, Ling‐Yu, Li, Jing, Zhang, Lu‐Dan, Guo, Ze‐Jun, Ma, Dong‐Na, Dai, Ming‐Jin, Li, Qing‐Hua, Liu, Jin‐Yu, Zheng, Hai‐Lei
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.05.2025
• Subjects: Annotations; Avicennia - genetics; Bioinformatics; coasts; Computational Biology - methods; data collection; Databases, Genetic; Datasets; economic valuation; environment; Experimental research; Flora; Gene expression; Gene Expression Profiling; gene expression regulation; Gene sequencing; genome; Genome, Plant - genetics; Genomes; Genomics; interactive web‐based data analysis; Internet; Intertidal zone; littoral zone; Mangroves; Multiomics; multi‐omics; Population structure; Principal components analysis; Rhizophoraceae - genetics; transcriptome; Transcriptome - genetics; Transcriptomes; visualization; Wetlands; Whole genome sequencing; database; interactive web‐based data analysis; visualization; mangroves; multi‐omics
• ISSN: 0140-7791; 1365-3040; 1365-3040
• DOI: 10.1111/pce.15318

ABSTRACT Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi‐omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole‐genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web‐based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue‐specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets. Summary statement We constructed a comprehension omics database for mangroves research community. MangroveDB provides several tools for data analysis, which facilitates further exploration, especially for researchers performing wet‐lab experiments.