对于植物病原真菌灰葡萄孢的综合基因表达分析,感染了许多植物类群,是全球农业重大损失的原因,我们开发了BEB,基于网络的B.cinerea基因表达浏览器。这种计算上便宜的基于网络的应用程序及其相关数据库包含用于灰霉病菌的手动管理的RNA-Seq数据。BEB通过提供描述转录水平的可发表热图,在不同培养条件下实现感兴趣基因的表达分析。不需要高级计算技能。BEB还提供了每个实验的详细信息以及用户定义的基因表达聚类和可视化选项。如果需要,基因表达值的表格可以下载进行进一步探索,包括,例如,差异表达基因的测定。BEB的实现是基于开源计算技术,可以部署到其他生物。在这种情况下,新的实施将仅受到纳入平台的转录组实验数量的限制。为了证明BEB的可用性和价值,我们分析了不同条件下的基因表达模式,专注于次级代谢物基因簇,全染色体基因表达,先前描述的毒力因子,和参考基因,提供了这些基因在该相关真菌植物病原体中的第一个全面表达概述。我们希望这个工具在B.cinerea研究中广泛有用,为功能测定的比较转录组学和候选基因鉴定提供基础。
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed
BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea.
BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills.
BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The
BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of
BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.