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Meng L, Su H, Qu Z, Lu P, Tao J, Li H, Zhang J, Zhang W, Liu N, Cao P, Jin J. Genome-wide identification and analysis of WD40 proteins reveal that NtTTG1 enhances drought tolerance in tobacco (Nicotiana tabacum). BMC Genomics 2024; 25:133. [PMID: 38302866 PMCID: PMC10835901 DOI: 10.1186/s12864-024-10022-w] [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: 07/19/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND WD40 proteins, which are highly prevalent in eukaryotes, play important roles in plant development and stress responses. However, systematic identification and exploration of WD40 proteins in tobacco have not yet been conducted. RESULTS In this study, a total of 399 WD40 regulatory genes were identified in common tobacco (Nicotiana tabacum). Gene structure and motif analysis revealed structural and functional diversity among different clades of tobacco WD40 regulatory genes. The expansion of tobacco WD40 regulatory genes was mainly driven by segmental duplication and purifying selection. A potential regulatory network of NtWD40s suggested that NtWD40s might be regulated by miRNAs and transcription factors in various biological processes. Expression pattern analysis via transcriptome analysis and qRT-PCR revealed that many NtWD40s exhibited tissue-specific expression patterns and might be involved in various biotic and abiotic stresses. Furthermore, we have validated the critical role of NtTTG1, which was located in the nuclei of trichome cells, in enhancing the drought tolerance of tobacco plants. CONCLUSIONS Our study provides comprehensive information to better understand the evolution of WD40 regulatory genes and their roles in different stress responses in tobacco.
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Grants
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
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Affiliation(s)
- Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Huan Su
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Zechao Qu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - He Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Wei Zhang
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Nan Liu
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
- Beijing Life Science Academy, Beijing, 102200, China.
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2
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Wang C, Tang Y, Li Y, Hu C, Li J, Lyu A. Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii. BMC Genomics 2023; 24:488. [PMID: 37633914 PMCID: PMC10463391 DOI: 10.1186/s12864-023-09604-x] [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: 04/26/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yafang Tang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, 264200, China
| | - Chao Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Jingyi Li
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Ang Lyu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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3
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Chen J, Liu Q, Yuan L, Shen W, Shi Q, Qi G, Chen T, Zhang Z. Osa-miR162a Enhances the Resistance to the Brown Planthopper via α-Linolenic Acid Metabolism in Rice ( Oryza sativa). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11847-11859. [PMID: 37493591 DOI: 10.1021/acs.jafc.3c02637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The brown planthopper (BPH) is the most serious pest causing yield losses in rice. MicroRNAs (miRNAs) are emerging as key modulators of plant-pest interactions. In the study, we found that osa-miR162a is induced in response to BPH attack in the seedling stage and tunes rice resistance to the BPH via the α-linolenic acid metabolism pathway as indicated by gas chromatography/liquid chromatography-mass spectrometry analysis. Overexpression of osa-miR162a inhibited the development and growth of the BPH and simultaneously reduced the release of 3-hexenal and 3-hexen-1-ol to block host recognition in the BPH. Moreover, knockdown of OsDCL1, which is targeted by osa-miR162a, inhibited α-linolenic acid metabolism to enhance the resistance to the BPH, which was similar to that in miR162a-overexpressing plants. Our study revealed a novel defense mechanism mediated by plant miRNAs developed during the long-term evolution of plant-host interaction, provided new ideas for the identification of rice resistance resources, and promoted a better understanding of pest control.
