Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum
Abstract Background Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes...
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3768-5 |
| _version_ | 1819291212867174400 |
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| author | Wei Wang Xiaopei Zhang Fenni Deng Rui Yuan Fafu Shen |
| author_facet | Wei Wang Xiaopei Zhang Fenni Deng Rui Yuan Fafu Shen |
| author_sort | Wei Wang |
| collection | DOAJ |
| description | Abstract Background Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton. Results In the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified and phylogenetically classified into five subgroups which corroborated their classifications based on gene-structure patterns and subcellular localizations. The GhSOD sequences were distributed at different densities across 12 of the 26 chromosomes. The conserved domains, gene family evolution cis-acting elements of promoter regions and miRNA-mediated posttranscriptional regulation were predicted and analyzed. In addition, the expression pattern of 18 GhSOD genes were tested in different tissues/organs and developmental stages, and different abiotic stresses and abscisic acid, which indicated that the SOD gene family possessed temporal and spatial specificity expression specificity and may play important roles in reactive oxygen species scavenging caused by various stresses in upland cotton. Conclusions This study describes the first genome-wide analysis of the upland cotton SOD gene family, and the results will help establish a foundation for the further cloning and functional verification of the GhSOD gene family during stress responses, leading to crop improvement. |
| first_indexed | 2024-12-24T03:35:03Z |
| format | Article |
| id | doaj.art-dd1d529c1b4d494c9ef4be97a6f38289 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-24T03:35:03Z |
| publishDate | 2017-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-dd1d529c1b4d494c9ef4be97a6f382892022-12-21T17:17:06ZengBMCBMC Genomics1471-21642017-05-0118112510.1186/s12864-017-3768-5Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutumWei Wang0Xiaopei Zhang1Fenni Deng2Rui Yuan3Fafu Shen4State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityAbstract Background Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton. Results In the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified and phylogenetically classified into five subgroups which corroborated their classifications based on gene-structure patterns and subcellular localizations. The GhSOD sequences were distributed at different densities across 12 of the 26 chromosomes. The conserved domains, gene family evolution cis-acting elements of promoter regions and miRNA-mediated posttranscriptional regulation were predicted and analyzed. In addition, the expression pattern of 18 GhSOD genes were tested in different tissues/organs and developmental stages, and different abiotic stresses and abscisic acid, which indicated that the SOD gene family possessed temporal and spatial specificity expression specificity and may play important roles in reactive oxygen species scavenging caused by various stresses in upland cotton. Conclusions This study describes the first genome-wide analysis of the upland cotton SOD gene family, and the results will help establish a foundation for the further cloning and functional verification of the GhSOD gene family during stress responses, leading to crop improvement.http://link.springer.com/article/10.1186/s12864-017-3768-5SODUpland cottonGenome wide analysisAbiotic stressExpression profiles |
| spellingShingle | Wei Wang Xiaopei Zhang Fenni Deng Rui Yuan Fafu Shen Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum BMC Genomics SOD Upland cotton Genome wide analysis Abiotic stress Expression profiles |
| title | Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum |
| title_full | Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum |
| title_fullStr | Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum |
| title_full_unstemmed | Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum |
| title_short | Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum |
| title_sort | genome wide characterization and expression analyses of superoxide dismutase sod genes in gossypium hirsutum |
| topic | SOD Upland cotton Genome wide analysis Abiotic stress Expression profiles |
| url | http://link.springer.com/article/10.1186/s12864-017-3768-5 |
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