FWAlgaeDB, an integrated genome database of freshwater algae

• Published in: Frontiers in environmental science Vol. 11
• Main Authors: Lai, Juan, Liang, Qiting, Zhang, Xin, Liu, Yongfeng, Wang, Miao, Yang, Wei, Sun, Taotao, Li, Yan, Jin, Huan, Liu, Ying, Li, Wei, Wu, Shenhao, Xie, Zixin, Zhou, Letian, Luo, Mingjie, Zeng, Lidong, Yan, Qin, Feng, Jie, Sun, Lei
• Format: Journal Article
• Language: English
• Published: Lausanne Frontiers Research Foundation 18.07.2023; Frontiers Media S.A
• Subjects: Algae; Annotations; Biodiversity; Bioinformatics; BLAST; Cyanobacteria; Data retrieval; Environmental science; Fresh water; freshwater algae; functional annotation; Gene clusters; Gene mapping; Gene sequencing; Genes; Genomes; genomic data; Genomics; Interfaces; Metagenomics; Morphology; Next-generation sequencing; Open access; Researchers; Software; species identification; Taxonomy; Water analysis; Water sampling; China
• ISSN: 2296-665X; 2296-665X
• DOI: 10.3389/fenvs.2023.1178097

Algal genomics research contributes to a deeper understanding of algal evolution and provides useful genomics inferences correlated with various functions. Published algal genome sequences are very limited owing to genome assembly challenges. Because genome data of freshwater algae are rapidly increasing with the recent boom in next-generation sequencing and bioinformatics, an interface to store, interlink, and display these data is needed. To provide a substantial genomic resource specifically for freshwater algae, we developed the Freshwater Algae Database (FWAlgaeDB), a user-friendly, constantly updated online repository for integrating genomic data and annotation information. This database, which includes information on 204 freshwater algae, allows easy access to gene repertoires and gene clusters of interest and facilitates potential applications. Three functional modules are integrated into FWAlgaeDB: a Basic Local Alignment Search Tool tool for similarity analyses, a Search tool for rapid data retrieval, and a Download function for data downloads. This database tool is freely available at http://www.fwalagedb.com/#/home . To demonstrate the utility of FWAlgaeDB, we also individually mapped metagenomic sequencing reads of 10 water samples to FWAlgaeDB and Nt algae databases we constructed to obtain taxonomic composition information. According to the mapping results, FWAlgaeDB may be a better choice for identifying algal species in freshwater samples, with fewer potential false positives because of its focus on freshwater algal species. FWAlgaeDB can therefore serve as an open-access, sustained platform to provide genomic data and molecular analysis tools specifically for freshwater algae.