Genome-wide identification and expression analysis of the NBS-LRR gene family in Citrus clementina

Citrus is a highly important global fruit crop that faces significant challenges from citrus Huanglongbing (HLB). The nucleotide binding site leucine-rich repeat (NBS-LRR) gene family plays a central role in plant immunity. However, comprehensive studies on the function of NBS-LRR genes in HLB resistance or tolerance remain limited. In this study, we identified 278 NBS-LRR genes from Citrus clementina. These genes exhibit 7 domain architectures. Physicochemical analyses revealed significant subfamily divergence in length (91-2101 aa), molecular weight (10.57-237.18 kDa), and isoelectric point (pI, 4.61-9.35). Over 82% of proteins localize to the nucleus/cytoplasm, indicating roles in signal transduction and transcriptional regulation. NBS-LRR genes cluster non-randomly among chromosomes, forming tandem repeats on chromosomes 3, 5, and 7. Phylogenetic analysis grouped the NBS-LRR family into 5 clades. Conserved domain analysis identified 10 motifs; Motif 1 and 2 are highly conserved, potentially involved in pathogen recognition. Promoter analysis detected 36 cis-acting elements linked to diverse processes (e.g., hormone/stress response). Synteny analysis revealed 9 genes are orthologous genes of Arabidopsis thaliana. Crucially, transcriptome data showed that significantly higher NBS-LRR expression in Huanglongbing-infected plants, pinpointing candidate gene Ciclev10018143m.1. This study provides a foundation for citrus disease resistance breeding and candidate genes for functional validation.