Diversity and Evolution of NLR Genes in Citrus Species

Simple Summary Citrus (Citrus spp.) is the world's largest fruit crop, both in terms of cultivation area and production. In recent years, the citrus industry in countries such as China, Brazil, and the United States has suffered significant damage due to the increasing severity of citrus diseases, such as Citrus Huanglongbing (HLB). Plant nucleotide-binding leucine-rich repeat (NLR) genes play a critical role in the plant immune system by helping plants resist pathogen infections. A thorough understanding of the diversity and evolution of citrus NLR genes is of great significance for the development of disease-resistant cultivars. In this study, we systematically identified 1585 NLR genes across 10 citrus genomes and conducted an in-depth analysis of their origins and evolutionary processes.Abstract NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR 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 NLR gene copy number in A. buxifolia. The citrus NLR 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 citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties.