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Wei X, Yuan M, Zheng BQ, Zhou L, Wang Y. Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development. FRONTIERS IN PLANT SCIENCE 2024; 15:1352119. [PMID: 38375086 PMCID: PMC10875090 DOI: 10.3389/fpls.2024.1352119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of TCP genes in Dendrobium nobile, a crucial parent in genetic breeding and an excellent model material to explore perianth development in Dendrobium, has not been conducted. We identified 23 DnTCP genes unevenly distributed across 19 chromosomes and classified them as Class I PCF (12 members), Class II: CIN (10 members), and CYC/TB1 (1 member) based on the conserved domain and phylogenetic analysis. Most DnTCPs in the same subclade had similar gene and motif structures. Segmental duplication was the predominant duplication event for TCP genes, and no tandem duplication was observed. Seven genes in the CIN subclade had potential miR319 and -159 target sites. Cis-acting element analysis showed that most DnTCP genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 DnTCP genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, DnTCP4 and DnTCP18 play a role in early perianth development, and DnTCP5 and DnTCP10 are significantly expressed during late perianth development. DnTCP17, 20, 21, and 22 are the most likely to be involved in perianth and leaf development. DnTCP11 was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most DnTCP genes putative promoters, and two Class I DnTCPs were in the nucleus and interacted with each other or with the MADS-box. The interactions between TCP and the MADS-box have been described for the first time in orchids, which broadens our understanding of the regulatory network of TCP involved in perianth development in orchids.
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Affiliation(s)
| | | | | | | | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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2
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Liu C, Lv T, Shen Y, Liu T, Liu M, Hu J, Liu S, Jiang Y, Zhang M, Zhao M, Wang K, Wang Y. Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng. BMC PLANT BIOLOGY 2024; 24:47. [PMID: 38216888 PMCID: PMC10787463 DOI: 10.1186/s12870-024-04729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Panax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.
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Affiliation(s)
- Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Tingting Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Yanhua Shen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Tao Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
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Zhang S, Han Y, Zeng Q, Wang C, Wang H, Zhang J, Cai M, Lu J, Chen T. Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum. Antioxidants (Basel) 2024; 13:94. [PMID: 38247518 PMCID: PMC10812421 DOI: 10.3390/antiox13010094] [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: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
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Huang Y, Zhao X, Zheng Q, He X, Zhang MM, Ke S, Li Y, Zhang C, Ahmad S, Lan S, Liu ZJ. Genome-Wide Identification of TCP Gene Family in Dendrobium and Their Expression Patterns in Dendrobium chrysotoxum. Int J Mol Sci 2023; 24:14320. [PMID: 37762622 PMCID: PMC10531990 DOI: 10.3390/ijms241814320] [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: 08/16/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The TCP gene family are plant-specific transcription factors that play important roles in plant growth and development. Dendrobium chrysotoxum, D. nobile, and D. huoshanense are orchids with a high ornamental value, but few studies have investigated the specific functions of TCPs in Dendrobium flower development. In this study, we used these three Dendrobium species to analyze TCPs, examining their physicochemical properties, phylogenetic relationships, gene structures, and expression profiles. A total of 50 TCPs were identified across three Dendrobium species; they were divided into two clades-Class-I (PCF subfamily) and Class-II (CIN and CYC/TB1 subfamilies)-based on their phylogenetic relationships. Our sequence logo analysis showed that almost all Dendrobium TCPs contain a conserved TCP domain, as well as the existence of fewer exons, and the cis-regulatory elements of the TCPs were mostly related to light response. In addition, our transcriptomic data and qRT-PCR results showed that DchTCP2 and DchTCP13 had a significant impact on lateral organs. Moreover, changes in the expression level of DchTCP4 suggested its important role in the phenotypic variation of floral organs. Therefore, this study provides a significant reference for the further exploration of TCP gene functions in the regulation of different floral organs in Dendrobium orchids.