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Affiliation(s)
- Jie Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Qin Liu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Longyu Yuan
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Wenzhong Shen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research Institute, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Qingxing Shi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Guojun Qi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Ting Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
| | - Zhenfei Zhang
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, Guangdong, China
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4
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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5
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Ji XL, Zhang M, Wang D, Li Z, Lang S, Song XS. Genome-wide identification of WD40 superfamily in Cerasus humilis and functional characteristics of ChTTG1. Int J Biol Macromol 2023; 225:376-388. [PMID: 36402390 DOI: 10.1016/j.ijbiomac.2022.11.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
The WD40 superfamily plays an important role in a wide range of developmental and physiological processes. It is a large gene family in eukaryotes. Unfortunately, the research on the WD40 superfamily genes in Cerasus humilis has not been reported. 198 ChWD40s were identified and analyzed in the present study, along with evolutionary relationships, gene structure, chromosome distribution, and collinearity. Then, 5 pairs of tandem duplication and 17 pairs of segmental duplication were found. Based on RNA-Seq data analysis, we screened 31 candidate genes whose expression was up-regulated during the four developmental stages of fruit peel. In addition, we also demonstrated that ChWD40-140, namely ChTTG1, located in the nucleus, cytoplasm, and cytomembrane, has transcriptional activation activity and can form homodimers. ChTTG1 is involved in anthocyanin biosynthesis through heterologous overexpression in Arabidopsis. These research results provide a reference for a comprehensive analysis of the functions of WD40 in the future.
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Affiliation(s)
- Xiao Long Ji
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Mingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Di Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Zhe Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shaoyu Lang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xing Shun Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin 150040, China.
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6
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Chen C, Yang Y, Pan L, Xia W, Xu L, Hua B, Zhang Z, Miao M. Genome-Wide Identification of WD40 Proteins in Cucurbita maxima Reveals Its Potential Functions in Fruit Development. Genes (Basel) 2023; 14:genes14010220. [PMID: 36672961 PMCID: PMC9859561 DOI: 10.3390/genes14010220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
WD40 proteins, a super gene family in eukaryotes, are involved in multiple biological processes. Members of this family have been identified in several plants and shown to play key roles in various development processes, including acting as scaffolding molecules with other proteins. However, WD40 proteins have not yet been systematically analyzed and identified in Cucurbita maxima. In this study, 231 WD40 proteins (CmWD40s) were identified in C. maxima and classified into five clusters. Eleven subfamilies were identified based on different conserved motifs and gene structures. The CmWD40 genes were distributed in 20 chromosomes; 5 and 33 pairs of CmWD40s were distinguished as tandem and segmental duplications, respectively. Overall, 58 pairs of orthologous WD40 genes in C. maxima and Arabidopsis thaliana, and 56 pairs of orthologous WD40 genes in C. maxima and Cucumis sativus were matched. Numerous CmWD40s had diverse expression patterns in fruits, leaf, stem, and root. Several genes were involved in responses to NaCl. The expression pattern of CmWD40s suggested their key role in fruit development and abiotic stress response. Finally, we identified 14 genes which might be involved in fruit development. Our results provide valuable basis for further functional verification of CmWD40s in C. maxima.
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Affiliation(s)
- Chen Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yating Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Liu Pan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Wenhao Xia
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lanruoyan Xu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Bing Hua
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhiping Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Minmin Miao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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7
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Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Basic WD40 proteins, which are characterized by a conserved WD40 domain, comprise a superfamily of regulatory proteins in plants and play important roles in plant growth and development. However, WD40 genes have been rarely studied in apple (Malus × domestica Borkh.). In this study, 346 WD40 genes classified in 12 subfamilies, were identified in the apple genome. Evolutionary analysis of WD40 proteins in apple and Arabidopsis revealed that the genes were classifiable into 14 groups, and the exon/intron structure of each group showed a similar structure. Analysis of collinearity showed that the large-scale amplification of WD40 genes in apple was largely attributable to recent whole-genome replication events. Nineteen candidate stress-related genes, selected by GO annotation and comparison with Arabidopsis homologs, showed different expression profiles in six organs at different developmental stages in response to exogenous abscisic acid (ABA), drought, and low temperature. Eight genes (MdWD40-17, 24, 70, 74, 219, 256, 283, and 307) showed a distinct response to one or more treatments (ABA, drought, and low temperature) as indicated by quantitative real-time PCR analysis. Taken together, these data provide rich resources for further study of MdWD40 genes and their potential roles in stress responses in apple.
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8
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Safder I, Shao G, Sheng Z, Hu P, Tang S. Genome-wide identification studies - A primer to explore new genes in plant species. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:9-22. [PMID: 34558163 DOI: 10.1111/plb.13340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.
