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Cao L, Wang J, Ren S, Jia Y, Liu Y, Yang S, Yu J, Guo X, Hou X, Xu J, Li S, Xing G. Genome-wide identification of the NAC family in Hemerocallis citrina and functional analysis of HcNAC35 in response to abiotic stress in watermelon. FRONTIERS IN PLANT SCIENCE 2024; 15:1474589. [PMID: 39469056 PMCID: PMC11513300 DOI: 10.3389/fpls.2024.1474589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/25/2024] [Indexed: 10/30/2024]
Abstract
Introduction NAC (NAM, ATAF, and CUC) transcription factor family, one of the important switches of transcription networks in plants, functions in plant growth, development, and stress resistance. Night lily (Hemerocallis citrina) is an important horticultural perennial monocot plant that has edible, medicinal, and ornamental values. However, the NAC gene family of night lily has not yet been analyzed systematically to date. Methods Therefore, we conducted a genome-wide study of the HcNAC gene family and identified a total of 113 HcNAC members from the Hemerocallis citrina genome. Results We found that 113 HcNAC genes were unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that they could be categorized into 16 instinct subgroups. Proteins clustering together exhibited similar conserved motifs and intron-exon structures. Collinearity analysis indicated that segmental and tandem duplication might contribute to the great expansion of the NAC gene family in night lily, whose relationship was closer with rice than Arabidopsis. Additionally, tissue-specific pattern analysis indicated that most HcNAC genes had relatively higher expression abundances in roots. RNA-Seq along with RT-qPCR results jointly showed HcNAC genes expressed differently under drought and salinity stresses. Interestingly, HcNAC35 was overexpressed in watermelon, and the stress resilience of transgenic lines was much higher than that of wild-type watermelon, which revealed its wide participation in abiotic stress response. Conclusion In conclusion, our findings provide a new prospect for investigating the biological roles of NAC genes in night lily.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Sen Li
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable
and Flower, College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Guoming Xing
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable
and Flower, College of Horticulture, Shanxi Agricultural University, Taigu, China
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Zhang J, Wang L, Wu D, Zhao H, Gong L, Xu J. Regulation of SmEXPA13 expression by SmMYB1R1-L enhances salt tolerance in Salix matsudana Koidz. Int J Biol Macromol 2024; 270:132292. [PMID: 38750858 DOI: 10.1016/j.ijbiomac.2024.132292] [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: 02/29/2024] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
Expansins, cell wall proteins, play a significant role in plant stress resistance. Our previous study confirmed the expression of the expansin gene SmEXPA13 from Salix matsudana Koidz. enhanced salt tolerance of plants. This report presented an assay that the expression of SmEXPA13 was higher in the salt-resistant willow variety 9901 than in the salt-sensitive variety Yanjiang. In order to understand the possible reasons, a study of the regulation process was conducted. Despite being cloned from both varieties, SmEXPA13 and its promotor showed no significant differences in the structure and sequence. A transcription factor (TF), SmMYB1R1-L, identified through screening the yeast library of willow cDNA, was found to regulate SmEXPA13. Yeast one-hybrid (Y1H) assay confirmed that SmMYB1R1-L could bind to the MYB element at the -520 bp site on the SmEXPA13 promotor. A dual-luciferase reporter assay also demonstrated that SmMYB1R1-L could greatly activate SmEXPA13 expression. The willow calli with over-expression of SmMYB1R1-L exhibited better physiological performance than the wild type under salt stress. Further testing the expression of SmMYB1R1-L displayed it significantly higher in 9901 willow than that in Yanjiang under salt stress. In conclusion, the high accumulation of SmMYB1R1-L in 9901 willow under salt stress led to the high expression of SmEXPA13, resulting in variations in salt stress resistance among willow varieties. The SmMYB1R1-L/SmEXPA13 cascade module in willow offers a new perspective on plant resistance mechanisms.
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Affiliation(s)
- Junkang Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Han Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Longfeng Gong
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jichen Xu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Jiao F, Zhang D, Chen Y, Wu J. Genome-Wide Identification of Members of the Soybean CBL Gene Family and Characterization of the Functional Role of GmCBL1 in Responses to Saline and Alkaline Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1304. [PMID: 38794375 PMCID: PMC11124892 DOI: 10.3390/plants13101304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024]
Abstract
Calcium ions function as key messengers in the context of intracellular signal transduction. The ability of plants to respond to biotic and abiotic stressors is highly dependent on the calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) signaling network. Here, a comprehensive effort was made to identify all members of the soybean CBL gene family, leading to the identification of 15 total genes distributed randomly across nine chromosomes, including 13 segmental duplicates. All the GmCBL gene subfamilies presented with similar gene structures and conserved motifs. Analyses of the expression of these genes in different tissues revealed that the majority of these GmCBLs were predominantly expressed in the roots. Significant GmCBL expression and activity increases were also observed in response to a range of stress-related treatments, including salt stress, alkaline stress, osmotic stress, or exposure to salicylic acid, brassinosteroids, or abscisic acid. Striking increases in GmCBL1 expression were observed in response to alkaline and salt stress. Subsequent analyses revealed that GmCBL1 was capable of enhancing soybean salt and alkali tolerance through the regulation of redox reactions. These results offer new insight into the complex mechanisms through which the soybean CBL gene family regulates the responses of these plants to environmental stressors, highlighting promising targets for efforts aimed at enhancing soybean stress tolerance.
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Affiliation(s)
| | | | | | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (F.J.); (D.Z.); (Y.C.)
