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Li H, Zou T, Chen S, Zhong M. Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato. PeerJ 2024; 12:e17537. [PMID: 38912042 PMCID: PMC11192028 DOI: 10.7717/peerj.17537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/19/2024] [Indexed: 06/25/2024] Open
Abstract
The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.
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Affiliation(s)
- Hui Li
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Tingrui Zou
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Shuisen Chen
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Ming Zhong
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
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2
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Luo C, Akhtar M, Min W, Bai X, Ma T, Liu C. Domain of unknown function (DUF) proteins in plants: function and perspective. PROTOPLASMA 2024; 261:397-410. [PMID: 38158398 DOI: 10.1007/s00709-023-01917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.
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Affiliation(s)
- Chengke Luo
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Maryam Akhtar
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Weifang Min
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xiaorong Bai
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Tianli Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Caixia Liu
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
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Han S, Han X, Qi C, Guo F, Yin J, Liu Y, Zhu Y. Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale. Int J Mol Sci 2024; 25:929. [PMID: 38256002 PMCID: PMC10815606 DOI: 10.3390/ijms25020929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
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Affiliation(s)
- Shuo Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Xiaowen Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Chuandong Qi
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Fengling Guo
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Junliang Yin
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yiqing Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
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4
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Dong W, Tu J, Deng W, Zhang J, Xu Y, Gu A, An H, Fan K, Wang R, Zhang J, Kui L, Li X. Genome-wide identification of DUF506 gene family in Oryzasativa and expression profiling under abiotic stresses. PeerJ 2023; 11:e16168. [PMID: 37790624 PMCID: PMC10544316 DOI: 10.7717/peerj.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023] Open
Abstract
The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future.
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Affiliation(s)
- Wei Dong
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jian Tu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Wei Deng
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jianhua Zhang
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Yuran Xu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Anyu Gu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Hua An
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Kui Fan
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | - Rui Wang
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | | | - Limei Kui
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Xiaolin Li
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
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Yuan Y, Yin X, Han X, Han S, Li Y, Ma D, Fang Z, Yin J, Gong S. Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat ( Triticum aestivum). Int J Mol Sci 2023; 24:14248. [PMID: 37762550 PMCID: PMC10531524 DOI: 10.3390/ijms241814248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat.
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Affiliation(s)
- Yi Yuan
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Xiaohui Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Xiaowen Han
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuo Han
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yiting Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Dongfang Ma
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Zhengwu Fang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Junliang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuangjun Gong
- Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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6
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Chen K, Wang Y, Nong X, Zhang Y, Tang T, Chen Y, Shen Q, Yan C, Lü B. Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.). BMC Genomics 2023; 24:544. [PMID: 37704940 PMCID: PMC10500787 DOI: 10.1186/s12864-023-09654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
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.
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Affiliation(s)
- Kai Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Yilin Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Xiaoyan Nong
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yichi Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Huaiyin Normal University, Huaian, 223300, China
| | - Yun Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qikun Shen
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Changjie Yan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Bing Lü
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
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Zaynab M, Sharif Y, Xu Z, Fiaz S, Al-Yahyai R, Yadikar HA, Al Kashgry NAT, Qari SH, Sadder M, Li S. Genome-Wide Analysis and Expression Profiling of DUF668 Genes in Glycine max under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2923. [PMID: 37631135 PMCID: PMC10459691 DOI: 10.3390/plants12162923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
The DUF668 gene performs a critical role in mitigating the impact of abiotic stress factors. In this study, we identified 30 DUF668 genes in a soybean genome, distributed across fifteen chromosomes. The phylogenetic analysis classified the DUF668 genes into three groups (group I, group II, and group III). Interestingly, gene structure analysis illustrated that several GmDUF668 genes were without introns. Furthermore, the subcellular localization results suggested that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane. GmDUF668 promoters were analyzed in silico to gain insight into the presence of regulatory sequences for TFs binding. The expression profiling illustrated that GmDUF668 genes showed expression in leaves, roots, nodules, and flowers. To investigate their response to salt stress, we utilized the RNA sequencing data of GmDUF668 genes. The results unveiled that GmDUF668-8, GmDUF668-20, and GmDUF668-30 genes were upregulated against salt stress treatment. We further validated these findings using qRT-PCR analysis. These findings provide a scientific basis to explore the functions of GmDUF668 genes against different stress conditions.