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Affiliation(s)
- Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Xin He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (X.Z.); (Q.Z.); (X.H.); (M.-M.Z.); (S.K.); (Y.L.); (C.Z.); (S.A.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhang Z, Zhao Y, Chen Y, Li Y, Pan L, Wang S, Wang P, Fan S. Overexpression of TCP9-like gene enhances salt tolerance in transgenic soybean. PLoS One 2023; 18:e0288985. [PMID: 37494336 PMCID: PMC10370689 DOI: 10.1371/journal.pone.0288985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/08/2023] [Indexed: 07/28/2023] Open
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors are a plant-specific family and play roles in plant growth, development, and responses to biotic and abiotic stresses. However, little is known about the functions of the TCP transcription factors in the soybean cultivars with tolerance to salt stress. In this study, TCP9-like, a TCP transcription factor, was identified in the soybean cultivars exposed to salt stress. The expression of TCP9-like gene in the roots of salt-tolerant soybean cultivars was higher than that in salt-sensitive cultivars treated with NaCl. The overexpression of TCP9-like enhanced the salt tolerance of the salt-sensitive soybean cultivar 'DN50'. In T2 generation, the plants with TCP9-like overexpression had significantly lower Na+ accumulation and higher K+ accumulation than the WT plants exposed to 200 or 250 mmol/L NaCl. The K+/Na+ ratio in the plants overexpressing TCP9-like was significantly higher than that in WT plants treated with 200 mmol/L NaCl. Meanwhile, the overexpression of TCP9-like up-regulated the expression levels of GmNHX1, GmNHX3, GmSOS1, GmSOS2-like, and GmHKT1, which were involved in the K+/Na+ homeostasis pathway. The findings indicated that TCP9-like mediated the regulation of both Na+ and K+ accumulation to improve the tolerance of soybean to salt stress.
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Affiliation(s)
- Zhuo Zhang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Yuanling Zhao
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People's Republic of China
| | - Yifan Chen
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Yueming Li
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Lijun Pan
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Siyu Wang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Piwu Wang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
| | - Sujie Fan
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People's Republic of China
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Xiong W, Zhao Y, Gao H, Li Y, Tang W, Ma L, Yang G, Sun J. Genomic characterization and expression analysis of TCP transcription factors in Setaria italica and Setaria viridis. PLANT SIGNALING & BEHAVIOR 2022; 17:2075158. [PMID: 35616063 PMCID: PMC9154779 DOI: 10.1080/15592324.2022.2075158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific TCP transcription factor plays important roles in plant development and environment adaptation. Setaria italica and Setaria viridis, the C4 model plants, can grow on drought or arid soils. However, there is no systematic information about the genomic dissection and the expression of Setaria TCP genes. A total of 22 TCP genes were both identified from S. italica and S. viridis genomes. They all contained bHLH domain and were grouped into three main clades (PCF, CIN, and CYC/TB1). The TCP genes in the same clades shared similar gene structures. Cis-element in the TCP promoter regions were analyzed and associated with hormones and stress responsiveness. Ten TCP genes were predicted to be targets of miRNA319. Moreover, gene ontology analysis indicated three SiTCP and three SvTCP genes were involved in the regulation of shoot development, and SiTCP16/SvTCP16 were clustered together with tillering controlling gene TB1. The TCP genes were differentially expressed in the organs, but SiTCP/SvTCP orthologs shared similar expression patterns. Ten SiTCP members were downregulated under drought or salinity stresses, indicating they may play regulatory roles in abiotic stresses. The study provides detailed information regarding Setaria TCP genes, providing the theoretical basis for agricultural applications.
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Affiliation(s)
- Wangdan Xiong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yiran Zhao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hanchi Gao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yinghui Li
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Lichao Ma
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
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Liu DK, Zhang C, Zhao X, Ke S, Li Y, Zhang D, Zheng Q, Li MH, Lan S, Liu ZJ. Genome-wide analysis of the TCP gene family and their expression pattern in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2022; 13:1068969. [PMID: 36570938 PMCID: PMC9772009 DOI: 10.3389/fpls.2022.1068969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
TCP gene family are specific transcription factors for plant, and considered to play an important role in development and growth. However, few related studies investigated the TCP gene trait and how it plays a role in growth and development of Orchidaceae. In this study, we obtained 14 TCP genes (CgTCPs) from the Spring Orchid Cymbidium goeringii genome. The classification results showed that 14 CgTCPs were mainly divided into two clades as follows: four PCF genes (Class I), nine CIN genes and one CYC gene (Class II). The sequence analysis showed that the TCP proteins of C. goeringii contain four conserved regions (basic Helix-Loop-Helix) in the TCP domain. The exon-intron structure varied in the clade according to a comparative investigation of the gene structure, and some genes had no introns. There are fewer CgTCP homologous gene pairs compared with Dendrobium catenatum and Phalaenopsis equestris, suggesting that the TCP genes in C. goeringii suffered more loss events. The majority of the cis-elements revealed to be enriched in the function of light responsiveness, followed by MeJA and ABA responsiveness, demonstrating their functions in regulating by light and phytohormones. The collinearity study revealed that the TCPs in D. catenatum, P. equestris and C. goeringii almost 1:1. The transcriptomic data and real-time reverse transcription-quantitative PCR (RT-qPCR) expression profiles showed that the flower-specific expression of the TCP class II genes (CgCIN2, CgCIN5 and CgCIN6) may be related to the regulation of florescence. Altogether, this study provides a comprehensive analysis uncovering the underlying function of TCP genes in Orchidaceae.