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Li Y, Li B, Pang Q, Lou Y, Wang D, Wang Z. Identification and expression analysis of expansin gene family in Salvia miltiorrhiza. Chin Med 2024; 19:22. [PMID: 38311790 PMCID: PMC10838462 DOI: 10.1186/s13020-023-00867-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Expansins (EXP) are important enzymes that are involved in the extension of plant cells and regulation of root configurations, which play important roles in resisting various stresses. As a model medicinal plant, Salvia miltiorrhiza is well recognized for treating coronary heart disease, myocardial infection, and other cardiovascular and cerebrovascular diseases; however, the SmEXP gene family has not yet been analyzed. METHODS The SmEXP family was systematically analyzed using bioinformatics. Quantitative real-time PCR was employed to analyze the tissue expression patterns of the SmEXP family, as well as its expression under abscisic acid (ABA) treatment and abiotic stress. Subcellular localization assay revealed the localization of SmEXLA1, SmEXLB1, and SmEXPA2. RESULTS This study identified 29 SmEXP that belonged to four different subfamilies. SmEXP promoter analysis suggested that it may be involved in the growth, development, and stress adaptation of S. miltiorrhiza. An analysis of the expression patterns of SmEXP revealed that ABA, Cu2+, and NaCl had regulatory effects on its expression. A subcellular localization assay showed that SmEXLA1 and SmEXLB1 were located on the nucleus and cell membrane, while SmEXPA2 was located on the cell wall. CONCLUSION For this study, the SmEXP family was systematically analyzed for the first time, which lays a foundation for further elucidating its physiological and biological functionality.
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Affiliation(s)
- Yunyun Li
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China
| | - Bin Li
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an, China
| | - Qiyue Pang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China
| | - Yaoyu Lou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China
| | - Donghao Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.
| | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.
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Hu Y, Li Y, Zhu B, Huang W, Chen J, Wang F, Chen Y, Wang M, Lai H, Zhou Y. Genome-wide identification of the expansin gene family in netted melon and their transcriptional responses to fruit peel cracking. FRONTIERS IN PLANT SCIENCE 2024; 15:1332240. [PMID: 38322822 PMCID: PMC10846642 DOI: 10.3389/fpls.2024.1332240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Introduction Fruit cracking not only affects the appearance of netted melons (Cucumis melo L. var. reticulatus Naud.) but also decreases their marketability. Methods Herein, to comprehensively understand the role of expansin (EXP) proteins in netted melon, bioinformatics methods were employed to discover the EXP gene family in the melon genome and analyze its characteristic features. Furthermore, transcriptomics analysis was performed to determine the expression patterns of melon EXP (CmEXP) genes in crack-tolerant and crack-susceptible netted melon varieties. Discussion Thirty-three CmEXP genes were identified. Chromosomal location analysis revealed that CmEXP gene distribution was uneven on 12 chromosomes. In addition, phylogenetic tree analysis revealed that CmEXP genes could be categorized into four subgroups, among which the EXPA subgroup had the most members. The same subgroup members shared similar protein motifs and gene structures. Thirteen duplicate events were identified in the 33 CmEXP genes. Collinearity analysis revealed that the CmEXP genes had 50, 50, and 44 orthologous genes with EXP genes in cucumber, watermelon, and Arabidopsis, respectively. However, only nine orthologous EXP genes were observed in rice. Promoter cis-acting element analysis demonstrated that numerous cis-acting elements in the upstream promoter region of CmEXP genes participate in plant growth, development, and environmental stress responses. Transcriptomics analysis revealed 14 differentially expressed genes (DEGs) in the non-cracked fruit peels between the crack-tolerant variety 'Xizhoumi 17' (N17) and the crack-susceptible variety 'Xizhoumi 25' (N25). Among the 14 genes, 11 were upregulated, whereas the remaining three were downregulated in N17. In the non-cracked (N25) and cracked (C25) fruit peels of 'Xizhoumi 25', 24 DEGs were identified, and 4 of them were upregulated, whereas the remaining 20 were downregulated in N25. In the two datasets, only CmEXPB1 exhibited consistently upregulated expression, indicating its importance in the fruit peel crack resistance of netted melon. Transcription factor prediction revealed 56 potential transcription factors that regulate CmEXPB1 expression. Results Our study findings enrich the understanding of the CmEXP gene family and present candidate genes for the molecular breeding of fruit peel crack resistance of netted melon.
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Affiliation(s)
- Yanping Hu
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Yuxin Li
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Haikou, China
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Baibi Zhu
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Wenfeng Huang
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Jianjun Chen
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
| | - Feng Wang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
| | - Yisong Chen
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Min Wang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, Haikou, China
| | - Hanggui Lai
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Haikou, China
| | - Yang Zhou
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Haikou, China
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Faris Abdulkhadum Al-Mamoorı D, Celik Altunoglu Y, Horuz E, Özkan Kök B. Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses. Biol Futur 2023; 74:295-307. [PMID: 37642915 DOI: 10.1007/s42977-023-00176-1] [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: 10/27/2022] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.
