Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.)
Abstract Background Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein fa...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09654-1 |
| _version_ | 1797577917876666368 |
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| author | Kai Chen Yilin Wang Xiaoyan Nong Yichi Zhang Tang Tang Yun Chen Qikun Shen Changjie Yan Bing Lü |
| author_facet | Kai Chen Yilin Wang Xiaoyan Nong Yichi Zhang Tang Tang Yun Chen Qikun Shen Changjie Yan Bing Lü |
| author_sort | Kai Chen |
| collection | DOAJ |
| description | Abstract Background Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein family is plant-specific and has not been described previously. A basic analysis and expression profiling was performed, and the co-expression and interaction networks were constructed to explore the functions of DUF568 family in rice. Results The phylogenetic tree showed that the 8, 9 and 11 DUF568 family members from rice, Arabidopsis and maize were divided into three groups. The evolutionary relationship between DUF568 members in rice and maize was close, while the genes in Arabidopsis were more distantly related. The cis-elements prediction showed that over 82% of the elements upstream of OsDUF568 genes were responsive to light and phytohormones. Gene expression profile prediction and RT-qPCR experiments revealed that OsDUF568 genes were highly expressed in leaves, stems and roots of rice seedling. The expression of some OsDUF568 genes varied in response to plant hormones (abscisic acid, 6-benzylaminopurine) and abiotic stress (drought and chilling). Further analysis of the co-expression and protein–protein interaction networks using gene ontology showed that OsDUF568 − related genes were enriched in cellular transports, metabolism and processes. Conclusions In summary, our findings suggest that the OsDUF568 family may be a vital gene family for the development of rice roots, leaves and stems. In addition, the OsDUF568 family may participate in abscisic acid and cytokinin signaling pathways, and may be related to abiotic stress resistance in these vegetative tissues of rice. |
| first_indexed | 2024-03-10T22:15:53Z |
| format | Article |
| id | doaj.art-e605efc12bba495195523f1137dfeba3 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:53Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e605efc12bba495195523f1137dfeba32023-11-19T12:28:24ZengBMCBMC Genomics1471-21642023-09-0124111710.1186/s12864-023-09654-1Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.)Kai Chen0Yilin Wang1Xiaoyan Nong2Yichi Zhang3Tang Tang4Yun Chen5Qikun Shen6Changjie Yan7Bing Lü8College of Bioscience and Biotechnology, Yangzhou UniversityCollege of Bioscience and Biotechnology, Yangzhou UniversityCollege of Bioscience and Biotechnology, Yangzhou UniversityCollege of Bioscience and Biotechnology, Yangzhou UniversityJiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Huaiyin Normal UniversityCollege of Bioscience and Biotechnology, Yangzhou UniversityJiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou UniversityKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou UniversityCollege of Bioscience and Biotechnology, Yangzhou UniversityAbstract Background Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein family is plant-specific and has not been described previously. A basic analysis and expression profiling was performed, and the co-expression and interaction networks were constructed to explore the functions of DUF568 family in rice. Results The phylogenetic tree showed that the 8, 9 and 11 DUF568 family members from rice, Arabidopsis and maize were divided into three groups. The evolutionary relationship between DUF568 members in rice and maize was close, while the genes in Arabidopsis were more distantly related. The cis-elements prediction showed that over 82% of the elements upstream of OsDUF568 genes were responsive to light and phytohormones. Gene expression profile prediction and RT-qPCR experiments revealed that OsDUF568 genes were highly expressed in leaves, stems and roots of rice seedling. The expression of some OsDUF568 genes varied in response to plant hormones (abscisic acid, 6-benzylaminopurine) and abiotic stress (drought and chilling). Further analysis of the co-expression and protein–protein interaction networks using gene ontology showed that OsDUF568 − related genes were enriched in cellular transports, metabolism and processes. Conclusions In summary, our findings suggest that the OsDUF568 family may be a vital gene family for the development of rice roots, leaves and stems. In addition, the OsDUF568 family may participate in abscisic acid and cytokinin signaling pathways, and may be related to abiotic stress resistance in these vegetative tissues of rice.https://doi.org/10.1186/s12864-023-09654-1DUF568 domainExpression patternGene familyPhylogenetic analysisRice |
| spellingShingle | Kai Chen Yilin Wang Xiaoyan Nong Yichi Zhang Tang Tang Yun Chen Qikun Shen Changjie Yan Bing Lü Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) BMC Genomics DUF568 domain Expression pattern Gene family Phylogenetic analysis Rice |
| title | Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
| title_full | Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
| title_fullStr | Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
| title_full_unstemmed | Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
| title_short | Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
| title_sort | characterization and in silico analysis of the domain unknown function duf568 containing gene family in rice oryza sativa l |
| topic | DUF568 domain Expression pattern Gene family Phylogenetic analysis Rice |
| url | https://doi.org/10.1186/s12864-023-09654-1 |
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