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Bian L, Fahim AM, Wu J, Liu L, Pu Y, Ma L, Fang Y, Zhang D, Yang G, Wang W, Fan T, Yang X, Wang J, Shi Y, Sun W. Systematic Analysis of the BrHAT Gene Family and Physiological Characteristics of Brassica rapa L. Treated with Histone Acetylase and Deacetylase Inhibitors under Low Temperature. Int J Mol Sci 2024; 25:9200. [PMID: 39273148 PMCID: PMC11395008 DOI: 10.3390/ijms25179200] [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: 06/19/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Brassica rapa L. is an important overwintering oilseed crop in Northwest China. Histone acetyltransferases (HATs) play an important role in epigenetic regulation, as well as the regulation of plant growth, development, and responses to abiotic stresses. To clarify the role of histone acetylation in the low-temperature response of B. rapa L., we identified 29 HAT genes in B. rapa L. using bioinformatics tools. We also conducted a comprehensive analysis of the physicochemical properties, gene structure, chromosomal localization, conserved structural domains and motifs, cis-acting regulatory elements, and evolutionary relationships of these genes. Using transcriptome data, we analyzed the expression patterns of BrHAT family members and predicted interactions between proteins; the results indicated that BrHATs play an important role in the low-temperature response of B. rapa L. HAT inhibitor (curcumin; CUR) and histone deacetylase inhibitor (Trichostatin A; TSA) were applied to four B. rapa L. varieties varying in cold resistance under the same low-temperature conditions, and changes in the physiological indexes of these four varieties were analyzed. The inhibitor treatment attenuated the effect of low temperature on seed germination, and curcumin treatment was most effective, indicating that the germination period was primarily regulated by histone acetylase. Both inhibitor treatments increased the activity of protective enzymes and the content of osmoregulatory substances in plants, suggesting that histone acetylation and deacetylation play a significant role in the response of B. rapa L. to low-temperature stress. The qRT-PCR analyses showed that the expression patterns of BrHATs were altered under different inhibitor treatments and low-temperature stress; meanwhile, we found three significantly differentially expressed genes. In sum, the process of histone acetylation is involved in the cold response and the BrHATs gene plays a role in the cold stress response.
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Affiliation(s)
- Liang Bian
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Abbas Muhammad Fahim
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junyan Wu
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijun Liu
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Li Ma
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yan Fang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Dan Zhang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Gang Yang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wangtian Wang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tingting Fan
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiuguo Yang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jingyu Wang
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yangyang Shi
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wancang Sun
- State Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Gao C, Li Z, Zhang H, Li C, Sun H, Li S, Ma N, Qi X, Cui Y, Yang P, Hu T. Genome-Wide Identification and Characterization of the GASA Gene Family in Medicago truncatula, and Expression Patterns under Abiotic Stress and Hormone Treatments. PLANTS (BASEL, SWITZERLAND) 2024; 13:2364. [PMID: 39273848 PMCID: PMC11396804 DOI: 10.3390/plants13172364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/09/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Medicago truncatula is a key model plant for studying legume plants, particularly alfalfa (Medicago sativa), due to its well-defined genetic background. Plant-specific GASA (Gibberellic Acid Stimulated Arabidopsis) genes play various roles in plant growth and development, abiotic stress, and hormone responses. However, limited information is available on GASA research in Medicago. In this study, 26 MtGASAs were identified and analyzed for its structure, evolution, and expressions. Sequence alignments and phylogeny revealed that 26 MtGASAs containing conserved GASA domains were classified into three clades. The chromosomal locations and gene synteny revealed segmental and tandem repetition evolution. Analysis of cis-regulatory elements indicates that family members likely influence various hormone signaling pathways and stress-related mechanisms. Moreover, the RNA-seq and qRT-PCR analyses revealed that 26 MtGASAs were extensively involved in abiotic stresses and hormone responses. Notably, seven MtGASA genes (MtGASA1, 10, 12, 17, 23, 25 and 26) were all dramatically activated by NaCl and Mannitol treatments, and four MtGASAs (MtGASA7, 10, 23 and 24) were significant activated by GA3, PBZ, ABA, and MeJA treatments. Collectively, this study is the first to identify and describe GASA genes in Medicago on a genome-wide scale. The results establish a basis for functional characterization, showing that these proteins are essential in responding to various abiotic stresses and hormonal signals.
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Affiliation(s)
- Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhongxing Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hanwen Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chun Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiangyu Qi
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yilin Cui
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
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103
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Li J, Li M, Shen T, Guo Q, Zhang R, Chen Y, Zhang Y, Luo K. Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance. Int J Biol Macromol 2024; 279:134846. [PMID: 39179062 DOI: 10.1016/j.ijbiomac.2024.134846] [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: 05/27/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024]
Abstract
The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.
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Affiliation(s)
- Junyi Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Tiantian Shen
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province/Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Kai Luo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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104
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Yue J, Dai X, Li Q, Wei M. Genome-Wide Characterization of the BTB Gene Family in Poplar and Expression Analysis in Response to Hormones and Biotic/Abiotic Stresses. Int J Mol Sci 2024; 25:9048. [PMID: 39201733 PMCID: PMC11354360 DOI: 10.3390/ijms25169048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
The BTB (Broad-complex, tramtrack, and bric-a-brac) gene family, characterized by a highly conserved BTB domain, is implicated in a spectrum of biological processes, encompassing growth and development, as well as stress responses. Characterization and functional studies of BTB genes in poplar are still limited, especially regarding their response to hormones and biotic/abiotic stresses. In this study, we conducted an HMMER search in conjunction with BLASTp and identified 95 BTB gene models in Populus trichocarpa. Through domain motif and phylogenetic relationship analyses, these proteins were classified into eight families, NPH3, TAZ, Ankyrin, only BTB, BACK, Armadillo, TPR, and MATH. Collinearity analysis of poplar BTB genes with homologs in six other species elucidated evolutionary relationships and functional conservations. RNA-seq analysis of five tissues of poplar identified BTB genes as playing a pivotal role during developmental processes. Comprehensive RT-qPCR analysis of 11 BTB genes across leaves, roots, and xylem tissues revealed their responsive expression patterns under diverse hormonal and biotic/abiotic stress conditions, with varying degrees of regulation observed in the results. This study marks the first in-depth exploration of the BTB gene family in poplar, providing insights into the potential roles of BTB genes in hormonal regulation and response to stress.
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Affiliation(s)
- Jing Yue
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (J.Y.); (X.D.); (Q.L.)
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (J.Y.); (X.D.); (Q.L.)
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (J.Y.); (X.D.); (Q.L.)
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Mingke Wei
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
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105
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Yu X, Huang Z, Cheng Y, Hu K, Zhou Y, Yao H, Shen J, Huang Y, Zhuang X, Cai Y. Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18507-18519. [PMID: 39113497 DOI: 10.1021/acs.jafc.4c03633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.