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Affiliation(s)
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
| | - Erdoğan Horuz
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Büşra Özkan Kök
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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Yin Z, Zhou F, Chen Y, Wu H, Yin T. Genome-Wide Analysis of the Expansin Gene Family in Populus and Characterization of Expression Changes in Response to Phytohormone (Abscisic Acid) and Abiotic (Low-Temperature) Stresses. Int J Mol Sci 2023; 24:ijms24097759. [PMID: 37175464 PMCID: PMC10178758 DOI: 10.3390/ijms24097759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Expansins are a group of cell wall enzyme proteins that help to loosen cell walls by breaking hydrogen bonds between cellulose microfibrils and hemicellulose. Expansins are essential plant proteins that are involved in several key processes, including seed germination, the growth of pollen tubes and root hairs, fruit ripening and abscission processes. Currently, there is a lack of knowledge concerning the role of expansins in woody plants. In this study, we analyzed expansin genes using Populus genome as the study target. Thirty-six members of the expansin gene family were identified in Populus that were divided into four subfamilies (EXPA, EXPB, EXLA and EXLB). We analyzed the molecular structure, chromosome localization, evolutionary relationships and tissue specificity of these genes and investigated expression changes in responses to phytohormone and abiotic stresses of the expansin genes of Populus tremula L. (PtEXs). Molecular structure analysis revealed that each PtEX protein had several conserved motifs and all of the PtEXs genes had multiple exons. Chromosome structure analysis showed that the expansin gene family is distributed on 14 chromosomes. The PtEXs gene family expansion patterns showed segmental duplication. Transcriptome data of Populus revealed that 36 PtEXs genes were differently expressed in different tissues. Cis-element analysis showed that the PtEXs were closely associated with plant development and responses to phytohormone and abiotic stress. Quantitative real-time PCR showed that abscisic acid (ABA) and low-temperature treatment affected the expression of some PtEXs genes, suggesting that these genes are involved in responses to phytohormone and abiotic stress. This study provides a further understanding of the expansin gene family in Populus and forms a basis for future functional research studies.
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Affiliation(s)
- Zhihui Yin
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Fangwei Zhou
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yingnan Chen
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Huaitong Wu
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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Genome-Wide Identification and Expression Analysis of the CAD Gene Family in Walnut (Juglans regia L.). Biochem Genet 2022; 61:1065-1085. [DOI: 10.1007/s10528-022-10303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022]
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Overexpression of AcEXPA23 Promotes Lateral Root Development in Kiwifruit. Int J Mol Sci 2022; 23:ijms23148026. [PMID: 35887372 PMCID: PMC9317778 DOI: 10.3390/ijms23148026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022] Open
Abstract
Kiwifruit is loved by consumers for its unique taste and rich vitamin C content. Kiwifruit are very sensitive to adverse soil environments owing to fleshy and shallow roots, which limits the uptake of water and nutrients into the root system, resulting in low yield and poor fruit quality. Lateral roots are the key organs for plants to absorb water and nutrients. Improving water and fertilizer use efficiency by promoting lateral root development is a feasible method to improve yield and quality. Expansin proteins plays a major role in lateral root growth; hence, it is important to identify expansin protein family members, screen key genes, and explore gene function in root development. In this study, 41 expansin genes were identified based on the genome of kiwifruit (‘Hongyang’, Actinidia chinensis). By clustering with the Arabidopsis thaliana expansin protein family, the 41 AcExpansin proteins were divided into four subfamilies. The AcExpansin protein family was further analysed by bioinformatics methods and was shown to be evolutionarily diverse and conserved at the DNA and protein levels. Based on previous transcriptome data and quantitative real-time PCR assays, we screened the candidate gene AcEXPA23. Overexpression of AcEXPA23 in kiwifruit increased the number of kiwifruit lateral roots.
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Feng X, Li C, He F, Xu Y, Li L, Wang X, Chen Q, Li F. Genome-Wide Identification of Expansin Genes in Wild Soybean ( Glycine soja) and Functional Characterization of Expansin B1 ( GsEXPB1) in Soybean Hair Root. Int J Mol Sci 2022; 23:5407. [PMID: 35628217 PMCID: PMC9140629 DOI: 10.3390/ijms23105407] [Citation(s) in RCA: 9] [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: 04/19/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Wild soybean, the progenitor and close relative of cultivated soybean, has an excellent environmental adaptation ability and abundant resistance genes. Expansins, as a class of cell wall relaxation proteins, have important functions in regulating plant growth and stress resistance. In the present study, we identified a total of 75 members of the expansin family on the basis of recent genomic data published for wild soybean. The predicted results of promoter elements structure showed that wild soybean expansin may be associated with plant hormones, stress responses, and growth. Basal transcriptome data of vegetative organs suggest that the transcription of expansin members has some organ specificity. Meanwhile, the transcripts of some members had strong responses to salt, low temperature and drought stress. We screened and obtained an expansin gene, GsEXPB1, which is transcribed specifically in roots and actively responds to salt stress. The results of A. tumefaciens transient transfection showed that this protein was localized in the cell wall of onion epidermal cells. We initially analyzed the function of GsEXPB1 by a soybean hairy root transformation assay and found that overexpression of GsEXPB1 significantly increased the number of hairy roots, root length, root weight, and the tolerance to salt stress. This research provides a foundation for subsequent studies of expansins in wild soybean.
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Affiliation(s)
- Xu Feng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Cuiting Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
| | - Fumeng He
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
| | - Yongqing Xu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
| | - Li Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
| | - Xue Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Fenglan Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (X.F.); (C.L.); (F.H.); (Y.X.); (L.L.); (X.W.)
