biostudies-literatureGuo BCNational Key R&D Program of ChinaNational Natural Science Foundation of ChinaChinese Universities Scientific Fundmsaf015https://www.ebi.ac.uk/biostudies/studies/S-EPMC11789945biostudies-literatureUnknown42(2)Nucleotide-binding leucine-rich repeat receptor (NLR) genes encode a pivotal class of plant immune receptors. However, their rampant duplication and loss have made inferring their genomic evolutionary trajectory difficult, exemplified by the loss of TNL family genes in monocots. In this study, we introduce a novel classification system for angiosperm NLR genes, grounded in network analysis of microsynteny information. This refined classification categorizes these genes into five classes: CNL_A, CNL_B, CNL_C, TNL, and RNL. Compared to the previous classification, we further subdivided CNLs into three subclasses. The credibility of this classification is supported by phylogenetic analysis and examination of protein domain structures. Importantly, this classification enabled a model to explaiMolecular biology and evolutionDeciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss.PMC117899452452021133321023382023YFD1202400Li XCMa FWZhang YRLiu ZGPing BYSun YQvan den Burg HGuo BCZhao TYu ZfalseDeciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss.Nucleotide-binding leucine-rich repeat receptor (NLR) genes encode a pivotal class of plant immune receptors. However, their rampant duplication and loss have made inferring their genomic evolutionary trajectory difficult, exemplified by the loss of TNL family genes in monocots. In this study, we introduce a novel classification system for angiosperm NLR genes, grounded in network analysis of microsynteny information. This refined classification categorizes these genes into five classes: CNL_A, CNL_B, CNL_C, TNL, and RNL. Compared to the previous classification, we further subdivided CNLs into three subclasses. The credibility of this classification is supported by phylogenetic analysis and examination of protein domain structures. Importantly, this classification enabled a model to explai2025-01-01T00:00:00Z2025 Feb2026-05-27T03:18:17.214Z2025-04-07T07:50:46.911ZS-EPMC117899453983572110.1093/molbev/msaf015