Sakai Toshiyuki, Toghani AmirAli, Adachi Hiroaki
Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto, Japan.
The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
Bio Protoc. 2024 Jul 5;14(13):e5023. doi: 10.21769/BioProtoc.5023.
In recent years, the increase in genome sequencing across diverse plant species has provided a significant advantage for phylogenomics studies, allowing the analysis of one of the most diverse gene families in plants: nucleotide-binding leucine-rich repeat receptors (NLRs). However, due to the sequence diversity of the NLR gene family, identifying key molecular features and functionally conserved sequence patterns is challenging through multiple sequence alignment. Here, we present a step-by-step protocol for a computational pipeline designed to identify evolutionarily conserved motifs in plant NLR proteins. In this protocol, we use a large-scale NLR dataset, including 1,862 NLR genes annotated from monocot and dicot species, to predict conserved sequence motifs, such as the MADA and EDVID motifs, within the coiled-coil (CC)-NLR subfamily. Our pipeline can be applied to identify molecular signatures that have remained conserved in the gene family over evolutionary time across plant species. Key features • Phylogenomics analysis of plant NLR immune receptor family. • Identification of functionally conserved sequence patterns among plant NLRs.
近年来，不同植物物种全基因组测序的增加为系统发育基因组学研究提供了显著优势，使得对植物中最多样化的基因家族之一——核苷酸结合富含亮氨酸重复序列受体（NLRs）进行分析成为可能。然而，由于NLR基因家族的序列多样性，通过多序列比对来识别关键分子特征和功能保守的序列模式具有挑战性。在此，我们提出了一个计算流程的分步方案，旨在识别植物NLR蛋白中进化上保守的基序。在本方案中，我们使用一个大规模的NLR数据集，包括从单子叶植物和双子叶植物物种中注释的1862个NLR基因，来预测卷曲螺旋（CC）-NLR亚家族内的保守序列基序，如MADA和EDVID基序。我们的流程可用于识别在整个植物物种进化过程中在该基因家族中保持保守的分子特征。关键特征 • 植物NLR免疫受体家族的系统发育基因组学分析。 • 识别植物NLR之间功能保守的序列模式。