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Genome-Wide Identification of the NAC Gene Family in Zanthoxylum bungeanum and Their Transcriptional Responses to Drought Stress. Int J Mol Sci 2022; 23:ijms23094769. [PMID: 35563160 PMCID: PMC9103986 DOI: 10.3390/ijms23094769] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the largest plant-specific TF families and play a pivotal role in adaptation to abiotic stresses. The genome-wide analysis of NAC TFs is still absent in Zanthoxylum bungeanum. Here, 109 ZbNAC proteins were identified from the Z. bungeanum genome and were classified into four groups with Arabidopsis NAC proteins. The 109 ZbNAC genes were unevenly distributed on 46 chromosomes and included 4 tandem duplication events and 17 segmental duplication events. Synteny analysis of six species pairs revealed the closely phylogenetic relationship between Z. bungeanum and C. sinensis. Twenty-four types of cis-elements were identified in the ZbNAC promoters and were classified into three types: abiotic stress, plant growth and development, and response to phytohormones. Co-expression network analysis of the ZbNACs revealed 10 hub genes, and their expression levels were validated by real-time quantitative polymerase chain reaction (qRT-PCR). Finally, ZbNAC007, ZbNAC018, ZbNAC047, ZbNAC072, and ZbNAC079 were considered the pivotal NAC genes for drought tolerance in Z. bungeanum. This study represented the first genome-wide analysis of the NAC family in Z. bungeanum, improving our understanding of NAC proteins and providing useful information for molecular breeding of Z. bungeanum.
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Genome-wide identification of expansin in Fragaria vesca and expression profiling analysis of the FvEXPs in different fruit development. Gene 2022; 814:146162. [PMID: 34995732 DOI: 10.1016/j.gene.2021.146162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022]
Abstract
Strawberry is a highly efficient and economical horticultural crop plant, and strawberry fruits are easy to soften after ripening and decay after harvest, which severely impacts the economic benefits. Expansins are plant cell-wall loosening proteins involved in the process of fruit softening, loosening cell walls and reducing fruit firmness. In this study, 35 FvEXPs genes were identified in the F. vesaca genome. These genes were divided into four subfamilies (27 FvEXPAs, 5 FvEXPBs, 1 FvEXLAs, and 2 FvEXLBs) and were unevenly distributed on 7 chromosomes. Gene structure and motif analysis showed the conserved structure and motif in same subgroup, however, the different motifs and structures may reveal functional divergence of multigene family members of FvEXPs in different developmental stages of fruits. The expression profiling by RNA-seq and qRT-PCR analysis revealed that the FvEXP genes have distinct expression patterns among different stages of strawberry development and ripening. Among them, 3 genes (FvEXPA9, FvEXPA12, and FvEXPA27) were highly expressed in the ripening stage, FvEXPA9 and FvEXPA12 were especially highly expressed in turning stage, whereas FvEXPA27 was especially highly expressed in red stage. Our study provides a better understanding of the FvEXP genes, which may benefit strawberry biotechnological breeding and genetic modification for improving fruit quality and delaying fruit softening.
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Li K, Ma B, Shen J, Zhao S, Ma X, Wang Z, Fan Y, Tang Q, Wei D. The evolution of the expansin gene family in Brassica species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:630-638. [PMID: 34479031 DOI: 10.1016/j.plaphy.2021.08.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Expansin gene (EXP) family plays important roles in plant growth and crop improvement. However, it has not been well studied in the Brassica genus that includes several important agricultural and horticultural crops. To get insight to the evolution and expansion of EXP family in Brassica, Brassica EXPs which are homologues of 35 known AtEXPs of Arabidopsis were comprehensively and systematically analyzed in the present study. In total, 340 Brassica EXPs were clustered into four groups that corresponded multiple alignment to four subfamilies of AtEXPs, with divergent conserved motifs and cis-acting elements among groups. To understand the expansion of EXP family, an integrated genomic block system was constructed among Arabidopsis and Brassica species based on 24 known ancestral karyotype blocks. Obvious gene loss, segmental duplication, tandem duplication and DNA sequence repeat events were found during the expansion of Brassica EXPs, of which the segmental duplication was possibly the major driving force. The divergence time was estimated in 1109 orthologs pairs of EXPs, revealing the divergence of Brassica EXPs from AtEXPs during ~30 MYA, and the divergence of EXPs among Brassica species during 13.50-17.94 MYA. Selective mode analysis revealed that the purifying selection was the major contributor to expansion of Brassica EXPs. This study provides new insights into the evolution and expansion of the EXP family in Brassica genus.
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Affiliation(s)
- Kui Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Jinjuan Shen
- Chongqing Yudongnan Academy of Agricultural Sciences, Fuling, 408000, China
| | - Sa Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Xiao Ma
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhimin Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yonghong Fan
- Chongqing Yudongnan Academy of Agricultural Sciences, Fuling, 408000, China
| | - Qinglin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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Mu Q, Li X, Luo J, Pan Q, Li Y, Gu T. Characterization of expansin genes and their transcriptional regulation by histone modifications in strawberry. PLANTA 2021; 254:21. [PMID: 34216276 DOI: 10.1007/s00425-021-03665-6] [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: 03/12/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
The possible candidate expansin genes, which may be important for strawberry fruit softening, have been identified in the diploid woodland strawberry Fragaria vesca and the octoploid cultivated strawberry Fragaria × ananassa and their transcriptional regulation by histone modifications has been studied. Softening process greatly affects fruit texture and shelf life. Expansins (EXPs) are a group of structural proteins participating in cell wall loosening, which break the hydrogen bonding between cellulose microfibrils and hemicelluloses. However, our knowledge on how EXP genes are regulated in fruit ripening, especially in non-climacteric fleshy fruits, is limited. Here, we have identified the EXP genes in both the octoploid cultivated strawberry (Fragaria × ananassa) and one of its diploid progenitor species, woodland strawberry (Fragaria vesca). We found that EXP proteins in F. × ananassa were structurally more divergent than the ones in F. vesca. Transcriptome data suggested that FaEXP88, FaEXP114, FveEXP11 and FveEXP33 were the four candidate EXP genes more likely involved in fruit softening, whose transcript levels dramatically increased when firmness decreased during fruit maturation. Phylogenetic analyses showed that those candidate genes were closely clustered, indicating the presence of homoeolog expression dominance in the EXP gene family in strawberry. Moreover, we have performed chromatin immunoprecipitation (ChIP) experiments to investigate the distribution of histone modifications along the promoters and genic regions of the EXP genes in F. vesca. ChIP data revealed that the transcript levels of EXP genes were highly correlated with the enrichment of H3K9/K14 acetylation and H3K27 tri-methylation. Collectively, this study identifies the key EXP genes involved in strawberry fruit softening and reveals a regulatory role of histone modifications in their transcriptional regulation, which would facilitate functional studies of the EXP genes in the ripening of non-climacteric fruits.