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Affiliation(s)
- Madiha Zaynab
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaoshi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Rashid Al-Yahyai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, P.O. Box 34, Muscat 123, Oman
| | - Hamad. A. Yadikar
- Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Najla Amin T. Al Kashgry
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Monther Sadder
- School of Agriculture, University of Jordan, Amman 11942, Jordan
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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Jayaraman K, Sevanthi AM, Raman KV, Jiwani G, Solanke AU, Mandal PK, Mohapatra T. Overexpression of a DUF740 family gene ( LOC_Os04g59420) imparts enhanced climate resilience through multiple stress tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 13:947312. [PMID: 36743581 PMCID: PMC9893790 DOI: 10.3389/fpls.2022.947312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Functional characterization of stress-responsive genes through the analysis of transgenic plants is a standard approach to comprehend their role in climate resilience and subsequently exploit them for sustainable crop improvement. In this study, we investigated the function of LOC_Os04g59420, a gene of DUF740 family (OsSRDP-Oryza sativa Stress Responsive DUF740 Protein) from rice, which showed upregulation in response to abiotic stress in the available global expression data, but is yet to be functionally characterized. Transgenic plants of the rice OsSRDP gene, driven by a stress-inducible promoter AtRd29A, were developed in the background of cv. Pusa Sugandh 2 (PS2) and their transgene integration and copy number were confirmed by molecular analysis. The three independent homozygous transgenic plants (AtRd29A::OsSRDP rice transformants) showed better resilience to drought, salinity, and cold stresses, but not heat stress, as compared to the non-transformed PS2, which corresponded with their respective relative transcript abundance for OsSRDP. Transgenic plants maintained higher RWC, photosynthetic pigments, and proline accumulation under drought and salinity stresses. Furthermore, they exhibited less accumulation of reactive oxygen species (ROS) than PS2 under drought stress, as seen from the transcript abundance studies of the ROS genes. Under cold stress, OsSRDP transgenic lines illustrated minimal cell membrane injury compared to PS2. Additionally, the transgenic plants showed resistance to a virulent strain of rice blast fungus, Magnaporthe oryzae (M. oryzae). The promoter analysis of the gene in N22 and PS2 revealed the presence of multiple abiotic and biotic stress-specific motif elements supporting our observation on multiple stress tolerance. Based on bioinformatics studies, we identified four potential candidate interaction partners for LOC_Os04g59420, of which two genes (LOC_Os05g09640 and LOC_Os06g50370) showed co-expression under biotic and drought stress along with OsSRDP. Altogether, our findings established that stress-inducible expression of OsSRDP can significantly enhance tolerance to multiple abiotic stresses and a biotic stress.
