Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation
Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation
复制标题
DOI：
10.1101/2024.02.14.580321
复制
发表时间：
2024-04
期刊：
影响因子：
--
通讯作者：
Moray Smith;John T. Jones;Ingo Hein
中科院分区：
文献类型：
--
作者：
Moray Smith;John T. Jones;Ingo Hein
背景核苷酸结合域富含亮氨酸重复序列（Nucleotide-bindingdomainLeucine-richRepeat，NLR）蛋白是植物天然免疫系统的重要组成部分。在植物基因组中，NLR表现出相当大的存在/不存在变异和序列多样性。测序技术的最新进展使得高质量的新型植物基因组组装的产生变得更加直接。从这些基因组中准确识别NLR是提高我们对NLR的理解和识别潜在的抗病性新来源的先决条件。结果虽然已经开发了几种工具来预测NLR，但它们的准确性、速度和可用性都很低。在这里，NLR注释工具Resistify被呈现。Resistify是一种易于使用，快速，准确的工具，用于从蛋白质序列中识别和分类NLR。将Resistify应用于RefPlantNLR数据库表明，它可以正确识别各种物种的NLR。应用Resistify与工具相结合，以确定转座因子的一组茄科基因组揭示了以前未描述的NLR和Helitron转座因子之间的关联。结论Resistify能够快速鉴定植物基因组中的NLR，并提供准确的结构分类。它的易用性和可访问性允许轻松集成到生物信息学工作流程和项目中，增强了对这一重要基因组的研究。将Resistify应用于茄科泛基因组揭示了NLR与转座因子之间未描述的关联。可用性：https://github.com/SwiftSeal/resistify
Background Nucleotide-binding domain Leucine-rich Repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying potential novel sources of disease resistance. Results Whilst several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements. Conclusion Resistify can rapidly identify NLRs within plant genomes and provides accurate structural classifications. Its ease of use and accessibility allows easy integration into bioinformatic workflows and projects, enhancing the study of this important group of genes. Applying Resistify to a Solanaceae pangenome reveals an undescribed association between NLRs and transposable elements. Availability: https://github.com/SwiftSeal/resistify