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Affiliation(s)
- I Safder
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - G Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Z Sheng
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - P Hu
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - S Tang
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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9
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Basso MF, Costa JA, Ribeiro TP, Arraes FBM, Lourenço-Tessutti IT, Macedo AF, Neves MRD, Nardeli SM, Arge LW, Perez CEA, Silva PLR, de Macedo LLP, Lisei-de-Sa ME, Santos Amorim RM, Pinto ERDC, Silva MCM, Morgante CV, Floh EIS, Alves-Ferreira M, Grossi-de-Sa MF. Overexpression of the CaHB12 transcription factor in cotton (Gossypium hirsutum) improves drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:80-93. [PMID: 34034163 DOI: 10.1016/j.plaphy.2021.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The Coffea arabica HB12 gene (CaHB12), which encodes a transcription factor belonging to the HD-Zip I subfamily, is upregulated under drought, and its constitutive overexpression (35S:CaHB12OX) improves the Arabidopsis thaliana tolerance to drought and salinity stresses. Herein, we generated transgenic cotton events constitutively overexpressing the CaHB12 gene, characterized these events based on their increased tolerance to water deficit, and exploited the gene expression level from the CaHB12 network. The segregating events Ev8.29.1, Ev8.90.1, and Ev23.36.1 showed higher photosynthetic yield and higher water use efficiency under severe water deficit and permanent wilting point conditions compared to wild-type plants. Under well-irrigated conditions, these three promising transformed events showed an equivalent level of Abscisic acid (ABA) and decreased Indole-3-acetic acid (IAA) accumulation, and a higher putrescine/(spermidine + spermine) ratio in leaf tissues was found in the progenies of at least two transgenic cotton events compared to non-transgenic plants. In addition, genes that are considered as modulated in the A. thaliana 35S:CaHB12OX line were also shown to be modulated in several transgenic cotton events maintained under field capacity conditions. The upregulation of GhPP2C and GhSnRK2 in transgenic cotton events maintained under permanent wilting point conditions suggested that CaHB12 might act enhancing the ABA-dependent pathway. All these data confirmed that CaHB12 overexpression improved the tolerance to water deficit, and the transcriptional modulation of genes related to the ABA signaling pathway or downstream genes might enhance the defense responses to drought. The observed decrease in IAA levels indicates that CaHB12 overexpression can prevent leaf abscission in plants under or after stress. Thus, our findings provide new insights on CaHB12 gene and identify several promising cotton events for conducting field trials on water deficit tolerance and agronomic performance.
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Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Julia Almeida Costa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; Catholic University of Brasília, Brasília, DF, 71966-700, Brazil
| | - Thuanne Pires Ribeiro
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Fabricio Barbosa Monteiro Arraes
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; Federal University of Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | | | | | | | | | - Luis Willian Arge
- Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-901, Brazil
| | | | - Paolo Lucas Rodrigues Silva
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; Catholic University of Brasília, Brasília, DF, 71966-700, Brazil
| | | | - Maria Eugênia Lisei-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil; EPAMIG, Uberaba, MG, 31170-495, Brazil
| | | | | | - Maria Cristina Mattar Silva
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Carolina Vianna Morgante
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil; Embrapa Semi-Arid, Petrolina, PE, 56302-970, Brazil
| | | | - Marcio Alves-Ferreira
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil; Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-901, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70297-400, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil; Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
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10
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Hafeez A, Razzaq A, Ahmed A, Liu A, Qun G, Junwen L, Shi Y, Deng X, Zafar MM, Ali A, Gong W, Yuan Y. Identification of hub genes through co-expression network of major QTLs of fiber length and strength traits in multiple RIL populations of cotton. Genomics 2021; 113:1325-1337. [PMID: 33713821 DOI: 10.1016/j.ygeno.2021.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022]
Abstract
The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL populations including sGK9708 × 0-153, LMY22 × LY343 and Lumianyan28 × Xinluzao24. The current study was conducted to identify the major common QTLs including fiber length and strength, and to identify the co-expression networks of fiber length and strength QTLs harbored genes to target the hub genes. The RNA-seq data of sGK9708 × 0-153 population highlighted 50 and 48 candidate genes of fiber length and fiber strength QTLs. A total of 29 and 21 hub genes were identified in fiber length and strength co-expression network modules. The absolute values of correlation coefficient close to 1 resulted highly positive correlation among hub genes. Results also suggested that the gene correlation significantly influence the gene expression at different fiber development stages. These results might provide useful reference for further experiments in multiple RIL populations and suggest potential candidate genes for functional studies in cotton.