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Affiliation(s)
- Qin Mu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xianyang Li
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jianhua Luo
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qinwei Pan
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA.
| | - Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Jin KM, Zhuo RY, Xu D, Wang YJ, Fan HJ, Huang BY, Qiao GR. Genome-Wide Identification of the Expansin Gene Family and Its Potential Association with Drought Stress in Moso Bamboo. Int J Mol Sci 2020; 21:E9491. [PMID: 33327419 PMCID: PMC7764852 DOI: 10.3390/ijms21249491] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 01/09/2023] Open
Abstract
Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.
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Affiliation(s)
- Kang-Ming Jin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Ren-Ying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Dong Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yu-Jun Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Hui-Jin Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Bi-Yun Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Gui-Rong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (K.-M.J.); (R.-Y.Z.); (D.X.); (Y.-J.W.); (H.-J.F.); (B.-Y.H.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Genome-wide identification, characterization, and expression analysis of the expansin gene family in watermelon ( Citrullus lanatus). 3 Biotech 2020; 10:302. [PMID: 32550119 DOI: 10.1007/s13205-020-02293-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/07/2020] [Indexed: 10/24/2022] Open
Abstract
Expansins are plant cell-wall loosening proteins involved in cell enlargement, adaptive responses to environmental stimuli, and various developmental processes. Although expansins have been characterized in many plant species, little is reported on this family in watermelon. In this study, 30 expansin genes in the watermelon genome (ClEXPs) were identified. These genes which were divided into four subfamilies (7 ClEXLAs, 2 ClEXLBs, 18 ClEXPAs, and 3 ClEXPBs) are unevenly distribute on 10 of 11 watermelon chromosomes. Chromosome mapping suggested that tandem duplication events may have played important roles in the expanding of watermelon expansins. Gene structure and motif identification revealed that same subfamily and subgroup have conserved gene structure and motif. Detection of cis-acting elements revealed that ClEXPs gene promoter regions were enriched with light-responsive elements, hormone-responsive, environmental stress-related, and development-related elements. Expression patterns of ClEXPs were investigated by qRT-PCR. The results showed that expression patterns of 15 ClEXP genes differed in three tissues. Through our own and public RNA-seq analysis, we found that ClEXPs had different expression patterns in fruit flesh, fruit rind, and seed at various developmental stages, and most of ClEXPs were highly responsive to abiotic and biotic stresses. Remarkably, 7 ClEXPs (ClEXLA1, ClEXLA6, ClEXLB1, ClEXLB2, ClEXPA5, ClEXPA10, and ClEXPA16) exhibited positive response to at least three kinds of stresses, suggesting that they might play important roles in the crosstalk of stress signal pathways. The results of this study provide useful insights for the functional identification of expansin gene family in watermelon.
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Mayorga-Gómez A, Nambeesan SU. Temporal expression patterns of fruit-specific α- EXPANSINS during cell expansion in bell pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2020; 20:241. [PMID: 32466743 PMCID: PMC7254744 DOI: 10.1186/s12870-020-02452-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Expansins (EXPs) facilitate non-enzymatic cell wall loosening during several phases of plant growth and development including fruit growth, internode expansion, pollen tube growth, leaf and root development, and during abiotic stress responses. In this study, the spatial and temporal expression patterns of C. annuum α- EXPANSIN (CaEXPA) genes were characterized. Additionally, fruit-specific CaEXPA expression was correlated with the rate of cell expansion during bell pepper fruit development. RESULTS Spatial expression patterns revealed that CaEXPA13 was up-regulated in vegetative tissues and flowers, with the most abundant expression in mature leaves. Expression of CaEXPA4 was associated with stems and roots. CaEXPA3 was expressed abundantly in flower at anthesis suggesting a role for CaEXPA3 in flower development. Temporal expression analysis revealed that 9 out of the 21 genes were highly expressed during fruit development. Of these, expression of six genes, CaEXPA5, CaEXPA7, CaEXPA12, CaEXPA14 CaEXPA17 and CaEXPA19 were abundant 7 to 21 days after anthesis (DAA), whereas CaEXPA6 was strongly expressed between 14 and 28 DAA. Further, this study revealed that fruit growth and cell expansion occur throughout bell pepper development until ripening, with highest rates of fruit growth and cell expansion occurring between 7 and 14 DAA. The expression of CaEXPA14 and CaEXPA19 positively correlated with the rate of cell expansion, suggesting their role in post-mitotic cell expansion-mediated growth of the bell pepper fruit. In this study, a ripening specific EXP transcript, CaEXPA9 was identified, suggesting its role in cell wall disassembly during ripening. CONCLUSIONS This is the first genome-wide study of CaEXPA expression during fruit growth and development. Identification of fruit-specific EXPAs suggest their importance in facilitating cell expansion during growth and cell wall loosening during ripening in bell pepper. These EXPA genes could be important targets for future manipulation of fruit size and ripening characteristics.
