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Zhang Y, Peng Y, Zhang H, Gao Q, Song F, Cui X, Mo F. Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times. Genes (Basel) 2024; 15:911. [PMID: 39062690 PMCID: PMC11276291 DOI: 10.3390/genes15070911] [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: 05/31/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yujiao Peng
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Huixin Zhang
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Qiuyu Gao
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Fangfei Song
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Xueyu Cui
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Fulei Mo
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
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Qin S, Wei G, Lin Q, Tang D, Li C, Tan Z, Yao L, Huang L, Wei F, Liang Y. Analysis of the Spatholobus suberectus full-length transcriptome identified an R2R3-MYB transcription factor-encoding gene SsMYB158 that regulates flavonoid biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108929. [PMID: 39002304 DOI: 10.1016/j.plaphy.2024.108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/14/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Spatholobus suberectus Dunn (Leguminosae) has been used for medicinal purposes for a long period. Flavonoids are the major bioactive components of S. suberectus. However, there is still limited knowledge of the exact method via which transcription factors (TFs) regulate flavonoid biosynthesis. The full-length transcriptome of S. suberectus was analyzed using SMRT sequencing; 61,548 transcripts were identified, including 12,311 new gene loci, 53,336 novel transcripts, 44,636 simple sequence repeats, 36,414 complete coding sequences, 871 long non-coding RNAs and 6781 TFs. The SsMYB158 TF, which is associated with flavonoid biosynthesis, belongs to the R2R3-MYB class and is localized subcellularly to the nucleus. The overexpression of SsMYB158 in Nicotiana benthamiana and the transient overexpression of SsMYB158 in S. suberectus resulted in a substantial enhancement in both flavonoids and catechin levels. In addition, there was a remarkable upregulation in the expression of essential enzyme-coding genes associated with the flavonoid biosynthesis pathways. Our study revealed SsMYB158 as a critical regulator of flavonoid biosynthesis in S. suberectus and laying the foundation for its molecular breeding.
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Affiliation(s)
- Shuangshuang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Guili Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Quan Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Cui Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhien Tan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lixiang Yao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lirong Huang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
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Li J, Guo S, Min Htwe Y, Sun X, Zhou L, Wang F, Zeng C, Chen S, Iqbal A, Yang Y. Genome-wide identification, classification and expression analysis of MYB gene family in coconut ( Cocos nucifera L.). FRONTIERS IN PLANT SCIENCE 2024; 14:1263595. [PMID: 38288415 PMCID: PMC10822967 DOI: 10.3389/fpls.2023.1263595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.
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Affiliation(s)
- Jing Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shukuan Guo
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Yin Min Htwe
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Xiwei Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Fangyuan Wang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Chunru Zeng
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
| | - Shuangyan Chen
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- School of Tropical Crops, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Amjad Iqbal
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
- Department of Food Science & Technology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, China
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