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Affiliation(s)
- Xiaosong Yu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Zhongchao Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yuanyuan Cheng
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Keyi Hu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yan Zhou
- Chengdu Lusyno Biotechnology Co., Ltd., Chengdu 610000, Sichuan, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 310000, Zhejiang, China
| | - Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
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106
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Lim H, Denison MIJ, Lee K, Natarajan S, Kim TL, Oh C. Genome-Wide Characterization of Glyceraldehyde-3-Phosphate Dehydrogenase Genes and Their Expression Profile under Drought Stress in Quercus rubra. PLANTS (BASEL, SWITZERLAND) 2024; 13:2312. [PMID: 39204748 PMCID: PMC11360533 DOI: 10.3390/plants13162312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is crucial in plant metabolism and responses to various abiotic stresses. In the glycolysis pathway, glyceraldehyde-3-phosphate (G3P) is oxidized to 1,3-bisphosphate glycerate (1,3-BPG) through the catalytic action of GAPDH. However, the GAPDH gene family in Quercus rubra has been minimally researched. In this study, we identified 13 GAPDH-encoding genes in Q. rubra through a bioinformatics analysis of genomic data. Evolutionary studies suggest that these QrGAPDH genes are closely related to those in Glycine max and Triticum aestivum. We conducted a comprehensive whole-genome study, which included predictions of subcellular localization, gene structure analysis, protein motif identification, chromosomal placement, and analysis of cis-acting regions. We also examined the expression of GAPDH proteins and genes in various tissues of Q. rubra and under drought stress. The results indicated diverse expression patterns across different tissues and differential expression under drought conditions. Notably, the expression of Qurub.02G290300.1, Qurub.10G209800.1, and Qrub.M241600.1 significantly increased in the leaf, stem, and root tissues under drought stress. This study provides a systematic analysis of QrGAPDH genes, suggesting their pivotal roles in the drought stress response of trees.
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Affiliation(s)
- Hyemin Lim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (K.L.); (T.-L.K.); (C.O.)
| | | | - Kyungmi Lee
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (K.L.); (T.-L.K.); (C.O.)
| | | | - Tae-Lim Kim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (K.L.); (T.-L.K.); (C.O.)
| | - Changyoung Oh
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea; (K.L.); (T.-L.K.); (C.O.)
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107
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Zhang A, Shang J, Xiao K, Zhang M, Wang S, Zhu W, Wu X, Zha D. WRKY transcription factor 40 from eggplant (Solanum melongena L.) regulates ABA and salt stress responses. Sci Rep 2024; 14:19289. [PMID: 39164381 PMCID: PMC11335892 DOI: 10.1038/s41598-024-69670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Plants are affected by many environmental factors during their various stages of growth, among which salt stress is a key factor. WRKY transcription factors play important roles in the response to stress in plants. In this study, SmWRKY40 from eggplant (Solanum melongena L.) was found to belong to the subfamily of WRKY transcription factor group II, closely related to the evolution of wild tomato ScWRKY40 (Solanum chilense). The expression of SmWRKY40 could be induced by several abiotic stresses (drought, salt, and high temperature) and ABA to different degrees, with salt stress being the most significant. In Arabidopsis thaliana, the seed germination rate of SmWRKY40 overexpression seedlings was significantly higher than those of the wild type under high concentrations of NaCl and ABA, and root elongation of overexpression lines was also longer than wild type under NaCl treatments. SmWRKY40 overexpression lines were found to enhance Arabidopsis tolerance to salt with lower ROS, MDA, higher soluble protein, proline accumulation, and more active antioxidant enzymes. The expression level of genes related to stress and ABA signaling displayed significant differences in SmWRKY40 overexpression line than that of WT. These results indicate that SmWRKY40 regulates ABA and salt stress responses in Arabidopsis.
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Affiliation(s)
- Aidong Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jing Shang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Xiao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Min Zhang
- Horticultural Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345, Hubei, China
| | - Shengjie Wang
- Shanghai Qiande Seed Industry Co., Ltd, Shanghai, 200235, China
| | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xuexia Wu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
| | - Dingshi Zha
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
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108
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Rao R, Huang X, Wang X, Li X, Liao H, Abuduwaili N, Wei X, Li D, Huang G. Genome-wide identification and analysis of DEAD-box RNA helicases in Gossypium hirsutum. Gene 2024; 920:148495. [PMID: 38663690 DOI: 10.1016/j.gene.2024.148495] [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: 11/25/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
DEAD-box RNA helicases, a prominent subfamily within the RNA helicase superfamily 2 (SF2), play crucial roles in the growth, development, and abiotic stress responses of plants. This study identifies 146 DEAD-box RNA helicase genes (GhDEADs) and categorizes them into four Clades (Clade A-D) through phylogenetic analysis. Promoter analysis reveals cis-acting elements linked to plant responses to light, methyl jasmonate (MeJA), abscisic acid (ABA), low temperature, and drought. RNA-seq data demonstrate that Clade C GhDEADs exhibit elevated and ubiquitous expression across different tissues, validating their connection to leaf development through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Notably, over half of GhDEADs display up-regulation in the leaves of virus-induced gene silencing (VIGS) plants of GhVIR-A/D (members of m6A methyltransferase complex, which regulate leaf morphogenesis). In conclusion, this study offers a comprehensive insight into GhDEADs, emphasizing their potential involvement in leaf development.
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Affiliation(s)
- Ruotong Rao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Xiaoyu Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xinting Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuelong Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Huiping Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Nigara Abuduwaili
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Xiuzhen Wei
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Dengdi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Gengqing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China.
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109
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Li S, Xu J, Cao Y, Wu J, Liu Q, Zhang D. Genome-Wide Analyses of CCHC Family Genes and Their Expression Profiles under Drought Stress in Rose ( Rosa chinensis). Int J Mol Sci 2024; 25:8983. [PMID: 39201669 PMCID: PMC11354476 DOI: 10.3390/ijms25168983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
CCHC-type zinc finger proteins (CCHC-ZFPs), ubiquitous across plant species, are integral to their growth, development, hormonal regulation, and stress adaptation. Roses (Rosa sp.), as one of the most significant and extensively cultivated ornamentals, account for more than 30% of the global cut-flower market. Despite its significance, the CCHC gene family in roses (Rosa sp.) remains unexplored. This investigation identified and categorized 41 CCHC gene members located on seven chromosomes of rose into 14 subfamilies through motif distribution and phylogenetic analyses involving ten additional plant species, including Ginkgo biloba, Ostreococcus lucimarinus, Arabidopsis thaliana, and others. This study revealed that dispersed duplication likely plays a crucial role in the diversification of the CCHC genes, with the Ka/Ks ratio suggesting a history of strong purifying selection. Promoter analysis highlighted a rich presence of cis-acting regulatory elements linked to both abiotic and biotic stress responses. Differential expression analysis under drought conditions grouped the 41 CCHC gene members into five distinct clusters, with those in group 4 exhibiting pronounced regulation in roots and leaves under severe drought. Furthermore, virus-induced gene silencing (VIGS) of the RcCCHC25 member from group 4 compromised drought resilience in rose foliage. This comprehensive analysis lays the groundwork for further investigations into the functional dynamics of the CCHC gene family in rose physiology and stress responses.
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Affiliation(s)
- Shijie Li
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jun Xu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Yong Cao
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jie Wu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT 2601, Australia;
| | - Deqiang Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
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Cazares-Álvarez JE, Báez-Astorga PA, Arroyo-Becerra A, Maldonado-Mendoza IE. Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection. Genes (Basel) 2024; 15:1087. [PMID: 39202446 PMCID: PMC11353892 DOI: 10.3390/genes15081087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.
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Affiliation(s)
- Jesús Eduardo Cazares-Álvarez
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Paúl Alán Báez-Astorga
- CONAHCYT—Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico;
| | - Ignacio Eduardo Maldonado-Mendoza
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
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111
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Duan X, Tian D, Gao P, Sun Y, Peng X, Wen J, Xie H, Wang ZY, Chai M. Transcriptome-Wide Identification of Dark- and Salt-Induced Senescence-Related NAC Gene Family Members in Alfalfa. Int J Mol Sci 2024; 25:8908. [PMID: 39201594 PMCID: PMC11354459 DOI: 10.3390/ijms25168908] [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: 06/29/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Leaves are a key forage part for livestock, and the aging of leaves affects forage biomass and quality. Preventing or delaying premature leaf senescence leads to an increase in pasture biomass accumulation and an improvement in alfalfa quality. NAC transcription factors have been reported to affect plant growth and abiotic stress responses. In this study, 48 NAC genes potentially associated with leaf senescence were identified in alfalfa under dark or salt stress conditions. A phylogenetic analysis divided MsNACs into six subgroups based on similar gene structure and conserved motif. These MsNACs were unevenly distributed in 26 alfalfa chromosomes. The results of the collinearity analysis show that all of the MsNACs were involved in gene duplication. Some cis-acting elements related to hormones and stress were screened in the 2-kb promoter regions of MsNACs. Nine of the MsNAC genes were subjected to qRT-PCR to quantify their expression and Agrobacterium-mediated transient expression to verify their functions. The results indicate that Ms.gene031485, Ms.gene032313, Ms.gene08494, and Ms.gene77666 might be key NAC genes involved in alfalfa leaf senescence. Our findings extend the understanding of the regulatory function of MsNACs in leaf senescence.
