Diversity and Evolution of NLR Genes in Citrus Species

<i>NLR</i> genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although <i>NLR</i> genes in many plant species have been extensively studied, the diversity of <i>NLR</i> genes in <i>citrus</i> remains largely unknown. Our analysis revealed significant variations in the copy numbers of <i>NLR</i> genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in <i>NLR</i> gene copy number in <i>A. buxifolia</i>. The <i>citrus NLR</i> genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that <i>citrus NLR</i> genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of <i>citrus</i>. This study provides important insights into the diversity of <i>citrus NLR</i> genes and serves as a foundational dataset for future research aimed at breeding disease-resistant <i>citrus</i> varieties.