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Affiliation(s)
- Ding-Kun Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-He Li
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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Genome-Wide Analysis of the WOX Transcription Factor Genes in Dendrobium catenatum Lindl. Genes (Basel) 2022; 13:genes13081481. [PMID: 36011392 PMCID: PMC9408443 DOI: 10.3390/genes13081481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
The WUSCHEL-related homeobox (WOX) proteins are a class of transcription factors exclusive to plants. They can promote cell division or inhibit stem cell differentiation to regulate plant growth and development. However, the WOX transcription factor genes in the monocotyledon Dendrobium catenatum Lindl. remain relatively uncharacterized. Specifically, the effects of phytohormones on their expression levels are unclear. In this study, we identified and analyzed 10 candidate DcaWOX transcription factor genes in D. catenatum. The DcaWOX family was divided into the modern/WUS, intermediate, and ancient clades. The subcellular localization analysis detected DcaWOX-GFP fusion proteins in the tobacco epidermal leaf cell nucleus. In DcaWOX, members of the WUS clade with the WUS-box motif can significantly activate the expression of TPL in vivo, while members of the intermediate and ancient clades cannot. The expression of the DcaWOX genes varied among the examined tissues. Moreover, the DcaWOX expression patterns were differentially affected by the phytohormone treatments, with differences detected even between homologs of the same gene. Furthermore, the gene expression patterns were consistent with the predicted cis-acting elements in the promoters. The above results suggest that DcaWOX may have an important role in its growth and development and resistance to stress. The results of this comprehensive investigation of the DcaWOX gene family provide the basis for future studies on the roles of WOX genes in D. catenatum.
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Jia R, Li C, Wang Y, Qin X, Meng L, Sun X. Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. Int J Mol Sci 2022; 23:ijms23042089. [PMID: 35216201 PMCID: PMC8877895 DOI: 10.3390/ijms23042089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In this study, a genome-wide analysis of LBD genes was performed in D. catenatum and 24 LBD genes were identified. The genes were classified into two classes (I and II) based on phylogenetic relationships and motif structure. Subcellular localization analysis for DcaLBD6 and DcaLBD18 from class I and DcaLBD37 and DcaLBD41 from class II revealed that the proteins were localized in the nucleus. Transient expression analysis of DcaLBD6, DcaLBD18, DcaLBD37, and DcaLBD41 indicated that class I and class II members have opposite roles in regulating VASCULAR-RELATED NAC-DOMAIN 7 (VND7) expression. DcaLBD genes showed diverse expression patterns in response to different phytohormone treatments. Heat maps revealed diverse patterns of DcaLBD gene expression in different organs. These results lay the foundation for further detailed studies of the LBD gene family in D. catenatum.
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Affiliation(s)
- Ru Jia
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Cheng Li
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Wang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangshi Qin
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Lihua Meng
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
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Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in Zea mays L. and Its Response to Heavy Metal Stresses. Int J Mol Sci 2022; 23:ijms23042109. [PMID: 35216220 PMCID: PMC8879807 DOI: 10.3390/ijms23042109] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter family is one of the largest eukaryotic protein families. Its members play roles in numerous metabolic processes in plants by releasing energy for substrate transport across membranes through hydrolysis of ATP. Maize belongs to the monocotyledonous plant family, Gramineae, and is one of the most important food crops in the world. We constructed a phylogenetic tree with individual ABC genes from maize, rice, sorghum, Arabidopsis, and poplar. This revealed eight families, each containing ABC genes from both monocotyledonous and dicotyledonous plants, indicating that the amplification events of ABC gene families predate the divergence of plant monocotyledons. To further understand the functions of ABC genes in maize growth and development, we analyzed the expression patterns of maize ABC family genes in eight tissues and organs based on the transcriptome database on the Genevestigator website. We identified 133 ABC genes expressed in most of the eight tissues and organs examined, especially during root and leaf development. Furthermore, transcriptome analysis of ZmABC genes showed that exposure to metallic lead induced differential expression of many maize ABC genes, mainly including ZmABC 012, 013, 015, 031, 040, 043, 065, 078, 080, 085, 088, 102, 107, 111, 130 and 131 genes, etc. These results indicated that ZmABC genes play an important role in the response to heavy metal stress. The comprehensive analysis of this study provides a foundation for further studies into the roles of ABC genes in maize.