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Affiliation(s)
- Xiangxue Duan
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Daicai Tian
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Peiran Gao
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Yue Sun
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaojing Peng
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Hongli Xie
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Zeng-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Maofeng Chai
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Yu J, Duan S, Shua Z, Li K, Xiang G, Baldwin TC, Lu Y, Liang Y. R2R3-MYB Gene Family in Coptis teeta Wall.: Genome-Wide Identification, Phylogeny, Evolutionary Expansion, and Expression Analyses during Floral Development. Int J Mol Sci 2024; 25:8902. [PMID: 39201588 PMCID: PMC11354770 DOI: 10.3390/ijms25168902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not been reported. Here, we describe the bioinformatic identification and characterization of 88 R2R3-MYB genes in this species, and the identification of members of the R2R3-MYB gene family in species within the order Ranales most closely related to Coptis teeta. The CteR2R3-MYB genes were shown to exhibit a higher degree of conservation compared to those of A. thaliana, as evidenced by phylogeny, conserved motifs, gene structure, and replication event analyses. Cis-acting element analysis confirmed the involvement of CteR2R3-MYB genes in a variety of developmental processes, including growth, cell differentiation, and reproduction mediated by hormone synthesis. In addition, through homology comparisons with the equivalent gene family in A. thaliana, protein regulatory network prediction and transcriptome data analysis of floral organs across three time periods of flower development, 17 candidate genes were shown to exhibit biased expression in two floral phenotypes of C. teeta. This suggests their potential involvement in floral development (anther development) in this species.
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Affiliation(s)
- Jichen Yu
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasm Innovation, Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.Y.); (K.L.); (G.X.)
| | - Shaofeng Duan
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasm Innovation, Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.Y.); (K.L.); (G.X.)
| | - Zhenyang Shua
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Kecheng Li
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasm Innovation, Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.Y.); (K.L.); (G.X.)
| | - Guisheng Xiang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasm Innovation, Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.Y.); (K.L.); (G.X.)
| | | | - Yingchun Lu
- College of Education and Vocational Education, Yunnan Agricultural University, Kunming 650201, China;
| | - Yanli Liang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasm Innovation, Utilization of Chinese Medicinal Materials in Southwest, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.Y.); (K.L.); (G.X.)
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Wang L, Zhao Z, Li H, Pei D, Ma Q, Huang Z, Wang H, Xiao L. Genome-Wide Identification and Molecular Evolutionary History of the Whirly Family Genes in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2024; 13:2243. [PMID: 39204679 PMCID: PMC11359715 DOI: 10.3390/plants13162243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Whirly transcription factors are unique to plants, playing pivotal roles in managing leaf senescence and DNA repair. While present in various species, their identification in Brassica napus L. (B. napus) and their differences during hybridization and polyploidy has been elusive. Addressing this, our study delves into the functional and evolutionary aspects of the Whirly gene family during the emergence of B. napus, applying bioinformatics and comparative genomics. We identified six Whirly genes in B. napus. In Brassica rapa L. (B. rapa), three Whirly genes were identified, while four were found in Brassica oleracea L. (B. oleracea). The results show that the identified Whirly genes not only have homology but also share the same chromosomal positions. Phylogenetic analysis indicates that Whirly genes in monocots and dicots exhibit high conservation. In the evolutionary process, the Whirly gene family in B. napus experienced events of intron/exon loss. Collinearity insights point to intense purifying selection post-duplication. Promoter regions housed diverse cis-acting elements linked to photoresponse, anaerobic initiation, and methyl jasmonate responsiveness. Notably, elements tied to abscisic acid signaling and meristem expression were prominent in diploid ancestors but subdued in tetraploid B. napus. Tissue-specific expression unveiled analogous patterns within subfamily genes. Subsequent qRT-PCR analysis spotlighted BnAWHY1b's potential significance in abiotic stress response, particularly drought. These findings can be used as theoretical foundations to understand the functions and effects of the Whirly gene family in B. napus, providing references for the molecular mechanism of gene evolution between this species and its diploid ancestors.
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Affiliation(s)
- Long Wang
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhi Zhao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Huaxin Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Damei Pei
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Qianru Ma
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Lu Xiao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
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114
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Wu H, Zhang R, Diao X. Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet ( Setaria italica). Int J Mol Sci 2024; 25:8804. [PMID: 39201492 PMCID: PMC11354513 DOI: 10.3390/ijms25168804] [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: 06/12/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 09/02/2024] Open
Abstract
The indeterminate domain proteins (IDD proteins) play essential roles in the growth and development of various plant tissues and organs across different developmental stages, but members of this gene family have not yet been characterized in foxtail millet (Setaria italica). To have a comprehensive understanding of the IDD gene family in foxtail millet, we performed a genome-wide characterization and haplotypic variation analysis of the IDD gene family in foxtail millet. In this study, sixteen IDD genes were identified across the reference genome of Yugu1, a foxtail millet cultivar. Phylogenetic analysis revealed that the Setaria italica IDD (SiIDD) proteins were clustered into four groups together with IDD proteins from Arabidopsis thaliana (dicot) and Oryza sativa (monocot). Conserved protein motif and gene structure analyses revealed that the closely clustered SiIDD genes were highly conserved within each subgroup. Furthermore, chromosomal location analysis showed that the SiIDD genes were unevenly distributed on nine chromosomes of foxtail millet and shared collinear relationships with IDD genes of other grass species. Transcriptional analysis revealed that the SiIDD genes differed greatly in their expression patterns, and paralogous genes shared similar expression patterns. In addition, superior haplotypes for two SiIDD genes (SiIDD8 and SiIDD14) were identified to correlate with traits of early heading date, and high thousand seed weight and molecular markers were designed for SiIDD8 and SiIDD14 to distinguish different haplotypes for breeding. Taken together, the results of this study provide useful information for further functional investigation of SiIDD genes, and the superior haplotypes of SiIDD8 and SiIDD14 will be particularly beneficial for improving heading date and yield of foxtail millet in breeding programs.
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Affiliation(s)
- Hongpo Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utlization of Ministry of Agriculture and Rural Affairs and State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.W.); (R.Z.)
| | - Renliang Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utlization of Ministry of Agriculture and Rural Affairs and State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.W.); (R.Z.)
| | - Xianmin Diao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utlization of Ministry of Agriculture and Rural Affairs and State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.W.); (R.Z.)
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453500, China
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115
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Huang W, Lin X, Li Z, Mai J, Hu M, Zhu H. Genome-Wide Identification and Expression Analysis of Growth-Regulating Factor Family in Sweet Potato and Its Two Relatives. Genes (Basel) 2024; 15:1064. [PMID: 39202424 PMCID: PMC11353427 DOI: 10.3390/genes15081064] [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: 06/18/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 09/03/2024] Open
Abstract
Growth-regulating factor (GRF) is a multi-gene family that plays an important role in plant growth and development and is widely present in plants. Currently, GRF gene members have been reported in many plants, but the GRF gene family has not been found in sweet potato. In this study, ten GRF genes were identified in sweet potato (Ipomoea batatas), twelve and twelve were identified in its two diploid relatives (Ipomoea trifida) and (Ipomoea triloba), which were unevenly distributed on nine different chromosomes. Subcellular localization analysis showed that GRF genes of sweet potato, I. trifida, and I. triloba were all located in the nucleus. The expression analysis showed that the expression of IbGRFs was diverse in different sweet potato parts, and most of the genes were upregulated and even had the highest expression in the vigorous growth buds. These findings provide molecular characterization of sweet potato and its two diploid relatives, the GRF families, further supporting functional characterization.
