Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses
Abstract Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an...
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BMC
2020-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-019-6389-3 |
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| author | Qi Yang Xiaocui Niu Xiaona Tian Xiujuan Zhang Jingyu Cong Ruigang Wang Guosheng Zhang Guojing Li |
| author_facet | Qi Yang Xiaocui Niu Xiaona Tian Xiujuan Zhang Jingyu Cong Ruigang Wang Guosheng Zhang Guojing Li |
| author_sort | Qi Yang |
| collection | DOAJ |
| description | Abstract Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future. |
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| language | English |
| last_indexed | 2024-12-17T04:58:09Z |
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| spelling | doaj.art-4e7ee0209f854badb8b90a9cce53b3362022-12-21T22:02:39ZengBMCBMC Genomics1471-21642020-01-0121111610.1186/s12864-019-6389-3Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stressesQi Yang0Xiaocui Niu1Xiaona Tian2Xiujuan Zhang3Jingyu Cong4Ruigang Wang5Guosheng Zhang6Guojing Li7College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityForestry College, Inner Mongolia Agricultural UniversityCollege of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural UniversityAbstract Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.https://doi.org/10.1186/s12864-019-6389-3DUF4228Phylogenetic analysisGenomic analysisAbiotic stress |
| spellingShingle | Qi Yang Xiaocui Niu Xiaona Tian Xiujuan Zhang Jingyu Cong Ruigang Wang Guosheng Zhang Guojing Li Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses BMC Genomics DUF4228 Phylogenetic analysis Genomic analysis Abiotic stress |
| title | Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses |
| title_full | Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses |
| title_fullStr | Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses |
| title_full_unstemmed | Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses |
| title_short | Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses |
| title_sort | comprehensive genomic analysis of the duf4228 gene family in land plants and expression profiling of atduf4228 under abiotic stresses |
| topic | DUF4228 Phylogenetic analysis Genomic analysis Abiotic stress |
| url | https://doi.org/10.1186/s12864-019-6389-3 |
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