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Affiliation(s)
- Andrés Mayorga-Gómez
- Department of Horticulture, University of Georgia, 120 Carlton Street, Athens, GA, 30602, USA
| | - Savithri U Nambeesan
- Department of Horticulture, University of Georgia, 120 Carlton Street, Athens, GA, 30602, USA.
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Lv LM, Zuo DY, Wang XF, Cheng HL, Zhang YP, Wang QL, Song GL, Ma ZY. Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton. BMC PLANT BIOLOGY 2020; 20:223. [PMID: 32429837 PMCID: PMC7236947 DOI: 10.1186/s12870-020-02362-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/24/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Expansins (EXPs), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family in cotton are still unknown. RESULTS In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum. These genes were classified into four subfamilies, including 67 GhEXPAs, 8 GhEXPBs, 6 GhEXLAs, and 12 GhEXLBs, and divided into 15 subgroups. The 93 expansin genes are distributed over 24 chromosomes, excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons, and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns among different stages of cotton fibre development. Among them, 3 genes (GhEXPA4o, GhEXPA1A, and GhEXPA8h) were highly expressed in the initiation stage, 9 genes (GhEXPA4a, GhEXPA13a, GhEXPA4f, GhEXPA4q, GhEXPA8f, GhEXPA2, GhEXPA8g, GhEXPA8a, and GhEXPA4n) had high expression during the fast elongation stage, and GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. CONCLUSIONS Our results provide a solid basis for further elucidation of the biological functions of expansin genes in relation to cotton fibre development and valuable genetic resources for future crop improvement.
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Affiliation(s)
- Li-Min Lv
- Hebei Research Base, State Key Laboratory of Cotton Biology in China, Hebei Agricultural University, Baoding, 071001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China
| | - Dong-Yun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China
| | - Xing-Fen Wang
- Hebei Research Base, State Key Laboratory of Cotton Biology in China, Hebei Agricultural University, Baoding, 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Hai-Liang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China
| | - You-Ping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China
| | - Qiao-Lian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China
| | - Guo-Li Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Zhi-Ying Ma
- Hebei Research Base, State Key Laboratory of Cotton Biology in China, Hebei Agricultural University, Baoding, 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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Liu W, Lyu T, Xu L, Hu Z, Xiong X, Liu T, Cao J. Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica. Int J Mol Sci 2020; 21:ijms21103424. [PMID: 32408673 PMCID: PMC7279145 DOI: 10.3390/ijms21103424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.
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Affiliation(s)
- Weimiao Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Liai Xu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Ziwei Hu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Tingting Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-571-8898-2597
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20
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Hepler NK, Bowman A, Carey RE, Cosgrove DJ. Expansin gene loss is a common occurrence during adaptation to an aquatic environment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:666-680. [PMID: 31627246 DOI: 10.1111/tpj.14572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 05/15/2023]
Abstract
Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.
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Affiliation(s)
- Nathan K Hepler
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Alexa Bowman
- Program in Biochemistry and Molecular Biology, Lebanon Valley College, 101 N. College Ave., Annville, PA, 17003, USA
| | - Robert E Carey
- Department of Biology, Lebanon Valley College, 101 N. College Ave., Annville, PA, 17003, USA
| | - Daniel J Cosgrove
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
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Hou L, Zhang Z, Dou S, Zhang Y, Pang X, Li Y. Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.). PLANTA 2019; 249:815-829. [PMID: 30411169 DOI: 10.1007/s00425-018-3020-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/23/2018] [Indexed: 05/10/2023]
Abstract
Main conclusion 30 expansin genes were identified in the jujube genome. Phylogenetic analysis classified expansins into 17 subgroups. Closely related expansins share a conserved gene structure. ZjEXPs had different expression patterns in different tissues. Plant-specific expansins were first discovered as pH-dependent cell-wall-loosening proteins involved in diverse physiological processes. No comprehensive analysis of the expansin gene family has yet been carried out at the whole genome level in Chinese jujube (Ziziphus jujuba Mill.). In this study, 30 expansin genes were identified in the jujube genome. These genes, which were distributed with varying densities across 10 of the 12 jujube chromosomes, could be divided into four subfamilies: 19 ZjEXPAs, 3 ZjEXPBs, 1 ZjEXLA, and 7 ZjEXLBs. Phylogenetic analysis of expansin genes in Arabidopsis, rice, apple, grape, and jujube classified these genes into 17 subgroups. Members of the same subfamily and subgroup shared conserved gene structure and motif compositions. Homology analysis identified 20 homologous gene pairs between jujube and Arabidopsis. Further analysis of ZjEXP gene promoter regions uncovered various growth, development and stress-responsive cis-acting elements. Expression analysis and transcript profiling revealed that ZjEXPs had different expression patterns in different tissues at various developmental stages. ZjEXPA4 and ZjEXPA6 were highly expressed in young fruits, ZjEXPA3 and ZjEXPA5 were significantly expressed in flowers, and ZjEXPA7 was specifically expressed in young leaves. The results of this study, the first systematic analysis of the jujube expansin gene family, can serve as a strong foundation for further elucidation of the physiological functions and biological roles of jujube expansin genes.
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Affiliation(s)
- Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Suhan Dou
- Henan Longyuan Flowers &Trees Co., Ltd., Xuchang, 461000, China
| | - Yadong Zhang
- Henan Longyuan Flowers &Trees Co., Ltd., Xuchang, 461000, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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22
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Guimaraes LA, Mota APZ, Araujo ACG, de Alencar Figueiredo LF, Pereira BM, de Passos Saraiva MA, Silva RB, Danchin EGJ, Guimaraes PM, Brasileiro ACM. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene. PLANT MOLECULAR BIOLOGY 2017; 94:79-96. [PMID: 28243841 PMCID: PMC5437183 DOI: 10.1007/s11103-017-0594-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/13/2017] [Indexed: 05/08/2023]
Abstract
Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.