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Affiliation(s)
| | | | | | | | | | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (W.H.); (X.L.); (Z.L.); (J.M.); (M.H.)
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116
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Chen S, Qiu Y, Lin Y, Zou S, Wang H, Zhao H, Shen S, Wang Q, Wang Q, Du H, Li J, Qu C. Genome-Wide Identification of B-Box Family Genes and Their Potential Roles in Seed Development under Shading Conditions in Rapeseed. PLANTS (BASEL, SWITZERLAND) 2024; 13:2226. [PMID: 39204662 PMCID: PMC11359083 DOI: 10.3390/plants13162226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.
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Affiliation(s)
- Si Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yushan Qiu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yannong Lin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Songling Zou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Hailing Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Huiyan Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Shulin Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Qinghui Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Qiqi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Hai Du
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (S.C.); (Y.Q.); (Y.L.); (S.Z.); (H.W.); (H.Z.); (S.S.); (Q.W.); (Q.W.); (H.D.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Yang Y, Li Y, Jin L, Li P, Zhou Q, Sheng M, Ma X, Shoji T, Hao X, Kai G. A transcription factor of SHI family AaSHI1 activates artemisinin biosynthesis genes in Artemisia annua. BMC Genomics 2024; 25:776. [PMID: 39123103 PMCID: PMC11312704 DOI: 10.1186/s12864-024-10683-7] [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: 02/22/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Transcription factors (TFs) of plant-specific SHORT INTERNODES (SHI) family play a significant role in regulating development and metabolism in plants. In Artemisia annua, various TFs from different families have been discovered to regulate the accumulation of artemisinin. However, specific members of the SHI family in A. annua (AaSHIs) have not been identified to regulate the biosynthesis of artemisinin. RESULTS We found five AaSHI genes (AaSHI1 to AaSHI5) in the A. annua genome. The expression levels of AaSHI1, AaSHI2, AaSHI3 and AaSHI4 genes were higher in trichomes and young leaves, also induced by light and decreased when the plants were subjected to dark treatment. The expression pattern of these four AaSHI genes was consistent with the expression pattern of four structural genes of artemisinin biosynthesis and their specific regulatory factors. Dual-luciferase reporter assays, yeast one-hybrid assays, and transient transformation in A. annua provided the evidence that AaSHI1 could directly bind to the promoters of structural genes AaADS and AaCYP71AV1, and positively regulate their expressions. This study has presented candidate genes, with AaSHI1 in particular, that can be considered for the metabolic engineering of artemisinin biosynthesis in A. annua. CONCLUSIONS Overall, a genome-wide analysis of the AaSHI TF family of A. annua was conducted. Five AaSHIs were identified in A. annua genome. Among the identified AaSHIs, AaSHI1 was found to be localized to the nucleus and activate the expression of structural genes of artemisinin biosynthesis including AaADS and AaCYP71AV1. These results indicated that AaSHI1 had positive roles in modulating artemisinin biosynthesis, providing candidate genes for obtaining high-quality new A. annua germplasms.
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Affiliation(s)
- Yinkai Yang
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yongpeng Li
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Jin
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Pengyang Li
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qin Zhou
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Miaomiao Sheng
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiaojing Ma
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tsubasa Shoji
- Institute of Natural Medicine, University of Toyama, Toyama, 930-0194, Japan
| | - Xiaolong Hao
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Guoyin Kai
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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Yang M, Song X, Li J, Wang S, Zhang M, Deng X, Wang H. Genome-wide identification and analysis of the EIN3/EIL gene family in broomcorn millet ( Panicum miliaceum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1440872. [PMID: 39170780 PMCID: PMC11335613 DOI: 10.3389/fpls.2024.1440872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024]
Abstract
The EIN3/EIL gene family holds a pivotal role as it encodes a crucial transcription factor in plants. During the process of polyploidization in broomcorn millet (Panicum miliaceum L.), there is an intriguing above-average amplification observed within the EIN3/EIL gene family. Nonetheless, our current knowledge of this gene family in broomcorn millet remains limited. Hence, in this study, we conducted a comprehensive analysis of the EIN3/EIL gene family in broomcorn millet, aiming to provide a deeper understanding of the potential evolutionary changes. Additionally, we analyzed the EIN3/EIL gene family of Panicum hallii L., a close relative of broomcorn millet, to enhance our characterization efforts. Within this study, we identified a total of 15 EIN3/EIL genes specific to broomcorn millet. Through covariance analysis, it was revealed that all PmEIL genes, except PmEIL1 and PmEIL15, had duplicate copies generated through genome-wide duplication events. Importantly, the Ka/Ks values of all duplicated genes were found to be less than 1, indicating strong purifying selection. Phylogenetic analysis showed that these genes could be categorized into four distinct evolutionary branches, showcasing similar characteristics among members within the same branch. However, there appeared to be an uneven distribution of cis-acting elements amid the EIN3/EIL genes. Further examination of transcriptomic data shed light on the diverse spatiotemporal and stress-related expression patterns exhibited by the EIN3/EIL genes in broomcorn millet. Notably, under cold stress, the expression of PmEIL3/4/8/14 was significantly up-regulated, while under drought stress, PmEIL4/5/6 displayed significant up-regulation. Intriguingly, the expression pattern of PmEIL15 showed an opposite pattern in resistant and sensitive cultivars. The findings of this study augment our understanding of the EIN3/EIL gene family in broomcorn millet and offer a valuable reference for future investigations into polyploid studies. Moreover, this study establishes a theoretical foundation for further exploration of the ethylene signaling pathway in broomcorn millet.
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Affiliation(s)
| | | | | | | | | | | | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang, China
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Tang J, Ling T, Li H, Fan C. Genome-wide analysis and identification of the TBL gene family in Eucalyptus grandis. FRONTIERS IN PLANT SCIENCE 2024; 15:1401298. [PMID: 39170793 PMCID: PMC11337025 DOI: 10.3389/fpls.2024.1401298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/17/2024] [Indexed: 08/23/2024]
Abstract
The TRICHOME BIREFRINGENCE-LIKE (TBL) gene encodes a class of proteins related to xylan acetylation, which has been shown to play an important role in plant response to environmental stresses. This gene family has been meticulously investigated in Arabidopsis thaliana, whereas there have been no related reports in Eucalyptus grandis. In this study, we identified 49 TBL genes in E. grandis. A conserved amino acid motif was identified, which plays an important role in the execution of the function of TBL gene family members. The expression of TBL genes was generally upregulated in jasmonic acid-treated experiments, whereas it has been found that jasmonic acid activates the expression of genes involved in the defense functions of the plant body, suggesting that TBL genes play an important function in the response of the plant to stress. The principle of the action of TBL genes is supported by the finding that the xylan acetylation process increases the rigidity of the cell wall of the plant body and thus improves the plant's resistance to stress. The results of this study provide new information about the TBL gene family in E. grandis and will help in the study of the evolution, inheritance, and function of TBL genes in E. grandis, while confirming their functions.