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Affiliation(s)
- Abdul Hafeez
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China; Sindh Agriculture University Tandojam, 70060 Hyderabad, Sindh, Pakistan
| | - Abdul Razzaq
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Aijaz Ahmed
- Sindh Agriculture University Tandojam, 70060 Hyderabad, Sindh, Pakistan
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Ge Qun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Li Junwen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.
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11
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Tan L, Salih H, Htet NNW, Azeem F, Zhan R. Genomic analysis of WD40 protein family in the mango reveals a TTG1 protein enhances root growth and abiotic tolerance in Arabidopsis. Sci Rep 2021; 11:2266. [PMID: 33500544 PMCID: PMC7838414 DOI: 10.1038/s41598-021-81969-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
WD40 domain-containing proteins constitute one of the most abundant protein families in all higher plants and play vital roles in the regulation of plant growth and developmental processes. To date, WD40 protein members have been identified in several plant species, but no report is available on the WD40 protein family in mango (Mangifera indica L.). In this study, a total of 315 WD40 protein members were identified in mango and further divided into 11 subgroups according to the phylogenetic tree. Here, we reported mango TRANSPARENT TESTA GLABRA 1 (MiTTG1) protein as a novel factor that functions in the regulation of Arabidopsis root growth and development. Bimolecular fluorescence complementation (BiFC) assay in tobacco leaves revealed that MiTTG1 protein physically interacts with MiMYB0, MiTT8 and MibHLH1, implying the formation of a new ternary regulatory complex (MYB-bHLH-WD40) in mango. Furthermore, the MiTTG1 transgenic lines were more adapted to abiotic stresses (mannitol, salt and drought stress) in terms of promoted root hairs and root lengths. Together, our findings indicated that MiTTG1 functions as a novel factor to modulate protein-protein interactions and enhance the plants abilities to adjust different abiotic stress responses.
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Affiliation(s)
- Lin Tan
- grid.453499.60000 0000 9835 1415Hainan Key Laboratory of Banana Genetic Improvement, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101 Hainan China
| | - Haron Salih
- grid.453499.60000 0000 9835 1415Hainan Key Laboratory of Banana Genetic Improvement, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101 Hainan China ,grid.442436.30000 0004 0447 7877Crop Sciences, Faculty of Agriculture, Zalingei University, Central Darfur, Sudan
| | - Nwe Ni Win Htet
- grid.453499.60000 0000 9835 1415Hainan Key Laboratory of Banana Genetic Improvement, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101 Hainan China ,Microbiology Laboratory, Biotechnology Research Department, Kyaukse, 05151 Myanmar
| | - Farrukh Azeem
- grid.453499.60000 0000 9835 1415Hainan Key Laboratory of Banana Genetic Improvement, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101 Hainan China
| | - Rulin Zhan
- grid.453499.60000 0000 9835 1415Hainan Key Laboratory of Banana Genetic Improvement, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101 Hainan China
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12
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Sun YB, Zhang XJ, Zhong MC, Dong X, Yu DM, Jiang XD, Wang D, Cui WH, Chen JH, Hu JY. Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae. PLANT MOLECULAR BIOLOGY 2020; 104:81-95. [PMID: 32621166 DOI: 10.1007/s11103-020-01026-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.
