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Li J, Sun H, Wang Y, Fan D, Zhu Q, Zhang J, Zhong K, Yang H, Chang W, Cao S. Genome-Wide Identification, Characterization, and Expression Analysis of the BES1 Family Genes under Abiotic Stresses in Phoebe bournei. Int J Mol Sci 2024; 25:3072. [PMID: 38474317 DOI: 10.3390/ijms25053072] [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: 01/27/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
The BRI1 EMS suppressor 1(BES1) transcription factor is a crucial regulator in the signaling pathway of Brassinosteroid (BR) and plays an important role in plant growth and response to abiotic stress. Although the identification and functional validation of BES1 genes have been extensively explored in various plant species, the understanding of their role in woody plants-particularly the endangered species Phoebe bournei (Hemsl.) Yang-remains limited. In this study, we identified nine members of the BES1 gene family in the genome of P. bournei; these nine members were unevenly distributed across four chromosomes. In our further evolutionary analysis of PbBES1, we discovered that PbBES1 can be divided into three subfamilies (Class I, Class II, and Class IV) based on the evolutionary tree constructed with Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum. Each subfamily contains 2-5 PbBES1 genes. There were nine pairs of homologous BES1 genes in the synteny analysis of PbBES1 and AtBES1. Three segmental replication events and one pair of tandem duplication events were present among the PbBES1 family members. Additionally, we conducted promoter cis-acting element analysis and discovered that PbBES1 contains binding sites for plant growth and development, cell cycle regulation, and response to abiotic stress. PbBES1.2 is highly expressed in root bark, stem bark, root xylem, and stem xylem. PbBES1.3 was expressed in five tissues. Moreover, we examined the expression profiles of five representative PbBES1 genes under heat and drought stress. These experiments preliminarily verified their responsiveness and functional roles in mediating responses to abiotic stress. This study provides important clues to elucidate the functional characteristics of the BES1 gene family, and at the same time provides new insights and valuable information for the regulation of resistance in P. bournei.
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Affiliation(s)
- Jingshu Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Honggang Sun
- Research Institute of Subtropical Forestry of Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yanhui Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dunjin Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qin Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiangyonghao Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Laboratory of Virtual Teaching and Research on Forest Therapy Specialty of Taiwan Strait, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Zhong
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hao Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiyin Chang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Laboratory of Virtual Teaching and Research on Forest Therapy Specialty of Taiwan Strait, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yu J, Yin K, Liu Y, Li Y, Zhang J, Han X, Tong Z. Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei. FRONTIERS IN PLANT SCIENCE 2024; 14:1297235. [PMID: 38259934 PMCID: PMC10800493 DOI: 10.3389/fpls.2023.1297235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Phoebe bournei is one of the main afforestation tree species in subtropical regions of China and is famous for its timber. Its distribution and growth are significantly impaired by water conditions. Thus, it is essential to understand the mechanism of the stress response in P. bournei. Here, we analyzed the phenotypic changes and transcriptomic rearrangement in the leaves and roots of P. bournei seedlings grown for 0 h, 1 h, 24 h, and 72 h under simulated drought conditions (10% PEG 6000). The results showed that drought stress inhibited plant photosynthesis and increased oxidoreductase activity and abscisic acid (ABA) accumulation. Spatio-temporal transcriptomic analysis identified 2836 and 3704 differentially expressed genes (DEGs) in leaves and roots, respectively. The responsive genes in different organs presented various expression profiles at different times. Gene co-expression network analysis identified two core transcription factors, TGA4 and APRR2, from two modules that showed a strong positive correlation with ABA accumulation. Our study investigated the different responses of aboveground and belowground organs of P. bournei to drought stress and provides critical information for improving the drought resistance of this timber species.