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Affiliation(s)
- Jiye Tang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Tenghong Ling
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Huiling Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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120
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Kim T, Egesa A, Qin C, Mather H, Sandoya G, Begcy K. Global identification of LIM genes in response to different heat stress regimes in Lactuca sativa. BMC PLANT BIOLOGY 2024; 24:751. [PMID: 39103763 DOI: 10.1186/s12870-024-05466-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND LIM (Lineage-11 (LIN-11), Insulin-1 (ISL-1), and Mechanotransduction-3 (MEC-3)) genes belong to a family that hold ubiquitous properties contributing to organ, seed, and pollen development as well as developmental and cellular responses to biotic and abiotic stresses. Lettuce (Lactuca sativa) is a highly consumed vegetable crop susceptible heat stress. High temperatures limit lettuce's overall yield, quality and marketability. Lettuce LIM genes have not been identified and their role in response to high temperatures is not known. Aiming to identify potential new targets for thermoresilience, we searched for LIM genes in lettuce and compared them with orthologous of several dicotyledons and monocotyledons plant species. RESULTS We identified fourteen lettuce LIM genes distributed into eight different subgroups using a genome-wide analysis strategy. Three belonging to DAR (DA means "large" in Chinese) class I, two DAR class II, one in the WLIM1, two in the WLIM2, one in the PLIM1, two in the PLIM2 class, one ßLIM and two δLIMs. No DAR-like were identified in any of the species analyzed including lettuce. Interestingly, unlike other gene families in lettuce which underwent large genome tandem duplications, LIM genes did not increase in number compared to other plant species. The response to heat stress induced a dynamic transcriptional response on LsLIM genes. All heat stress regimes, including night stress, day stress and day and night stress were largely responsible for changes in LIM transcriptional expression. CONCLUSIONS Our global analysis at the genome level provides a detailed identification of LIM genes in lettuce and other dicotyledonous and monocotyledonous plant species. Gene structure, physical and chemical properties as well as chromosomal location and Cis-regulatory element analysis together with our gene expression analysis under different temperature regimes identified LsWLIM1, LsWLIM2b, LsDAR3 and LsDAR5 as candidate genes that could be used by breeding programs aiming to produce lettuce varieties able to withstand high temperatures.
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Affiliation(s)
- Taehoon Kim
- Environmental Horticulture Department, University of Florida, Gainesville, FL, 32611, USA
| | - Andrew Egesa
- Environmental Horticulture Department, University of Florida, Gainesville, FL, 32611, USA
| | - Claire Qin
- Environmental Horticulture Department, University of Florida, Gainesville, FL, 32611, USA
- Student Science Training Program, University of Florida, Gainesville, FL, 32611, USA
| | - Hannah Mather
- Environmental Horticulture Department, University of Florida, Gainesville, FL, 32611, USA
- Horticultural Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Germán Sandoya
- Horticultural Science Department, University of Florida, Gainesville, FL, 32611, USA
- Everglades Research and Education Center, Horticultural Sciences Department, University of Florida IFAS, Belle Glade, FL, 33430, USA
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, 32611, USA.
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Liu Y, Li D, Liu Y, Wang J, Liu C. Genome-Wide Identification and Evolution-Profiling Analysis of TPS Gene Family in Triticum Plants. Int J Mol Sci 2024; 25:8546. [PMID: 39126114 PMCID: PMC11312503 DOI: 10.3390/ijms25158546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Terpenoids play a crucial role in plant growth and development, as well as in regulating resistance mechanisms. Terpene synthase (TPS) serves as the final step in the synthesis process of terpenoids. However, a comprehensive bioinformatics analysis of the TPS gene family in Triticum plants had not previously been systematically undertaken. In this study, a total of 531 TPS members were identified in Triticum plants. The evolutionary tree divided the TPS proteins into five subfamilies: Group1, Group2, Group3, Group4, and Group5. The results of the duplication events analysis showed that TD and WGD were major driving forces during the evolution of the TPS family. The cis-element analysis showed that the TPS genes were related to plant growth and development and environmental stress. Moreover, the GO annotation displayed that the biological function of TPS was relatively conserved in wheat plants. The RNA-seq data showed that the rice and wheat TPS genes responded to low-temperature stress and exhibited significantly different expression patterns. This research shed light on the functions of TPSs in responding to abiotic stress and demonstrated their modulatory potential during root development. These findings provide a foundation for further and deeper investigation of the TPSs' functions in Triticum plants.
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Affiliation(s)
- Yiyang Liu
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Dongyang Li
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China;
| | - Yue Liu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110866, China
| | - Jiazheng Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China;
| | - Chang Liu
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China;
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Wei Z, Wu ZC, Zang J, Zhao D, Guo W, Dai H. Genome-Wide Identification and Expression Pattern Analysis of the WNK Gene Family in Apple under Abiotic Stress and Colletotrichum siamense Infection. Int J Mol Sci 2024; 25:8528. [PMID: 39126096 PMCID: PMC11313067 DOI: 10.3390/ijms25158528] [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: 06/29/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
With-no-lysine kinase (WNK) is a unique serine/threonine kinase family member. WNK differs from other protein kinases by not having a standard lysine in subdomain II of the universally preserved kinase catalytic region. Conversely, the amino acid lysine located in subdomain I plays a crucial role in its phosphorylation. The WNK family has been reported to regulate Arabidopsis flowering, circadian rhythm, and abiotic stress. Eighteen members of the WNK gene family were discovered in apples in this research, and they were primarily grouped into five categories on the phylogenetic tree. Conserved domains and motifs also confirmed their identity as members of the WNK family. Promoter cis-acting element analysis indicated their potential role in responses to both abiotic stress and phytohormones. Furthermore, qRT-PCR analysis showed that the expression of MdWNK family genes was stimulated to different extents by Colletotrichum siamense, NaCl, mannitol, ABA, JA, and SA, with Colletotrichum siamense being the most prominent stimulant. MdWNK family genes were expressed across all apple tissues, with young fruits showing the greatest expression and roots showing the least expression. The research offered detailed insights into the MdWNK gene family, serving as a crucial basis for investigating the biological roles of MdWNK genes.
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Affiliation(s)
- Ziwen Wei
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China;
| | - Zheng-Chao Wu
- Analytical and Testing Center, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; (Z.-C.W.); (J.Z.); (D.Z.)
| | - Jian Zang
- Analytical and Testing Center, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; (Z.-C.W.); (J.Z.); (D.Z.)
| | - Di Zhao
- Analytical and Testing Center, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; (Z.-C.W.); (J.Z.); (D.Z.)
| | - Wei Guo
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China;
- Analytical and Testing Center, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; (Z.-C.W.); (J.Z.); (D.Z.)
| | - Hongyan Dai
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China;
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Konieczna W, Turkan S, Warchoł M, Skrzypek E, Dąbrowska GB, Mierek-Adamska A. The Contribution of Trichoderma viride and Metallothioneins in Enhancing the Seed Quality of Avena sativa L. in Cd-Contaminated Soil. Foods 2024; 13:2469. [PMID: 39123659 PMCID: PMC11312241 DOI: 10.3390/foods13152469] [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: 07/02/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Pollution of arable land with heavy metals is a worldwide problem. Cadmium (Cd) is a toxic metal that poses a severe threat to humans' and animals' health and lives. Plants can easily absorb Cd from the soil, and plant-based food is the main means of exposure to this hazardous element for humans and animals. Phytoremediation is a promising plant-based approach to removing heavy metals from the soil, and plant growth-promoting micro-organisms such as the fungi Trichoderma can enhance the ability of plants to accumulate metals. Inoculation of Avena sativa L. (oat) with Trichoderma viride enhances germination and seedling growth in the presence of Cd and, in this study, the growth of 6-month-old oat plants in Cd-contaminated soil was not increased by inoculation with T. viride, but a 1.7-fold increase in yield was observed. The content of Cd in oat shoots depended on the Cd content in the soil. Still, it was unaffected by the inoculation with T. viride. A. sativa metallothioneins (AsMTs) participate in plant-fungi interaction, however, their role in this study depended on MT type and Cd concentration. The inoculation of A. sativa with T. viride could be a promising approach to obtaining a high yield in Cd-contaminated soil without increasing the Cd content in the plant.