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Affiliation(s)
- Yi-Bo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Jia Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Dong-Mei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang-Hua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Kunming, 650223, Yunnan, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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13
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Mistry BV, Alanazi M, Fitwi H, Al-Harazi O, Rajab M, Altorbag A, Almohanna F, Colak D, Assiri AM. Expression profiling of WD40 family genes including DDB1- and CUL4- associated factor (DCAF) genes in mice and human suggests important regulatory roles in testicular development and spermatogenesis. BMC Genomics 2020; 21:602. [PMID: 32867693 PMCID: PMC7457511 DOI: 10.1186/s12864-020-07016-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The WD40-repeat containing proteins, including DDB1-CUL4-associated factors (DCAFs), are abundant and conserved proteins that play important roles in different cellular processes including spermatogenesis. DCAFs are subset of WD40 family proteins that contain WDxR motif and have been proposed to function as substrate receptor for Cullin4-RING-based E3 ubiquitin ligase complexes to recruit diverse proteins for ubiquitination, a vital process in spermatogenesis. Large number of WD40 genes has been identified in different species including mouse and human. However, a systematic expression profiling of WD40 genes in different tissues of mouse and human has not been investigated. We hypothesize that large number of WD40 genes may express highly or specifically in the testis, where their expression is uniquely regulated during testis development and spermatogenesis. Therefore, the objective of this study is to mine and characterize expression patterns of WD40 genes in different tissues of mouse and human with particular emphasis on DCAF genes expressions during mouse testicular development. RESULTS Publically available RNA sequencing (RNA seq) data mining identified 347 and 349 WD40 genes in mouse and human, respectively. Hierarchical clustering and heat map analyses of RNA seq datasets revealed differential expression patterns of WD40 genes with around 60-73% of the genes were highly or specifically expressed in testis. Similarly, around 74-83% of DCAF genes were predominantly or specifically expressed in testis. Moreover, WD40 genes showed distinct expression patterns during embryonic and postnatal testis development in mice. Finally, different germ cell populations of testis showed specific patterns of WD40 genes expression. Predicted gene ontology analyses revealed more than 80% of these proteins are implicated in cellular, metabolic, biological regulation and cell localization processes. CONCLUSIONS We have identified large number of WD40 family genes that are highly or specifically expressed in the testes of mouse and human. Moreover, WD40 genes have distinct expression patterns during embryonic and postnatal development of the testis in mice. Further, different germ cell populations within the testis showed specific patterns of WD40 genes expression. These results provide foundation for further research towards understanding the functional genomics and molecular mechanisms of mammalian testis development and spermatogenesis.
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Affiliation(s)
- Bhavesh V Mistry
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Maha Alanazi
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Hanae Fitwi
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Mohamed Rajab
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Abdullah Altorbag
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Falah Almohanna
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Dilek Colak
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abdullah M Assiri
- Department of Comparative Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia. .,Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia. .,Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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14
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Li XP, Ma XC, Wang H, Zhu Y, Liu XX, Li TT, Zheng YP, Zhao JQ, Zhang JW, Huang YY, Pu M, Feng H, Fan J, Li Y, Wang WM. Osa-miR162a fine-tunes rice resistance to Magnaporthe oryzae and Yield. RICE (NEW YORK, N.Y.) 2020; 13:38. [PMID: 32524307 PMCID: PMC7287001 DOI: 10.1186/s12284-020-00396-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/27/2020] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in rice immunity against Magnaporthe oryzae, the causative agent of rice blast disease. Here we demonstrate that Osa-miR162a fine-tunes rice immunity against M. oryzae and yield traits. Overexpression of Osa-miR162a enhances rice resistance to M. oryzae accompanying enhanced induction of defense-related genes and accumulation of hydrogen peroxide (H2O2). In contrast, blocking Osa-miR162 by overexpressing a target mimic of Osa-miR162a enhances susceptibility to blast fungus associating with compromised induction of defense-related gene expression and H2O2 accumulation. Moreover, the transgenic lines overexpressing Osa-miR162a display decreased seed setting rate resulting in slight reduced yield per plant, whereas the transgenic lines blocking Osa-miR162 show an increased number of grains per panicle, resulting in increased yield per plant. Altered accumulation of Osa-miR162 had a limited impact on the expression of rice Dicer-like 1 (OsDCL1) in these transgenic lines showing normal gross morphology, and silencing of OsDCL1 led to enhanced resistance to blast fungus similar to that caused by overexpression of Osa-miR162a, suggesting the involvement of OsDCL1 in Osa-miR162a-regulated resistance. Together, our results indicate that Osa-miR162a is involved in rice immunity against M. oryzae and fine-tunes resistance and yield.
