Genome-wide identification and comparative analyses of NLR gene families in Cucumis sativus and its related species

• By using bioinformatics tools, a total of 63, 67, and 89 NLR genes were identified in Cucumis sativus, C. sativus var. hardwickii and C. hystrix , which were categorized into N, NL, TNL, CNL , and RNL classes. • Cucumber had a closer synteny relationship with C. sativus var. hardwickii than with C. hystrix , and protein motif analyses revealed that unique motifs were found in C. hystrix NLR proteins . • The NLR genes from various genotypes and tissues exhibited distinct expression patterns over time under different biotic and abiotic stresses. • A total of 830 NLR genes were identified in 14 cucurbit species, revealed the diversity and molecular phylogenetic relationships among them. Cucumber ( Cucumis sativus L.) is a globally significant economic crop vulnerable to a multitude of diseases. Its two relatives, C. sativus var. hardwickii and C. hystrix , possess strong disease resistances and are valuable for cucumber resistance breeding . Nucleotide binding site leucine-rich repeat ( NLR ) genes are crucial in regulating resistance against phytopathogens and insects. However, their characteristics and resistance mechanisms in cucumber and its wild relatives remain poorly understood. Therefore, we conducted a comprehensive genome-wide analysis of the NLR gene families in cucumber, C. sativus var. hardwickii , and C. hystrix using bioinformatics tools. A total of 63, 67, and 89 NLR genes were identified in the three genomes and were categorized into N, NL, TNL, CNL , and RNL classes. More than 50 % of the NLRs contained only 1–3 exons, and most cis-acting regulatory elements in the NLR gene promoters were disease resistance related- and phytohormone-responsive. Cucumber had a closer synteny relationship with C. sativus var. hardwickii than with C. hystrix , and unique motifs were found in C. hystrix NLR proteins . Moreover, the expression patterns of the NLR genes in cucumber and C. hystrix demonstrated specific transciptional responses and genotype/tissue-dependent expression variations under biotic and abiotic stresses, suggesting distinct defense adaptation strategies. Additionally, this study revealed the diversity and molecular phylogenetic relationships of 830 NLR genes in 14 cucurbit species. Overall, these findings advance our understanding of plant defense mechanisms and broaden the NLR gene pool that could be utilized in cucumber resistance breeding.