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11
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Yang X, Chen Z, Yin X, Wang Y, Yang Y, Yang Y. Genome-Wide Survey Indicates Diverse Physiological Roles of Dendrobium officinale Calcium-Dependent Protein Kinase Genes. Int J Mol Sci 2022; 23:ijms23031298. [PMID: 35163223 PMCID: PMC8835911 DOI: 10.3390/ijms23031298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/03/2022] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are crucial calcium ions (Ca2+) sensors in plants with important roles in signal transduction, plant growth, development, and stress responses. Here, we identified 24 genes encoding CDPKs in Dendrobium officinale using genome-wide analysis. The phylogenetic analysis revealed that these genes formed four groups, with similar structures in the same group. The gene expression patterns following hormone treatments and yeast two-hybrid of homologous CDPK gene pairs with Rbohs showed differences, indicating functional divergence between homologous genes. In addition, the rapid accumulation of hydrogen peroxide (H2O2) and stomatal closure was observed in response to salicylic acid (SA)/jasmonic acid (JA) stress. Our data showed that CDPK9-2 and CDPK20-4 interacted with Rboh D and Rboh H, respectively, and were implicated in the generation of H2O2 and regulation of the stomatal aperture in response to salicylic acid/jasmonic acid treatment. We believe these results can provide a foundation for the functional divergence of homologous genes in D. officinale.
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Affiliation(s)
- Xingyu Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.Y.); (Z.C.); (X.Y.)
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Academy of Biological Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Chen
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.Y.); (Z.C.); (X.Y.)
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Academy of Biological Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yin
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.Y.); (Z.C.); (X.Y.)
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yuhua Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| | - Yunqiang Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.Y.); (Z.C.); (X.Y.)
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (Y.Y.); (Y.Y.)
| | - Yongping Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (X.Y.); (Z.C.); (X.Y.)
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (Y.Y.); (Y.Y.)
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12
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Song C, Ma J, Li G, Pan H, Zhu Y, Jin Q, Cai Y, Han B. Natural Composition and Biosynthetic Pathways of Alkaloids in Medicinal Dendrobium Species. FRONTIERS IN PLANT SCIENCE 2022; 13:850949. [PMID: 35599884 PMCID: PMC9121007 DOI: 10.3389/fpls.2022.850949] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/30/2022] [Indexed: 05/12/2023]
Abstract
Dendrobium is the second biggest genus in the Orchidaceae family, some of which have both ornamental and therapeutic values. Alkaloids are a group of active chemicals found in Dendrobium plants. Dendrobine has emerged specific pharmacological and therapeutic properties. Although Dendrobium alkaloids have been isolated and identified since the 1930s, the composition of alkaloids and their biosynthesis pathways, including metabolic intermediates, alkaloid transporters, concrete genes involved in downstream pathways, and associated gene clusters, have remained unresolved scientific issues. This paper comprehensively reviews currently identified and tentative alkaloids from the aspect of biogenic pathways or metabolic genes uncovered based on the genome annotations. The biosynthesis pathways of each class of alkaloids are highlighted. Moreover, advances of the high-throughput sequencing technologies in the discovery of Dendrobium alkaloid pathways have been addressed. Applications of synthetic biology in large-scale production of alkaloids are also described. This would serve as the basis for further investigation into Dendrobium alkaloids.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an, China
| | - Jingbo Ma
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Guohui Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Haoyu Pan
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yanfang Zhu
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Qing Jin
- College of Life Sciences, Anhui Agricultural University, Hefei, China
- *Correspondence: Qing Jin,
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei, China
- Yongping Cai,
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an, China
- Bangxing Han,
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