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Affiliation(s)
- Wiktoria Konieczna
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; (W.K.); (S.T.); (G.B.D.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Sena Turkan
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; (W.K.); (S.T.); (G.B.D.)
| | - Marzena Warchoł
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland; (M.W.); (E.S.)
| | - Edyta Skrzypek
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland; (M.W.); (E.S.)
| | - Grażyna B. Dąbrowska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; (W.K.); (S.T.); (G.B.D.)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; (W.K.); (S.T.); (G.B.D.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
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Singh CM, Singh BK, Purwar S, Nair B, Ruchi, Patel A, Singh S, Kaur V. Comprehensive characterization of protease inhibiting gene family, cis-regulatory elements, and protein interaction network in linseed and their expression upon bud fly infestation. Sci Rep 2024; 14:17907. [PMID: 39095443 PMCID: PMC11297176 DOI: 10.1038/s41598-024-68943-1] [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: 01/06/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
Linseed, also known as flax is an important oilseed crop with many potential uses in paint, textile, food and pharmaceutical industries. Susceptibility to bud fly (Dasyneura lini Barnes) infestation is a serious biotic concern leading to severe yield penalty in linseed. Protease inhibitors (PIs) are potential candidates that activate during the insect-pest attack and modulate the resistance. In the present study, we explored the PI candidates in the linseed genome and a total of 100 LuPI genes were identified and grouped into five distinct subgroups. The analysis of cis-acting elements revealed that almost all LuPI promoters contain several regulatory elementary related to growth and development, hormonal regulation and stress responses. Across the subfamilies of PIs, the specific domains are consistently found conserved in all protein sequences. The tissue-specific in-silico expression pattern via RNA-seq revealed that all the genes were regulated during different stress. The expression through qRT-PCR of 15 genes revealed the significant up-regulation of LuPI-24, LuPI-40, LuPI-49, LuPI-53, and LuPI-63 upon bud fly infestation in resistant genotype EC0099001 and resistant check variety Neela. This study establishes a foundation resource for comprehending the structural, functional, and evolutionary dimensions of protease inhibitors in linseed.
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Affiliation(s)
- Chandra Mohan Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, Uttar Pradesh, 210 001, India
| | - Bhupendra Kumar Singh
- Department of Entomology, Banda University of Agriculture and Technology, Banda, Uttar Pradesh, 210 001, India.
| | - Shalini Purwar
- Department of Basic and Social Sciences, Banda University of Agriculture and Technology, Banda, Uttar Pradesh, 210 001, India
| | - Beena Nair
- AICRP on Linseed and Mustard, College of Agriculture, Dr. PDKV-Akola, Nagpur, Maharashtra, 440 001, India
| | - Ruchi
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, Uttar Pradesh, 210 001, India
| | - Amar Patel
- AICRP on Linseed and Sesame, Oilseed Research Station, Banda University of Agriculture and Technology, Mauranipur, Uttar Pradesh, 282 204, India
| | - Saurabh Singh
- AICRP on Linseed and Sesame, Oilseed Research Station, Banda University of Agriculture and Technology, Mauranipur, Uttar Pradesh, 282 204, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, 110 012, India.
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Xu Z, Zhang G, Chen J, Ying Y, Yao L, Li X, Teixeira da Silva JA, Yu Z. Role of Rubus chingii BBX gene family in anthocyanin accumulation during fruit ripening. FRONTIERS IN PLANT SCIENCE 2024; 15:1427359. [PMID: 39157519 PMCID: PMC11327127 DOI: 10.3389/fpls.2024.1427359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/17/2024] [Indexed: 08/20/2024]
Abstract
The B-box (BBX) family, which is a class of zinc finger transcription factors, exhibits special roles in plant growth and development as well as in plants' ability to cope with various stresses. Even though Rubus chingii is an important traditional medicinally edible plant in east Asia, there are no comprehensive studies of BBX members in R. chingii. In this study, 32 RcBBX members were identified, and these were divided into five groups. A collinearity analysis showed that gene duplication events were common, and when combined with a motif analysis of the RcBBX genes, it was concluded that group V genes might have undergone deletion of gene fragments or mutations. Analysis of cis-acting elements revealed that each RcBBX gene contained hormone-, light-, and stress-related elements. Expression patterns of the 32 RcBBX genes during fruit ripening revealed that highest expression occurred at the small green fruit stage. Of note, the expression of several RcBBX genes increased rapidly as fruit developed. These findings, combined with the expression profiles of anthocyanin biosynthetic genes during fruit ripening, allowed us to identify the nuclear-targeted RcBBX26, which positively promoted anthocyanin production in R. chingii. The collective findings of this study shed light on the function of RcBBX genes in different tissues, developmental stages, and in response to two abiotic stresses.
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Affiliation(s)
- Zhangting Xu
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | | | - Junyu Chen
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuxin Ying
- College of Food and Health, Zhejiang A & F University, Hangzhou, China
| | - Lingtiao Yao
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoxian Li
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | | | - Zhenming Yu
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Songyang Institute of Zhejiang Chinese Medical University, Lishui, China
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Zhu C, Lin Z, Liu Y, Li H, Di X, Li T, Wang J, Gao Z. A bamboo bHLH transcription factor PeRHL4 has dual functions in enhancing drought and phosphorus starvation tolerance. PLANT, CELL & ENVIRONMENT 2024; 47:3015-3029. [PMID: 38644587 DOI: 10.1111/pce.14920] [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: 01/16/2024] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
ROOTHAIRLESS (RHL) is a typical type of basic helix-loop-helix (bHLH) transcription factor (TF), which has been reported to participate in various aspects of plant growth and in response to stress. However, the functions of RHL subfamily members in moso bamboo (Phyllostachys edulis) remain unknown. In this study, we identified 14 bHLH genes (PeRHL1-PeRHL14) in moso bamboo. Phylogenetic tree and conserved motif analyses showed that PeRHLs were clustered into three clades. The expression analysis suggested that PeRHL4 was co-expressed with PeTIP1-1 and PePHT1-1 in moso bamboo. Moreover, these three genes were all up-regulated in moso bamboo under drought stress and phosphate starvation. Y1H, DLR and EMSA assays demonstrated that PeRHL4 could activate the expression of PeTIP1-1 and PePHT1-1. Furthermore, overexpression of PeRHL4 could increase both drought and phosphate starvation tolerance in transgenic rice, in which the expression of OsTIPs and OsPHT1s was significantly improved, respectively. Overall, our results indicated that drought stress and phosphate starvation could induce the expression of PeRHL4, which in turn activated downstream genes involved in water and phosphate transport. Collectively, our findings reveal that PeRHL4 acting as a positive regulator contributes to enhancing the tolerance of moso bamboo under drought stress and phosphate starvation.