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Affiliation(s)
- Larissa Arrais Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Ana Paula Zotta Mota
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Claudia Guerra Araujo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | | | - Bruna Medeiros Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | - Raquel Bispo Silva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRA, University of Nice Sophia Antipolis, CNRS, 06900, Sophia Antipolis, France
| | - Patricia Messenberg Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
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Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ. Application of Genomic Technologies to the Breeding of Trees. Front Genet 2016; 7:198. [PMID: 27895664 PMCID: PMC5109026 DOI: 10.3389/fgene.2016.00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022] Open
Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
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Affiliation(s)
- Maria L Badenes
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - Angel Fernández I Martí
- Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain
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24
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Xu R, Liu C, Li N, Zhang S. Global identification and expression analysis of stress-responsive genes of the Argonaute family in apple. Mol Genet Genomics 2016; 291:2015-2030. [PMID: 27475441 DOI: 10.1007/s00438-016-1236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/27/2016] [Indexed: 11/26/2022]
Abstract
Argonaute (AGO) proteins, which are found in yeast, animals, and plants, are the core molecules of the RNA-induced silencing complex. These proteins play important roles in plant growth, development, and responses to biotic stresses. The complete analysis and classification of the AGO gene family have been recently reported in different plants. Nevertheless, systematic analysis and expression profiling of these genes have not been performed in apple (Malus domestica). Approximately 15 AGO genes were identified in the apple genome. The phylogenetic tree, chromosome location, conserved protein motifs, gene structure, and expression of the AGO gene family in apple were analyzed for gene prediction. All AGO genes were phylogenetically clustered into four groups (i.e., AGO1, AGO4, MEL1/AGO5, and ZIPPY/AGO7) with the AGO genes of Arabidopsis. These groups of the AGO gene family were statistically analyzed and compared among 31 plant species. The predicted apple AGO genes are distributed across nine chromosomes at different densities and include three segment duplications. Expression studies indicated that 15 AGO genes exhibit different expression patterns in at least one of the tissues tested. Additionally, analysis of gene expression levels indicated that the genes are mostly involved in responses to NaCl, PEG, heat, and low-temperature stresses. Hence, several candidate AGO genes are involved in different aspects of physiological and developmental processes and may play an important role in abiotic stress responses in apple. To the best of our knowledge, this study is the first to report a comprehensive analysis of the apple AGO gene family. Our results provide useful information to understand the classification and putative functions of these proteins, especially for gene members that may play important roles in abiotic stress responses in M. hupehensis.
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Affiliation(s)
- Ruirui Xu
- Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, China.
| | - Caiyun Liu
- Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, China
| | - Ning Li
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Technology, Shandong Agricultural University, 61# Daizong Street, Tai'an, Shandong, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Technology, Shandong Agricultural University, 61# Daizong Street, Tai'an, Shandong, 271018, China.
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25
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Ding A, Marowa P, Kong Y. Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum). Mol Genet Genomics 2016; 291:1891-907. [PMID: 27329217 DOI: 10.1007/s00438-016-1226-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022]
Abstract
Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants' ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.
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Affiliation(s)
- Anming Ding
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China
| | - Prince Marowa
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China
| | - Yingzhen Kong
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China.
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26
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Dheilly E, Gall SL, Guillou MC, Renou JP, Bonnin E, Orsel M, Lahaye M. Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes. BMC PLANT BIOLOGY 2016; 16:201. [PMID: 27630120 PMCID: PMC5024441 DOI: 10.1186/s12870-016-0887-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/01/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Fruit quality depends on a series of biochemical events that modify appearance, flavour and texture throughout fruit development and ripening. Cell wall polysaccharide remodelling largely contributes to the elaboration of fleshy fruit texture. Although several genes and enzymes involved in cell wall polysaccharide biosynthesis and modifications are known, their coordinated activity in these processes is yet to be discovered. RESULTS Combined transcriptomic and biochemical analyses allowed the identification of putative enzymes and related annotated members of gene families involved in cell wall polysaccharide composition and structural changes during apple fruit growth and ripening. The early development genes were mainly related to cell wall biosynthesis and degradation with a particular target on hemicelluloses. Fine structural evolutions of galactoglucomannan were strongly correlated with mannan synthase, glucanase (GH9) and β-galactosidase gene expression. In contrast, fewer genes related to pectin metabolism and cell expansion (expansin genes) were observed in ripening fruit combined with expected changes in cell wall polysaccharide composition. CONCLUSIONS Hemicelluloses undergo major structural changes particularly during early fruit development. The high number of early expressed β-galactosidase genes questions their function on galactosylated structures during fruit development and storage. Their activity and cell wall substrate remains to be identified. Moreover, new insights into the potential role of peroxidases and transporters, along with cell wall metabolism open the way to further studies on concomitant mechanisms involved in cell wall assembly/disassembly during fruit development and storage.