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Affiliation(s)
- Karikalan Jayaraman
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Kalappan Venkat Raman
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Gitanjali Jiwani
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Amolkumar U. Solanke
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Pranab Kumar Mandal
- Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, New Delhi, India
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Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under Drought and Salt Stresses in Sweet Potato [ Ipomoea batatas (L.) Lam]. Genes (Basel) 2023; 14:genes14010217. [PMID: 36672958 PMCID: PMC9858669 DOI: 10.3390/genes14010217] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The domain of unknown function 668 (DUF668) is a gene family that plays a vital role in responses to adversity coercion stresses in plant. However, the function of the DUF668 gene family is not fully understood in sweet potato. In this study, bioinformatics methods were used to analyze the number, physicochemical properties, evolution, structure, and promoter cis-acting elements of the IbDUF668 family genes, and RNA-seq and qRT-PCR were performed to detect gene expression and their regulation under hormonal and abiotic stress. A total of 14 IbDUF668 proteins were identified in sweet potato, distributed on nine chromosomes. By phylogenetic analysis, IbDUF668 proteins can be divided into two subfamilies. Transcriptome expression profiling revealed that many genes from DUF668 in sweet potato showed specificity and differential expression under cold, heat, drought, salt and hormones (ABA, GA3 and IAA). Four genes (IbDUF668-6, 7, 11 and 13) of sweet potato were significantly upregulated by qRT-PCR under ABA, drought and NaCl stress. Results suggest that the DUF668 gene family is involved in drought and salt tolerance in sweet potato, and it will further provide the basic information of DUF668 gene mechanisms in plants.
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Uribe F, Henríquez-Valencia C, Arenas-M A, Medina J, Vidal EA, Canales J. Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency. PLANTS 2022; 11:plants11121526. [PMID: 35736678 PMCID: PMC9229004 DOI: 10.3390/plants11121526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022]
Abstract
LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein–protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta-specific gene family and their response to S deficiency is conserved in angiosperms.
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Affiliation(s)
- Felipe Uribe
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
| | - Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
| | - Anita Arenas-M
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, INIA-CSIC-Universidad Politécnica de Madrid, 28223 Madrid, Spain;
| | - Elena A. Vidal
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
- Correspondence:
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11
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Fang Y, Cao D, Yang H, Guo W, Ouyang W, Chen H, Shan Z, Yang Z, Chen S, Li X, Chen L, Zhou X. Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses. Int J Mol Sci 2021; 22:12515. [PMID: 34830397 PMCID: PMC8624885 DOI: 10.3390/ijms222212515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.
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Affiliation(s)
- Yisheng Fang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China;
| | - Dong Cao
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Hongli Yang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Wei Guo
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Wenqi Ouyang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Haifeng Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Zhihui Shan
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Zhonglu Yang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Shuilian Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China;
| | - Limiao Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Xinan Zhou
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
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12
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Chen C, Chu Y, Huang Q, Zhang W, Ding C, Zhang J, Li B, Zhang T, Li Z, Su X. Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency. BMC Genomics 2021; 22:697. [PMID: 34579659 PMCID: PMC8474845 DOI: 10.1186/s12864-021-07991-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency (NUE) of poplar. Results In this study, three N-efficient genotypes (A1-A3) and three N-inefficient genotypes (C1-C3) of Populus deltoides were cultured under low N stress (5 μM NH4NO3) and normal N supply (750 μM NH4NO3). The dry matter mass, leaf morphology, and chlorophyll content of both genotypes decreased under N starvation. The low nitrogen adaptation coefficients of the leaves and stems biomass of group A were significantly higher than those of group C (p < 0.05). Interestingly, N starvation induced fine root growth in group A, but not in group C. Next, a detailed time-course analysis of enzyme activities and gene expression in leaves identified 2062 specifically differentially expressed genes (DEGs) in group A and 1118 in group C. Moreover, the sensitivity to N starvation of group A was weak, and DEGs related to hormone signal transduction and stimulus response played an important role in the low N response this group. Weighted gene co-expression network analysis identified genes related to membranes, catalytic activity, enzymatic activity, and response to stresses that might be critical for poplar’s adaption to N starvation and these genes participated in the negative regulation of various biological processes. Finally, ten influential hub genes and twelve transcription factors were identified in the response to N starvation. Among them, four hub genes were related to programmed cell death and the defense response, and PodelWRKY18, with high connectivity, was involved in plant signal transduction. The expression of hub genes increased gradually with the extension of low N stress time, and the expression changes in group A were more obvious than those in group C. Conclusions Under N starvation, group A showed stronger adaptability and better NUE than group C in terms of morphology and physiology. The discovery of hub genes and transcription factors might provide new information for the analysis of the molecular mechanism of NUE and its improvement in poplar. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07991-7.
