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

IF 4.2 2区农林科学 Q1 HORTICULTURE

Scientia Horticulturae Pub Date : 2025-09-01 DOI:10.1016/j.scienta.2025.114382

Shu-Yan Xie , Min Wang , Songguang Yang , Qingwu Peng , Wenrui Liu , Jinqiang Yan , Jinsen Cai , Dasen Xie , Biao Jiang , Yu’e Lin , Lin Chen

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引用次数: 0

Abstract

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.

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黄瓜及其近缘种NLR基因家族的全基因组鉴定与比较分析

黄瓜（Cucumis sativus L.）是一种全球重要的经济作物，易患多种病害。其两个亲缘种C. sativus var. hardwickii和C. hystrix均具有较强的抗病性，在黄瓜抗病育种中具有重要价值。核苷酸结合位点富亮氨酸重复序列（NLR）基因在植物对病原菌和昆虫的抗性调控中起着重要作用。然而，它们在黄瓜及其野生近缘种中的特性和抗性机制尚不清楚。因此，我们利用生物信息学工具对黄瓜、C. sativus var. hardwickii和C. hystrix的NLR基因家族进行了全面的全基因组分析。在3个基因组中共鉴定出63、67和89个NLR基因，分为N、NL、TNL、CNL和RNL类。超过50%的NLR基因仅包含1-3个外显子，NLR基因启动子中的大多数顺式调控元件是抗病相关的和植物激素响应的。黄瓜与C. sativus var. hardwickii的同源性比与C. hystrix的同源性更密切，并且在C. hystrix NLR蛋白中发现了独特的基序。此外，在生物胁迫和非生物胁迫下，黄瓜和黄瓜NLR基因的表达模式表现出特定的转录反应和基因型/组织依赖的表达变化，表明不同的防御适应策略。此外，本研究还揭示了14种瓜类830个NLR基因的多样性及其分子系统发育关系。总之，这些发现促进了我们对植物防御机制的理解，拓宽了NLR基因库，可用于黄瓜抗性育种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Scientia Horticulturae 农林科学-园艺

CiteScore

8.60

自引率

4.70%

发文量

796

审稿时长

47 days

期刊介绍： Scientia Horticulturae is an international journal publishing research related to horticultural crops. Articles in the journal deal with open or protected production of vegetables, fruits, edible fungi and ornamentals under temperate, subtropical and tropical conditions. Papers in related areas (biochemistry, micropropagation, soil science, plant breeding, plant physiology, phytopathology, etc.) are considered, if they contain information of direct significance to horticulture. Papers on the technical aspects of horticulture (engineering, crop processing, storage, transport etc.) are accepted for publication only if they relate directly to the living product. In the case of plantation crops, those yielding a product that may be used fresh (e.g. tropical vegetables, citrus, bananas, and other fruits) will be considered, while those papers describing the processing of the product (e.g. rubber, tobacco, and quinine) will not. The scope of the journal includes all horticultural crops but does not include speciality crops such as, medicinal crops or forestry crops, such as bamboo. Basic molecular studies without any direct application in horticulture will not be considered for this journal.