Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies
Plants in their natural habitat frequently face different biotic and abiotic stresses, which lead to the production of reactive oxygen species (ROS) that can damage cell membranes, cause peroxidation and deterioration of macromolecules, and ultimately result in cell death. Superoxide dismutase (SOD)...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/7/781 |
| _version_ | 1797436047421865984 |
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| author | Wasi Ullah Khan Latif Ullah Khan Dan Chen Fei Chen |
| author_facet | Wasi Ullah Khan Latif Ullah Khan Dan Chen Fei Chen |
| author_sort | Wasi Ullah Khan |
| collection | DOAJ |
| description | Plants in their natural habitat frequently face different biotic and abiotic stresses, which lead to the production of reactive oxygen species (ROS) that can damage cell membranes, cause peroxidation and deterioration of macromolecules, and ultimately result in cell death. Superoxide dismutase (SOD), a class of metalloenzymes, is primarily found in living organisms and serves as the principal line of defense against ROS. The <i>SOD</i> gene family has not yet been characterized in any species of water lily from the genus <i>Nymphaea</i>. The present study aims to conduct a genome-wide study to discover <i>SOD</i> genes in four representative water lily species. In our present comparative study, we discovered 43 <i>SOD</i> genes in the genomes of four water lily species. The phylogenetic investigation results revealed that <i>SOD</i> genes from water lily and closely related plant species formed two distinct groups, as determined by their binding domains with high bootstrap values. Enzymatic ion-binding classified the <i>SOD</i> gene family into three groups, <i>FeSOD</i>, <i>Cu</i>/<i>ZnSOD</i>, and <i>MnSOD</i>. The analysis of gene structure indicated that the <i>SOD</i> gene family exhibited a relatively conserved organization of exons and introns, as well as motif configuration. Moreover, we discovered that the promoters of water lily <i>SODs</i> contained five phytohormones, four stress-responsive elements, and numerous light-responsive <i>cis</i>-elements. The predicted 3D protein structures revealed water lily <i>SODs</i> form conserved protein dimer signatures that were comparable to each other. Finally, the RT-qPCR gene expression analysis of nine <i>NcSOD</i> genes revealed their responsiveness to heat, saline, cold, cadmium chloride, and copper sulphate stress. These findings establish a basis for further investigation into the role of the <i>SOD</i> gene family in <i>Nymphaea colorata</i> and offer potential avenues for genetic enhancement of water lily aquaculture. |
| first_indexed | 2024-03-09T10:56:03Z |
| format | Article |
| id | doaj.art-2b4b4025bfba4cfab9ae49c54da7b3e5 |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-09T10:56:03Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-2b4b4025bfba4cfab9ae49c54da7b3e52023-12-01T01:34:48ZengMDPI AGHorticulturae2311-75242023-07-019778110.3390/horticulturae9070781Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water LiliesWasi Ullah Khan0Latif Ullah Khan1Dan Chen2Fei Chen3Sanya Nanfan Research Institute, Hainan University, Sanya 572025, ChinaSanya Nanfan Research Institute, Hainan University, Sanya 572025, ChinaHainan Institute of Zhejiang University, Sanya 572025, ChinaSanya Nanfan Research Institute, Hainan University, Sanya 572025, ChinaPlants in their natural habitat frequently face different biotic and abiotic stresses, which lead to the production of reactive oxygen species (ROS) that can damage cell membranes, cause peroxidation and deterioration of macromolecules, and ultimately result in cell death. Superoxide dismutase (SOD), a class of metalloenzymes, is primarily found in living organisms and serves as the principal line of defense against ROS. The <i>SOD</i> gene family has not yet been characterized in any species of water lily from the genus <i>Nymphaea</i>. The present study aims to conduct a genome-wide study to discover <i>SOD</i> genes in four representative water lily species. In our present comparative study, we discovered 43 <i>SOD</i> genes in the genomes of four water lily species. The phylogenetic investigation results revealed that <i>SOD</i> genes from water lily and closely related plant species formed two distinct groups, as determined by their binding domains with high bootstrap values. Enzymatic ion-binding classified the <i>SOD</i> gene family into three groups, <i>FeSOD</i>, <i>Cu</i>/<i>ZnSOD</i>, and <i>MnSOD</i>. The analysis of gene structure indicated that the <i>SOD</i> gene family exhibited a relatively conserved organization of exons and introns, as well as motif configuration. Moreover, we discovered that the promoters of water lily <i>SODs</i> contained five phytohormones, four stress-responsive elements, and numerous light-responsive <i>cis</i>-elements. The predicted 3D protein structures revealed water lily <i>SODs</i> form conserved protein dimer signatures that were comparable to each other. Finally, the RT-qPCR gene expression analysis of nine <i>NcSOD</i> genes revealed their responsiveness to heat, saline, cold, cadmium chloride, and copper sulphate stress. These findings establish a basis for further investigation into the role of the <i>SOD</i> gene family in <i>Nymphaea colorata</i> and offer potential avenues for genetic enhancement of water lily aquaculture.https://www.mdpi.com/2311-7524/9/7/781<i>NcSOD</i> genessequence analysisabiotic stressesexpression pattern |
| spellingShingle | Wasi Ullah Khan Latif Ullah Khan Dan Chen Fei Chen Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies Horticulturae <i>NcSOD</i> genes sequence analysis abiotic stresses expression pattern |
| title | Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies |
| title_full | Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies |
| title_fullStr | Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies |
| title_full_unstemmed | Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies |
| title_short | Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies |
| title_sort | comparative analyses of superoxide dismutase sod gene family and expression profiling under multiple abiotic stresses in water lilies |
| topic | <i>NcSOD</i> genes sequence analysis abiotic stresses expression pattern |
| url | https://www.mdpi.com/2311-7524/9/7/781 |
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