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Affiliation(s)
- Cun Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Yanguang Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Qinjun Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Bo Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Zhenghong Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu Province, China.
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Zhao J, Wang P, Gao W, Long Y, Wang Y, Geng S, Su X, Jiao Y, Chen Q, Qu Y. Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. BMC Genomics 2021; 22:395. [PMID: 34044774 PMCID: PMC8162019 DOI: 10.1186/s12864-021-07716-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited. Results Our study was conducted based on the DUF668 gene family identified from cotton genome sequencing. Phylogenetic analysis showed that the DUF668 family genes can be classified into four subgroups in cotton. We identified 32 DUF668 genes, which are distributed on 17 chromosomes and most of them located in the nucleus of Gossypium hirsutum. Gene structure and motif analyses revealed that the members of the DUF668 gene family can be clustered in G. hirsutum into two broad groups, which are relatively evolutionarily conserved. Transcriptome data analysis showed that the GhDUF668 genes are differentially expressed in different tissues under various stresses (cold, heat, drought, salt, and Verticillium dahliae), and expression is generally increased in roots and stems. Promoter and expression analyses indicated that Gh_DUF668–05, Gh_DUF668–08, Gh_DUF668–11, Gh_DUF668–23 and Gh_DUF668–28 in G. hirsutum might have evolved resistance to adverse stress. Additionally, qRT-PCR revealed that these 5 genes in four cotton lines, KK1543 (drought resistant), Xinluzao 26 (drought sensitive), Zhongzhimian 2 (disease resistant) and Simian 3 (susceptible), under drought and Verticillium wilt stress were all significantly induced. Roots had the highest expression of these 5 genes before and after the treatment. Among them, the expression levels of Gh_DUF668–08 and Gh_DUF668–23 increased sharply at 6 h and reached a maximum at 12 h under biotic and abiotic stress, which showed that they might be involved in the process of adverse stress resistance in cotton. Conclusion The significant changes in GhDUF668 expression in the roots after adverse stress indicate that GhDUF668 is likely to increase plant resistance to stress. This study provides an important theoretical basis for further research on the function of the DUF668 gene family and the molecular mechanism of adverse stress resistance in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07716-w.
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Affiliation(s)
- Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Peng Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yilei Long
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Xuening Su
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yang Jiao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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Waseem M, Aslam MM, Shaheen I. The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. GM CROPS & FOOD 2021; 12:586-599. [PMID: 34379048 PMCID: PMC8820248 DOI: 10.1080/21645698.2021.1962207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. To understand the role of DDP proteins in tomato, a comprehensive genome-wide analysis was performed in the tomato genome. A total of 12 DDP genes were identified and distributed in 8 chromosomes in the tomato genome. Phylogenetically all SlDDPs were clustered into four clades, subsequently supported by their gene structure and conserved motifs distribution. The SlDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. The tissue-specific expression profile analysis revealed the constitutive expression of SlDDPs in roots, leaves, and developmental phases of fruit. It was found that SlDDP1, SlDDP3, SlDDP4, SlDDP9, SlDDP10, and SlDDP12 exhibited high expression levels in fruits at different development stages. Of these genes, SlDDP12 contained ethylene (ERE) responsive elements in their promoter regions, suggesting its role in ethylene-dependent fruit ripening. It was found that a single SlDDP induced by two or more abiotic and phytohormone stresses. These include, SlDDP1, SlDDP2, SlDDP3, SlDDP4, SlDDP7, SlDDP8, and SlDDP10 was induced under salt, drought, ABA, and IAA stresses. Moreover, tomato SlDDPs were targeted by multiple miRNA gene families as well. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in plants, particularly tomato, rice, and other economically important crop plant species.
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Affiliation(s)
- Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | | | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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