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Affiliation(s)
- Emmanuelle Dheilly
- INRA UR 1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Sophie Le Gall
- INRA UR 1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Marie-Charlotte Guillou
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Jean-Pierre Renou
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Estelle Bonnin
- INRA UR 1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Mathilde Orsel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Marc Lahaye
- INRA UR 1268 Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
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27
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Li N, Pu Y, Gong Y, Yu Y, Ding H. Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0446-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Seader VH, Thornsberry JM, Carey RE. Utility of the Amborella trichopoda expansin superfamily in elucidating the history of angiosperm expansins. JOURNAL OF PLANT RESEARCH 2016; 129:199-207. [PMID: 26646380 DOI: 10.1007/s10265-015-0772-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/29/2015] [Indexed: 05/15/2023]
Abstract
Expansins form a superfamily of plant proteins that assist in cell wall loosening during growth and development. The superfamily is divided into four families: EXPA, EXPB, EXLA, and EXLB (Sampedro and Cosgrove in Genome Biol 6:242, 2005. doi: 10.1186/gb-2005-6-12-242 ). Previous studies on Arabidopsis, rice, and Populus trichocarpa have clarified the evolutionary history of expansins in angiosperms (Sampedro et al. in Plant J 44:409-419, 2005. doi: 10.1111/j.1365-313X.2005.02540.x ). Amborella trichopoda is a flowering plant that diverged very early. Thus, it is a sister lineage to all other extant angiosperms (Amborella Genome Project in 342:1241089, 2013. doi: 10.1126/science.1241089 ). Because of this relationship, comparing the A. trichopoda expansin superfamily with those of other flowering plants may indicate which expansin genes were present in the last common ancestor of all angiosperms. The A. trichopoda expansin superfamily was assembled using BLAST searches with angiosperm expansin queries. The search results were analyzed and annotated to isolate the complete A. trichopoda expansin superfamily. This superfamily is similar to other angiosperm expansin superfamilies, but is somewhat smaller. This is likely because of a lack of genome duplication events (Amborella Genome Project 2013). Phylogenetic and syntenic analyses of A. trichopoda expansins have improved our understanding of the evolutionary history of expansins in angiosperms. Nearly all of the A. trichopoda expansins were placed into an existing Arabidopsis-rice expansin clade. Based on the results of phylogenetic and syntenic analyses, we estimate there were 12-13 EXPA genes, 2 EXPB genes, 1 EXLA gene, and 2 EXLB genes in the last common ancestor of all angiosperms.
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Affiliation(s)
- Victoria H Seader
- Program in Biochemistry and Molecular Biology, Lebanon Valley College, Annville, PA, 17003-1400, USA
| | - Jennifer M Thornsberry
- Department of Biology, Lebanon Valley College, 101 N. College Ave, Annville, PA, 17003-1400, USA
| | - Robert E Carey
- Department of Biology, Lebanon Valley College, 101 N. College Ave, Annville, PA, 17003-1400, USA.
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29
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Characterization and expression analysis of the expansin gene NnEXPA1 in lotus Nelumbo nucifera. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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30
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Cosgrove DJ. Plant expansins: diversity and interactions with plant cell walls. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:162-72. [PMID: 26057089 PMCID: PMC4532548 DOI: 10.1016/j.pbi.2015.05.014] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/11/2015] [Accepted: 05/15/2015] [Indexed: 05/18/2023]
Abstract
Expansins were discovered two decades ago as cell wall proteins that mediate acid-induced growth by catalyzing loosening of plant cell walls without lysis of wall polymers. In the interim our understanding of expansins has gotten more complex through bioinformatic analysis of expansin distribution and evolution, as well as through expression analysis, dissection of the upstream transcription factors regulating expression, and identification of additional classes of expansin by sequence and structural similarities. Molecular analyses of expansins from bacteria have identified residues essential for wall loosening activity and clarified the bifunctional nature of expansin binding to complex cell walls. Transgenic modulation of expansin expression modifies growth and stress physiology of plants, but not always in predictable or even understandable ways.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA.
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31
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Flaishman MA, Peles Y, Dahan Y, Milo-Cochavi S, Frieman A, Naor A. Differential response of cell-cycle and cell-expansion regulators to heat stress in apple (Malus domestica) fruitlets. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:82-94. [PMID: 25711816 DOI: 10.1016/j.plantsci.2015.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Temperature is one of the most significant factors affecting physiological and biochemical aspects of fruit development. Current and progressing global warming is expected to change climate in the traditional deciduous fruit tree cultivation regions. In this study, 'Golden Delicious' trees, grown in a controlled environment or commercial orchard, were exposed to different periods of heat treatment. Early fruitlet development was documented by evaluating cell number, cell size and fruit diameter for 5-70 days after full bloom. Normal activities of molecular developmental and growth processes in apple fruitlets were disrupted under daytime air temperatures of 29°C and higher as a result of significant temporary declines in cell-production and cell-expansion rates, respectively. Expression screening of selected cell cycle and cell expansion genes revealed the influence of high temperature on genetic regulation of apple fruitlet development. Several core cell-cycle and cell-expansion genes were differentially expressed under high temperatures. While expression levels of B-type cyclin-dependent kinases and A- and B-type cyclins declined moderately in response to elevated temperatures, expression of several cell-cycle inhibitors, such as Mdwee1, Mdrbr and Mdkrps was sharply enhanced as the temperature rose, blocking the cell-cycle cascade at the G1/S and G2/M transition points. Moreover, expression of several expansin genes was associated with high temperatures, making them potentially useful as molecular platforms to enhance cell-expansion processes under high-temperature regimes. Understanding the molecular mechanisms of heat tolerance associated with genes controlling cell cycle and cell expansion may lead to the development of novel strategies for improving apple fruit productivity under global warming.
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Affiliation(s)
- Moshe A Flaishman
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel.
| | - Yuval Peles
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
| | - Yardena Dahan
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel.
| | - Shira Milo-Cochavi
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
| | - Aviad Frieman
- Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel.
| | - Amos Naor
- The Golan Research Institute, University of Haifa, P.O. Box 97, Kazrin 12900, Israel.
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