背景:镰刀菌属对全球粮食安全和安全构成重大威胁,因为许多真菌物种会在作物中引起破坏性疾病和/或霉菌毒素污染。气候变化的不利影响正在加剧一些现有的威胁,并造成新的问题。这些挑战凸显了对创新解决方案的需求,包括开发先进的工具来识别控制策略的目标。
方法:为了应对这些挑战,我们开发了镰刀菌蛋白工具包(FPT),一种基于网络的工具,允许用户询问镰刀菌泛基因组中的结构和变异景观。该工具显示来自六个镰刀菌物种的AlphaFold和ESMFold生成的蛋白质结构模型。这些结构可通过用户友好的门户网站访问,并便于比较分析,功能注释推断,以及相关蛋白质结构的鉴定。使用蛋白质语言模型,FPT预测,在两个最重要的农业物种中,有超过2.7亿个编码变体的影响。禾谷镰刀菌和轮生镰刀菌。为了便于评估自然发生的遗传变异,FPT提供了基于22种不同物种的镰刀菌全基因组中蛋白质的变异效应评分。评分指示氨基酸取代的潜在功能后果,并使用PanEffect框架显示为直观热图。
结论:FPT通过提供以前无法获得的工具来评估镰刀菌产生的蛋白质的结构和错义变异,填补了知识空白。FPT有可能加深我们对镰刀菌致病机制的理解,并帮助确定减少作物疾病和霉菌毒素污染的控制策略的遗传目标。这些目标对于解决镰刀菌引起的农业问题至关重要,特别是气候变化带来的不断变化的威胁。因此,FPT有可能为改善全球粮食安全和安全做出贡献。
BACKGROUND: The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or mycotoxin contamination in crops. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets for control strategies.
METHODS: In response to these challenges, we developed the Fusarium Protein Toolkit (FPT), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum and F. verticillioides. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome based on 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework.
CONCLUSIONS: FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium. FPT has the potential to deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets for control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats resulting from climate change. Thus, FPT has the potential to contribute to improving food security and safety worldwide.