Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops
The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and evolutiona...
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MDPI AG
2022-05-01
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| author | Chenhao Zhang Xin Nie Weilong Kong Xiaoxiao Deng Tong Sun Xuhui Liu Yangsheng Li |
| author_facet | Chenhao Zhang Xin Nie Weilong Kong Xiaoxiao Deng Tong Sun Xuhui Liu Yangsheng Li |
| author_sort | Chenhao Zhang |
| collection | DOAJ |
| description | The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of <i>GAox</i> genes in six Gramineae representative crops, namely, <i>Setaria italica</i> (Si), <i>Zea mays</i> (Zm), <i>Sorghum bicolor</i> (Sb), <i>Hordeum vulgare</i> (Hv), <i>Brachypodium distachyon</i> (Bd), and <i>Oryza sativa</i> (Os). A total of 105 <i>GAox</i> genes were identified in these six crop genomes, belonging to the <i>C</i><sub>19</sub><i>-GA2ox, C</i><sub>20</sub><i>-GA2ox, GA3ox,</i> and <i>GA20ox</i> subfamilies. Based on orthogroup (OG) analysis, <i>GAox</i> genes were divided into nine OGs and the number of <i>GAox</i> genes in each of the OGs was similar among all tested crops, which indicated that <i>GAox</i> genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C<sub>19</sub>-GA2ox, and C<sub>20</sub>-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that <i>GAox</i> genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more <i>GAox</i> genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that <i>GAox</i> genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that <i>GAox</i> genes were predominantly expressed in the panicles of the above two plants and the expression of several <i>GAox</i> genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into <i>GAox</i> genes’ evolutionary differences among six representative Gramineae and highlighted <i>GAox</i> genes that may play a role in abiotic stress. |
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| spelling | doaj.art-9f64a4430ed74bc2a9a29059d6b3acba2023-11-23T11:10:40ZengMDPI AGGenes2073-44252022-05-0113586310.3390/genes13050863Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae CropsChenhao Zhang0Xin Nie1Weilong Kong2Xiaoxiao Deng3Tong Sun4Xuhui Liu5Yangsheng Li6State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaThe plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of <i>GAox</i> genes in six Gramineae representative crops, namely, <i>Setaria italica</i> (Si), <i>Zea mays</i> (Zm), <i>Sorghum bicolor</i> (Sb), <i>Hordeum vulgare</i> (Hv), <i>Brachypodium distachyon</i> (Bd), and <i>Oryza sativa</i> (Os). A total of 105 <i>GAox</i> genes were identified in these six crop genomes, belonging to the <i>C</i><sub>19</sub><i>-GA2ox, C</i><sub>20</sub><i>-GA2ox, GA3ox,</i> and <i>GA20ox</i> subfamilies. Based on orthogroup (OG) analysis, <i>GAox</i> genes were divided into nine OGs and the number of <i>GAox</i> genes in each of the OGs was similar among all tested crops, which indicated that <i>GAox</i> genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C<sub>19</sub>-GA2ox, and C<sub>20</sub>-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that <i>GAox</i> genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more <i>GAox</i> genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that <i>GAox</i> genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that <i>GAox</i> genes were predominantly expressed in the panicles of the above two plants and the expression of several <i>GAox</i> genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into <i>GAox</i> genes’ evolutionary differences among six representative Gramineae and highlighted <i>GAox</i> genes that may play a role in abiotic stress.https://www.mdpi.com/2073-4425/13/5/863Gramineaegibberellin oxidaseorthogroupsabiotic stressexpression patterns |
| spellingShingle | Chenhao Zhang Xin Nie Weilong Kong Xiaoxiao Deng Tong Sun Xuhui Liu Yangsheng Li Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops Genes Gramineae gibberellin oxidase orthogroups abiotic stress expression patterns |
| title | Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops |
| title_full | Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops |
| title_fullStr | Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops |
| title_full_unstemmed | Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops |
| title_short | Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops |
| title_sort | genome wide identification and evolution analysis of the gibberellin oxidase gene family in six gramineae crops |
| topic | Gramineae gibberellin oxidase orthogroups abiotic stress expression patterns |
| url | https://www.mdpi.com/2073-4425/13/5/863 |
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