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

Tuo Yin; Peichen Han; Dengxian Xi; Wencai Yu; Ling Zhu; Chaojin Du; Na Yang; Xiaozhen Liu; Hanyao Zhang

doi:10.1016/j.gene.2022.147117

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

Gene. 2023 Feb 20:854:147117. doi: 10.1016/j.gene.2022.147117. Epub 2022 Dec 13.

Authors

Tuo Yin¹, Peichen Han², Dengxian Xi³, Wencai Yu⁴, Ling Zhu⁵, Chaojin Du⁶, Na Yang⁷, Xiaozhen Liu⁸, Hanyao Zhang⁹

Affiliations

¹ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China. Electronic address: yintuo@swfu.edu.cn.
² Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China. Electronic address: hanpeichen@swfu.edu.cn.
³ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China. Electronic address: xidx@swfu.edu.cn.
⁴ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China. Electronic address: ywckgh@163.com.
⁵ Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China. Electronic address: zhuling@swfu.edu.cn.
⁶ Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China. Electronic address: duchaojin@swfu.edu.cn.
⁷ Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China. Electronic address: yangna1999@swfu.edu.cn.
⁸ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China. Electronic address: 15198729095@swfu.edu.cn.
⁹ Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China. Electronic address: zhanghanyao@swfu.edu.cn.

PMID: 36526123
DOI: 10.1016/j.gene.2022.147117

Abstract

Background: 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.

Methods: 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).

Results: 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 tandem duplication genes underwent purifying selection. Transcriptome data analysis showed a significant number of NBS-LRR genes expressed under biotic and abiotic stresses, and some reached significantly different levels of expression. It indicates that the NBS-LRR gene family is vital in resistance to biotic and abiotic stresses in sweet oranges.

Conclusion: Our study provides the first comprehensive framework on the NBS-LRR family of genes, which provides a basis for further in-depth studies on the biological functions of NBS-LRR in growth, development, and response to abiotic stresses in sweet orange.

Keywords: Abiotic and biotic stress; Citrus sinensis; Expression pattern; Genome-wide characterization; NBS-LRR gene.

MeSH terms

Citrus sinensis* / genetics
Citrus* / genetics
Genes, Plant
Genome, Plant
Multigene Family
Phylogeny
Plant Proteins / metabolism

Substances

Plant Proteins