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Affiliation(s)
| | | | | | | | | | - Xiao Han
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Tang Y, Li J, Song Q, Cheng Q, Tan Q, Zhou Q, Nong Z, Lv P. Transcriptome and WGCNA reveal hub genes in sugarcane tiller seedlings in response to drought stress. Sci Rep 2023; 13:12823. [PMID: 37550374 PMCID: PMC10406934 DOI: 10.1038/s41598-023-40006-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023] Open
Abstract
Drought stress can severely affect sugarcane growth and yield. The objective of this research was to identify candidate genes in sugarcane tillering seedlings in response to drought stress. We performed a comparative phenotypic, physiological and transcriptomic analysis of tiller seedlings of drought-stressed and well-watered "Guire 2" sugarcane, in a time-course experiment (5 days, 9 days and 15 days). Physiological examination reviewed that SOD, proline, soluble sugars, and soluble proteins accumulated in large amounts in tiller seedlings under different intensities of drought stress, while MDA levels remained at a stable level, indicating that the accumulation of osmoregulatory substances and the enhancement of antioxidant enzyme activities helped to limit further damage caused by drought stress. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify genes and modules associated with sugarcane tillering seedlings in response to drought stress. Drought stress induced huge down-regulated in gene expression profiles, most of down-regulated genes were mainly associated with photosynthesis, sugar metabolism and fatty acid synthesis. We obtained four gene co-expression modules significantly associated with the physiological changes under drought stress (three modules positively correlated, one module negatively correlated), and found that LSG1-2, ERF1-2, SHKA, TIL, HSP18.1, HSP24.1, HSP16.1 and HSFA6A may play essential regulatory roles as hub genes in increasing SOD, Pro, soluble sugar or soluble protein contents. In addition, one module was found mostly involved in tiller stem diameter, among which members of the BHLH148 were important nodes. These results provide new insights into the mechanisms by which sugarcane tillering seedlings respond to drought stress.
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Affiliation(s)
- Yuwei Tang
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Jiahui Li
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China.
| | - Qiqi Song
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Qin Cheng
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Qinliang Tan
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Quanguang Zhou
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Zemei Nong
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
| | - Ping Lv
- Guangxi Subtropical Crops Research Institute, 22 Yongwu Road, Xingning District, Nanning, 530001, Guangxi Province, China
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Yin Z, Liao W, Li J, Pan J, Yang S, Chen S, Cao S. Genome-Wide Identification of GATA Family Genes in Phoebe bournei and Their Transcriptional Analysis under Abiotic Stresses. Int J Mol Sci 2023; 24:10342. [PMID: 37373489 DOI: 10.3390/ijms241210342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
GATA transcription factors are crucial proteins in regulating transcription and are characterized by a type-IV zinc finger DNA-binding domain. They play a significant role in the growth and development of plants. While the GATA family gene has been identified in several plant species, it has not yet been reported in Phoebe bournei. In this study, 22 GATA family genes were identified from the P. bournei genome, and their physicochemical properties, chromosomal distribution, subcellular localization, phylogenetic tree, conserved motif, gene structure, cis-regulatory elements in promoters, and expression in plant tissues were analyzed. Phylogenetic analysis showed that the PbGATAs were clearly divided into four subfamilies. They are unequally distributed across 11 out of 12 chromosomes, except chromosome 9. Promoter cis-elements are mostly involved in environmental stress and hormonal regulation. Further studies showed that PbGATA11 was localized to chloroplasts and expressed in five tissues, including the root bark, root xylem, stem bark, stem xylem, and leaf, which means that PbGATA11 may have a potential role in the regulation of chlorophyll synthesis. Finally, the expression profiles of four representative genes, PbGATA5, PbGATA12, PbGATA16, and PbGATA22, under drought, salinity, and temperature stress, were detected by qRT-PCR. The results showed that PbGATA5, PbGATA22, and PbGATA16 were significantly expressed under drought stress. PbGATA12 and PbGATA22 were significantly expressed after 8 h of low-temperature stress at 10 °C. This study concludes that the growth and development of the PbGATA family gene in P. bournei in coping with adversity stress are crucial. This study provides new ideas for studying the evolution of GATAs, provides useful information for future functional analysis of PbGATA genes, and helps better understand the abiotic stress response of P. bournei.
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Affiliation(s)
- Ziyuan Yin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingshu Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinxi Pan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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