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Affiliation(s)
- Chenglei Zhu
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Zeming Lin
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Yan Liu
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Hui Li
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Xiaolin Di
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Tiankuo Li
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Jiangfei Wang
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Zhimin Gao
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
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Khalvandi M, Aghaie P, Siosemardeh A, Hosseini SJ, Ghorbanpour M, Reiahisamani N, Amerian M. Genome-wide study of UDP-glycosyltransferases gene family in Cannabis sativa. 3 Biotech 2024; 14:183. [PMID: 39050981 PMCID: PMC11263533 DOI: 10.1007/s13205-024-04025-3] [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: 04/06/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
The research focused on analyzing the UGT gene family in Cannabis sativa, which plays a crucial role in the plant's metabolism and glycosylation of secondary metabolites. The study identified 125 UGTs using conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. These UGT genes were categorized into 17 groups (A-Q) through phylogenetic analysis, showing their distribution across 10 chromosomes in C. sativa. The expansion of the CsUGT gene family was attributed to tandem and duplication events, as suggested by gene duplication analysis. Furthermore, the study found various cis-acting regulatory elements related to phytohormones and stress responses in CsUGT promoter regions. Subcellular localization analysis revealed that CsUGT is present in the cytoplasm, chloroplast, and nucleus. The study revealed that CsUGT plays a significant role in various biological processes, cellular components, and molecular functions as highlighted by Gene Ontology analysis. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that some CsUGTs are associated with the biosynthesis of secondary metabolites. This research provides valuable insights into the genomic organization, evolutionary history, and potential regulatory mechanisms of UGT genes in C. sativa. It lays the foundation for further exploration of their specific biological roles and potential applications in the plant's metabolism and stress responses. These findings contribute to a better understanding of the UGT gene family and its relevance to the metabolic pathways in C. sativa. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04025-3.
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Affiliation(s)
- Masoumeh Khalvandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Peyman Aghaie
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Adel Siosemardeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | | | - Mansour Ghorbanpour
- Department of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran
| | | | - Mohammadreza Amerian
- Department of Agronomy, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
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128
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Shahzad A, Fan Y, Qian M, Khan SU, Mahmood U, Wei L, Qu C, Lu K. Genome-wide characterization of Related to ABI3/VP1 transcription factors among U's triangle Brassica species reveals a negative role for BnaA06.RAV3L in seed size. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108854. [PMID: 38901228 DOI: 10.1016/j.plaphy.2024.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
The transcription factors Related to ABI3/VP1 (RAV) are crucial for various plant processes and stress responses. Although the U's triangle Brassica species genomes have been released, the knowledge regarding the RAV family is still limited. In this study, we identified 123 putative RAV genes across the six U's triangle Brassica species (Brassica rapa, 14; Brassica oleracea, 14; Brassica nigra, 13; Brassica carinata, 27; Brassica juncea, 28; Brassica napus, 27). Phylogenetic analysis categorized them into three groups. The RAV genes exhibited diversity in both functional and structural aspects, particularly in gene structure and cis-acting elements within their promoters. The expression analysis revealed that BnaRAV genes in Group 1/2 exhibited diverse expression patterns across various tissues, while those in Group 3 did not show expression except for BnaRAV3L-2 and BnaRAV3L-6, which were exclusively expressed in seeds. Furthermore, the seed-specific expression of BnaA06. RAV3L (BnaRAV3L-2) was confirmed through promoter-GUS staining. Subcellular localization studies demonstrated that BnaA06.RAV3L is localized to the nucleus. The overexpression of BnaA06. RAV3L in Arabidopsis led to a remarkable inhibition of seed-specific traits such as seed width, seed length, seed area, and seed weight. This study provides insights into the functional evolution of the RAV gene family in U triangle Brassica species. It establishes a foundation for uncovering the molecular mechanisms underlying the negative role of RAV3L in seed development.
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Affiliation(s)
- Ali Shahzad
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Lijuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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129
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Jara-Cornejo K, Zúñiga PE, Rivera-Mora C, Bustos E, Garrido-Bigotes A, Ruiz-Lara S, Figueroa CR. YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:735-748. [PMID: 38924267 DOI: 10.1111/plb.13656] [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: 09/12/2023] [Accepted: 04/02/2024] [Indexed: 06/28/2024]
Abstract
YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.
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Affiliation(s)
- K Jara-Cornejo
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - P E Zúñiga
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C Rivera-Mora
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - E Bustos
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - A Garrido-Bigotes
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
| | - S Ruiz-Lara
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C R Figueroa
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
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130
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Khan ZA, Gupta K, Dasgupta I. Transient expression analysis of promoters of okra enation leaf curl virus in Nicotiana benthamiana, cotton and okra plants. Virus Genes 2024; 60:412-422. [PMID: 38727968 DOI: 10.1007/s11262-024-02074-7] [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: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 07/13/2024]
Abstract
Viral promoters can be used to drive heterologous gene expression in transgenic plants. As part of our quest to look for new promoters, we have explored, for the first time, the promoters of okra enation leaf curl virus (OELCuV), a begomovirus infecting okra (Abelmoschus esculentus). The Rep and CP promoters of OELCuV fused with the gfp reporter gene, were expressed transiently in the natural host okra and the laboratory host cotton and Nicotiana benthamiana. The expression levels of the promoters were quantified through confocal laser scanning microscopy and GFP assay in N. benthamiana and okra. The results indicated that the Rep promoter was more active than the CP promoter, whose activity was similar to that of CaMV 35S promoter. Additionally, the Rep and CP promoters showed increase of expression, probably due to transactivation, when assayed following inoculation of OELCuV and betasatellite DNAs in cotton plants. A moderate increase in promoter activity in N. benthamiana was also seen, when assayed following the inoculation of the heterologous begomovirus Sri Lankan cassava mosaic virus.
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Affiliation(s)
- Zainul A Khan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Kanika Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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131
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Silva SA, Bezerra VBF, Teixeira FC, Roque EMS, do Nascimento JIB, Aguiar AM, de Carvalho HH, Alves MS. Genome-wide identification and characterization of SNW/SKIP domain-containing proteins in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:705-714. [PMID: 38899579 DOI: 10.1111/plb.13676] [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: 02/20/2024] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Sessile organisms, such as plants, developed various ways to sense and respond to external and internal stimuli to maximize their fitness through evolutionary time. Transcripts and protein regulation are, among many, the main mechanisms that plants use to respond to environmental changes. SKIP protein is one such, presenting an SNKW interacting domain, which is highly conserved among eukaryotes, where SKI interacting protein acts in regulating key processes. In the present work, many bioinformatics tools, such as phylogenetic relationships, gene structure, physical-chemical properties, conserved motifs, prediction of regulatory cis-elements, chromosomal localization, and protein-protein interaction network, were used to better understand the genome-wide SNW/SKIP domain-containing proteins. In total, 28 proteins containing the SNW/SKIP domain were identified in different plant species, including plants of agronomic interest. Two main protein clusters were formed in phylogenetic analysis, and gene structure analysis revealed that, in general, the coding region had no introns. Also, expression of these genes is possibly induced by abiotic stress stimuli. Primary structure analysis of the proteins revealed the existence of an evolutionarily conserved functional unit. But physicochemical properties show that proteins containing the SNW/SKIP domain are commonly unstable under in vivo conditions. In addition, the protein network, demonstrated that SKIP homologues could act by modulating plant fitness through gene expression regulation at the transcriptional and post-transcriptional levels. This could be corroborated by the expression number of gene copies of SKIP proteins in many species, highlighting it's crucial role in plant development and tolerance through the course of evolution.
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Affiliation(s)
- S A Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - V B F Bezerra
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - F C Teixeira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - E M S Roque
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - J I B do Nascimento
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - A M Aguiar
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - H H de Carvalho
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - M S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
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132
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Rawale KS, Gutierrez-Zamora GR, Venditto NA, Gill KS. Identification of Pathogen-Specific Novel Sources of Genetic Resistance Against Ascochyta Blight and Identification of Their Underlying Genetic Control. PLANT DISEASE 2024; 108:2367-2375. [PMID: 38332491 DOI: 10.1094/pdis-10-23-2176-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Global chickpea production is restricted by Ascochyta blight caused by the necrotrophic fungi Ascochyta rabiei. Developing locally adapted disease-resistant cultivars is an economically and environmentally sustainable approach to combat this disease. However, the lack of genetic variability in cultivated chickpeas and breeder-friendly markers poses a significant challenge to Ascochyta blight-resistant breeding efforts in chickpeas. In this study, we screened the mini-core germplasm of Cicer reticulatum against a local pathotype of A. rabiei. A modified mini-dome screening approach resulted in the identification of five accessions showing a high level of resistance. The mean disease score of resistant accessions ranged between 1.75 ± 0.3 and 2.88 ± 0.4 compared to susceptible accessions, where the mean disease score ranged between 3.59 ± 0.62 and 8.86 ± 0.14. Genome-wide association study revealed a strong association on chromosome 5, explaining ∼58% of the phenotypic variance. The underlying region contained two candidate genes (Cr_14190.1_v2 and Cr_14189.1_v2), the characterization of which showed the presence of a DNA-binding domain (cl28899 and cd18793) in Cr_14190.1_v2 and its orthologs in C. arietinum, whereas Cr_14190.1_v2 carried an additional N-terminal domain (cl31759). qPCR expression analysis in resistant and susceptible accessions revealed ∼3- and ∼110-fold higher transcript abundance for Cr_14189.1 and Cr_14190.1, respectively.
