Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis)

•Through our research and analysis, we found that the genes containing only the NBS structural domain in the sweet orange NBS-LRR genes are much older, which differs significantly from previous studies and indicates that the sweet orange NBS-LRR gene family has evolved in a way that differs from other species significantly.•Our study also found that 204 miRNAs out of 246 published miRNAs interacted with 107 NBS-LRR genes, suggesting that miRNAs play a vital role in regulating NBS-LRR gene expression.•For the first time, the NBS-LRR gene of sweet orange was found to be involved in abiotic stress response in addition to plant resistance to various biotic stresses. The NBS-LRR (nucleotide-binding site-leucine-rich repeat gene) gene family, known as the plant R (resistance) gene family with the most members, plays a significant role in plant resistance to various external adversity stresses. The NBS-LRR gene family has been researched in many plant species. Citrus is one of the most vital global cash crops, the number one fruit group, and the third most traded agricultural product world wild. However, as one of the largest citrus species, a comprehensive study of the NBS-LRR gene family has not been reported on sweet oranges. In this study, NBS-LRR genes were identified from the Citrus sinensis genome (v3.0), with a comprehensive analysis of this gene family performed, including phylogenetic analysis, gene structure, cis-acting element of a promoter, and chromosomal localization, among others. The expression pattern of NBS-LRR genes was analyzed when sweet orange fruits were infected by Penicillium digitatum, employing experimental data from our research group. It first reported the expression patterns of NBS-LRR genes under abiotic stresses, using three transcript data from NCBI (National Center for Biotechnology Information). In this study, 111 NBS-LRR genes were identified in the C. sinensis genome (v3.0) and classified into seven subfamilies according to their N-terminal and C-terminal domains. The phylogenetic tree results indicate that genes containing only the NBS structural domain are more ancient in the sweet orange NBS-LRR gene family. The chromosome localization results showed that 111 NBS-LRR genes were distributed unevenly on nine chromosomes, with the most genes distributed on chromosome 1. In addition, we identified a total of 18 tandem duplication gene pairs in the sweet orange NBS-LRR gene family, and based on the Ka/Ks ratio, all of the tande