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Affiliation(s)
- Xu-Pu Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Chun Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Xin-Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Ting-Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Ya-Ping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Ji-Qun Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Hui Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China.
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China.
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15
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Genome-wide identification and functional analysis of the WDR protein family in potato. 3 Biotech 2019; 9:432. [PMID: 31696037 DOI: 10.1007/s13205-019-1965-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022] Open
Abstract
WD-repeat (WDR) proteins are highly abundant and participate in a seemingly wide range of interactions and cellular functions acting as scaffolding molecules. However, WDR identification in potato has not been conducted so far. In this study, we demonstrated the presence of at least 168 WDR genes in potato (Solanum tuberosum L.) which can be subdivided into five discrete clusters (Cluster I-V) and 10 classes inferred from their phylogenetic features of the constituent genes and the distribution of domains. These genes are distributed on all 12 chromosomes, of which chromosome 3 carries the most genes with 26 StWDRs. The expression of potato WDR genes showed tissue specificity with a high expression in carpels, callus and roots, and the expression patterns were obviously different among different genes. Transcript profiling of 168 StWDR genes revealed the particular tissues in which the 168 StWDR are expressed, and displayed a high expression in carpels, callus and roots. Most StWDRs were modulated by salt, ABA and Verticillium dahliae stresses, of which StWD092 was found to be highly expressed under all the three stresses. These outcomes revealed the intricate crosstalk between WDRs and other regulatory networks in the event of adverse milieu.
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16
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Salih H, Gong W, He S, Xia W, Odongo MR, Du X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genomics 2019; 20:661. [PMID: 31426741 PMCID: PMC6700839 DOI: 10.1186/s12864-019-5978-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development. Results In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development. Conclusion The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality. Electronic supplementary material The online version of this article (10.1186/s12864-019-5978-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Wang Xia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Magwanga Richard Odongo
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
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17
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Chen Q, Chen QJ, Sun GQ, Zheng K, Yao ZP, Han YH, Wang LP, Duan YJ, Yu DQ, Qu YY. Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense. Int J Mol Sci 2019; 20:E349. [PMID: 30654456 PMCID: PMC6359516 DOI: 10.3390/ijms20020349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 11/17/2022] Open
Abstract
Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.
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Affiliation(s)
- Qin Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Quan-Jia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Guo-Qing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Zheng-Pei Yao
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Yu-Hui Han
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Li-Ping Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Ya-Jie Duan
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Dao-Qian Yu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yan-Ying Qu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China.
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18
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Hu R, Xiao J, Gu T, Yu X, Zhang Y, Chang J, Yang G, He G. Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). BMC Genomics 2018; 19:803. [PMID: 30400808 PMCID: PMC6219084 DOI: 10.1186/s12864-018-5157-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signal transduction. WD40 proteins are regarded as crucial regulators of plant development processes. However, the systematic identification and analysis of WD40 proteins have yet to be reported in wheat. RESULTS In this study, a total of 743 WD40 proteins were identified in wheat, and they were grouped into 5 clusters and 11 subfamilies. Their gene structures, chromosomal locations, and evolutionary relationships were analyzed. Among them, 39 and 46 pairs of TaWD40s were distinguished as tandem duplication and segmental duplication genes. The 123 OsWD40s were identified to exhibit synteny with TaWD40s. TaWD40s showed the specific characteristics at the reproductive developmental stage, and numerous TaWD40s were involved in responses to stresses, including cold, heat, drought, and powdery mildew infection pathogen, based on the result of RNA-seq data analysis. The expression profiles of some TaWD40s in wheat seed development were confirmed through qRT-PCR technique. CONCLUSION In this study, 743 TaWD40s were identified from the wheat genome. As the main driving force of evolution, duplication events were observed, and homologous recombination was another driving force of evolution. The expression profiles of TaWD40s revealed their importance for the growth and development of wheat and their response to biotic and abiotic stresses. Our study also provided important information for further functional characterization of some WD40 proteins in wheat.
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Affiliation(s)
- Rui Hu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Jie Xiao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Ting Gu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Yang Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.
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