Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.)
The NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually....
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MDPI AG
2022-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/9/5048 |
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| author | Wanlu Zhang Qi Yuan Yiduo Wu Jing Zhang Jingtao Nie |
| author_facet | Wanlu Zhang Qi Yuan Yiduo Wu Jing Zhang Jingtao Nie |
| author_sort | Wanlu Zhang |
| collection | DOAJ |
| description | The NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually. To characterize and understand the role of the <i>CC-NBS-LRR</i>(<i>CNL</i>) family of genes in disease defense response in cucumber plants, we performed bioinformatical analysis to characterize these genes systematically. We identified 33 members of the <i>CNL</i> gene family in cucumber plants, and they are distributed on each chromosome with chromosome 4 harboring the largest cluster of five different genes. The corresponding <i>CNL</i> family member varies in the number of amino acids and exons, molecular weight, theoretical isoelectric point (pI) and subcellular localization. <i>Cis</i>-acting element analysis of the <i>CNL</i> genes reveals the presence of multiple phytohormone, abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones and stress. Phylogenetic and synteny analysis indicated that the CNL proteins are conserved evolutionarily in different plant species, and they can be divided into four subfamilies based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of CNLs. Further DNA sequence analysis suggests that <i>CsCNL</i> genes might be subject to the regulation of different miRNAs upon PM infection. By mining available RNA-seq data followed by real-time quantitative PCR (qRT-PCR) analysis, we characterized expression patterns of the <i>CNL</i> genes, and found that those genes exhibit a temporospatial expression pattern, and their expression is also responsive to PM infection, ethylene, salicylic acid, and methyl jasmonate treatment in cucumber plants. Finally, the <i>CNL</i> genes targeted by miRNAs were predicted in cucumber plants. Our results in this study provided some basic information for further study of the functions of the <i>CNL</i> gene family in cucumber plants. |
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| language | English |
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| spelling | doaj.art-c68a9e22bd404e5182671fe77201a2ae2023-11-23T08:26:16ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-05-01239504810.3390/ijms23095048Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.)Wanlu Zhang0Qi Yuan1Yiduo Wu2Jing Zhang3Jingtao Nie4College of Horticulture Science, Zhejiang AF University, Hangzhou 311300, ChinaCollege of Horticulture Science, Zhejiang AF University, Hangzhou 311300, ChinaCollege of Horticulture Science, Zhejiang AF University, Hangzhou 311300, ChinaCollege of Horticulture Science, Zhejiang AF University, Hangzhou 311300, ChinaCollege of Horticulture Science, Zhejiang AF University, Hangzhou 311300, ChinaThe NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually. To characterize and understand the role of the <i>CC-NBS-LRR</i>(<i>CNL</i>) family of genes in disease defense response in cucumber plants, we performed bioinformatical analysis to characterize these genes systematically. We identified 33 members of the <i>CNL</i> gene family in cucumber plants, and they are distributed on each chromosome with chromosome 4 harboring the largest cluster of five different genes. The corresponding <i>CNL</i> family member varies in the number of amino acids and exons, molecular weight, theoretical isoelectric point (pI) and subcellular localization. <i>Cis</i>-acting element analysis of the <i>CNL</i> genes reveals the presence of multiple phytohormone, abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones and stress. Phylogenetic and synteny analysis indicated that the CNL proteins are conserved evolutionarily in different plant species, and they can be divided into four subfamilies based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of CNLs. Further DNA sequence analysis suggests that <i>CsCNL</i> genes might be subject to the regulation of different miRNAs upon PM infection. By mining available RNA-seq data followed by real-time quantitative PCR (qRT-PCR) analysis, we characterized expression patterns of the <i>CNL</i> genes, and found that those genes exhibit a temporospatial expression pattern, and their expression is also responsive to PM infection, ethylene, salicylic acid, and methyl jasmonate treatment in cucumber plants. Finally, the <i>CNL</i> genes targeted by miRNAs were predicted in cucumber plants. Our results in this study provided some basic information for further study of the functions of the <i>CNL</i> gene family in cucumber plants.https://www.mdpi.com/1422-0067/23/9/5048cucumber<i>CC-NBS-LRR</i>bioinformaticgene expressionmiRNA |
| spellingShingle | Wanlu Zhang Qi Yuan Yiduo Wu Jing Zhang Jingtao Nie Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) International Journal of Molecular Sciences cucumber <i>CC-NBS-LRR</i> bioinformatic gene expression miRNA |
| title | Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) |
| title_full | Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) |
| title_fullStr | Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) |
| title_full_unstemmed | Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) |
| title_short | Genome-Wide Identification and Characterization of the <i>CC-NBS-LRR</i> Gene Family in Cucumber (<i>Cucumis sativus</i> L.) |
| title_sort | genome wide identification and characterization of the i cc nbs lrr i gene family in cucumber i cucumis sativus i l |
| topic | cucumber <i>CC-NBS-LRR</i> bioinformatic gene expression miRNA |
| url | https://www.mdpi.com/1422-0067/23/9/5048 |
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