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Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.)
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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500787/ https://www.ncbi.nlm.nih.gov/pubmed/37704940 http://dx.doi.org/10.1186/s12864-023-09654-1 |
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author | Chen, Kai Wang, Yilin Nong, Xiaoyan Zhang, Yichi Tang, Tang Chen, Yun Shen, Qikun Yan, Changjie Lü, Bing |
author_facet | Chen, Kai Wang, Yilin Nong, Xiaoyan Zhang, Yichi Tang, Tang Chen, Yun Shen, Qikun Yan, Changjie Lü, Bing |
author_sort | Chen, Kai |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09654-1. |
format | Online Article Text |
id | pubmed-10500787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-105007872023-09-15 Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) Chen, Kai Wang, Yilin Nong, Xiaoyan Zhang, Yichi Tang, Tang Chen, Yun Shen, Qikun Yan, Changjie Lü, Bing BMC Genomics Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09654-1. BioMed Central 2023-09-13 /pmc/articles/PMC10500787/ /pubmed/37704940 http://dx.doi.org/10.1186/s12864-023-09654-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Chen, Kai Wang, Yilin Nong, Xiaoyan Zhang, Yichi Tang, Tang Chen, Yun Shen, Qikun Yan, Changjie Lü, Bing Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.) |
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 | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500787/ https://www.ncbi.nlm.nih.gov/pubmed/37704940 http://dx.doi.org/10.1186/s12864-023-09654-1 |
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