Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
Insect Sci. 2021 Jun;28(3):590-601. doi: 10.1111/1744-7917.12903. Epub 2021 Jan 29.
Fall armyworm (Spodoptera frugiperda), a native insect species in the Americas, is rapidly becoming a major agricultural pest worldwide and is causing great damage to corn, rice, soybeans, and other crops. To control this pest, scientists have accumulated a great deal of high-throughput data of fall armyworm, and nine versions of its genomes and transcriptomes have been published. However, easily accessing and performing integrated analysis of these omics data sets is challenging. Here, we developed the Fall Armyworm Genome Database (FAWMine, http://159.226.67.243:8080/fawmine/) to maintain genome sequences, structural and functional annotations, transcriptomes, co-expression, protein interactions, homologs, pathways, and single-nucleotide variations. FAWMine provides a powerful framework that helps users to perform flexible and customized searching, present integrated data sets using diverse visualization methods, output results tables in a range of file formats, analyze candidate gene lists using multiple widgets, and query data available in other InterMine systems. Additionally, stand-alone JBrowse and BLAST services are also established, allowing the users to visualize RNA-Seq data and search genome and annotated gene sequences. Altogether, FAWMine is a useful tool for querying, visualizing, and analyzing compiled data sets rapidly and efficiently. FAWMine will be continually updated to function as a community resource for fall armyworm genomics and pest control research.
草地贪夜蛾（Spodoptera frugiperda），一种原产于美洲的昆虫物种，正在迅速成为全球主要的农业害虫，并对玉米、水稻、大豆和其他作物造成巨大破坏。为了控制这种害虫，科学家们积累了大量草地贪夜蛾的高通量数据，已经发布了其九个版本的基因组和转录组。然而，轻松访问和执行这些组学数据集的综合分析具有挑战性。在这里，我们开发了草地贪夜蛾基因组数据库（FAWMine，http://159.226.67.243:8080/fawmine/）来维护基因组序列、结构和功能注释、转录组、共表达、蛋白质相互作用、同源物、途径和单核苷酸变异。FAWMine 提供了一个强大的框架，帮助用户灵活地执行自定义搜索，使用多种可视化方法呈现集成数据集，以多种文件格式输出结果表，使用多个小部件分析候选基因列表，并查询其他 InterMine 系统中的数据。此外，还建立了独立的 JBrowse 和 BLAST 服务，允许用户可视化 RNA-Seq 数据并搜索基因组和注释基因序列。总之，FAWMine 是一个快速高效查询、可视化和分析编译数据集的有用工具。FAWMine 将不断更新，作为草地贪夜蛾基因组学和害虫控制研究的社区资源。