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133
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Sun J, Liu Y, Zheng Y, Xue Y, Fan Y, Ma X, Ji Y, Liu G, Zhang X, Li Y, Wang S, Tian Z, Zhao L. The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1603-1619. [PMID: 38869305 DOI: 10.1111/jipb.13682] [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: 02/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 06/14/2024]
Abstract
Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, The Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Zheng
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Yongguo Xue
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yuhuan Fan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaofei Ma
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yujia Ji
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Gaoyuan Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Li
- Depatment of Environmental and Plant Biology, Ohio University, Athens, 45701, Ohio, USA
| | - Shuming Wang
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
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134
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Zhang Z, Zhang J, Wang C, Chang Y, Han K, Gao Y, Xie J. Characterization of GPX Gene Family in Pepper ( Capsicum annuum L.) under Abiotic Stress and ABA Treatment. Int J Mol Sci 2024; 25:8343. [PMID: 39125911 PMCID: PMC11313330 DOI: 10.3390/ijms25158343] [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: 06/28/2024] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Plant glutathione peroxidases (GPXs) are important enzymes for removing reactive oxygen species in plant cells and are closely related to the stress resistance of plants. This study identified the GPX gene family members of pepper (Capsicum annuum L.), "CM333", at the whole-genome level to clarify their expression patterns and enzyme activity changes under abiotic stress and ABA treatment. The results showed that eight CaGPX genes were unevenly distributed across four chromosomes and one scaffold of the pepper genome, and their protein sequences had Cys residues typical of the plant GPX domains. The analysis of collinearity, phylogenetic tree, gene structure, and conserved motifs indicated that the CaGPX gene sequence is conserved, structurally similar, and more closely related to the sequence structure of Arabidopsis. Meanwhile, many cis elements involved in stress, hormones, development, and light response were found in the promoter region of the CaGPX gene. In addition, CaGPX1/4 and CaGPX6 were basically expressed in all tissues, and their expression levels were significantly upregulated under abiotic stress and ABA treatment. Subcellular localization showed that CaGPX1 and CaGPX4 are localized in chloroplasts. Additionally, the variations in glutathione peroxidase activity (GSH-Px) mostly agreed with the variations in gene expression. In summary, the CaGPXs gene may play an important role in the development of peppers and their response to abiotic stress and hormones.
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Affiliation(s)
| | | | | | | | | | | | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (Z.Z.); (J.Z.); (C.W.); (Y.C.); (K.H.); (Y.G.)
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135
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Yin X, Liu Y, Gong Y, Ding G, Zhao C, Li Y. Genomic characterization of bZIP gene family and patterns of gene regulation on Cercospora beticola Sacc resistance in sugar beet ( Beta vulgaris L.). Front Genet 2024; 15:1430589. [PMID: 39139817 PMCID: PMC11319121 DOI: 10.3389/fgene.2024.1430589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Sugar beet (Beta vulgaris L.) is one of the most important sugar crops, accounting for nearly 30% of the world's annual sugar production. And it is mainly distributed in the northwestern, northern, and northeastern regions of China. However, Cercospora leaf spot (CLS) is the most serious and destructive foliar disease during the cultivation of sugar beet. In plants, the bZIP gene family is one of important family of transcription factors that regulate many biological processes, including cell and tissue differentiation, pathogen defense, light response, and abiotic stress signaling. Although the bZIP gene family has been mentioned in previous studies as playing a crucial role in plant defense against diseases, there has been no comprehensive study or functional analysis of the bZIP gene family in sugar beet with respect to biotic stresses. In this study, we performed a genome-wide analysis of bZIP family genes (BvbZIPs) in sugar beet to investigate their phylogenetic relationships, gene structure and chromosomal localization. At the same time, we observed the stomatal and cell ultrastructure of sugar beet leaf surface during the period of infestation by Cercospora beticola Sacc (C. beticola). And identified the genes with significant differential expression in the bZIP gene family of sugar beet by qRT-PCR. Finally we determined the concentrations of SA and JA and verified the associated genes by qRT-PCR. The results showed that 48 genes were identified and gene expression analysis indicated that 6 BvbZIPs were significantly differential expressed in C. beticola infection. It is speculated that these BvbZIPs are candidate genes for regulating the response of sugar beet to CLS infection. Meanwhile, the observation stomata of sugar beet leaves infected with C. beticola revealed that there were also differences in the surface stomata of the leaves at different periods of infection. In addition, we further confirmed that the protein encoded by the SA signaling pathway-related gene BVRB_9g222570 in high-resistant varieties was PR1, which is closely related to systemic acquired resistance. One of the protein interaction modes of JA signal transduction pathway is the response of MYC2 transcription factor caused by JAZ protein degradation, and there is a molecular interaction between JA signal transduction pathway and auxin. Despite previous reports on abiotic stresses in sugar beet, this study provides very useful information for further research on the role of the sugar beet bZIP gene family in sugar beet through experiments. The above research findings can promote the development of sugar beet disease resistance breeding.
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Affiliation(s)
- Xiao Yin
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
| | - Yu Liu
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
| | - Yunhe Gong
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
| | - Guangzhou Ding
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
- Sugar Beet Engineering Research Center of Heilongjiang, Harbin, China
| | - Chunlei Zhao
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
| | - Yanli Li
- College of Modern Agriculture and Ecologcial Environment, Heilongjiang University, Harbin, China
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Chen R, Gu G, Zhang B, Du C, Lin X, Cai W, Zheng Y, Li T, Wang R, Xie X. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to bacterial wilt resistance in tobacco ( Nicotiana tabacum L.) and eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1425651. [PMID: 39139726 PMCID: PMC11319268 DOI: 10.3389/fpls.2024.1425651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
The E3 enzyme in the UPS pathway is a crucial factor for inhibiting substrate specificity. In Solanaceae, the U-box E3 ubiquitin ligase has a complex relationship with plant growth and development, and plays a pivotal role in responding to various biotic and abiotic stresses. The analysis of the U-box gene family in Solanaceae and its expression profile under different stresses holds significant implications. A total of 116 tobacco NtU-boxs and 56 eggplant SmU-boxs were identified based on their respective genome sequences. Phylogenetic analysis of U-box genes in tobacco, eggplant, tomato, Arabidopsis, pepper, and potato revealed five distinct subgroups (I-V). Gene structure and protein motifs analysis found a high degree of conservation in both exon/intron organization and protein motifs among tobacco and eggplant U-box genes especially the members within the same subfamily. A total of 15 pairs of segmental duplication and 1 gene pair of tandem duplication were identified in tobacco based on the analysis of gene duplication events, while 10 pairs of segmental duplication in eggplant. It is speculated that segmental duplication events are the primary driver for the expansion of the U-box gene family in both tobacco and eggplant. The promoters of NtU-box and SmU-box genes contained cis-regulatory elements associated with cellular development, phytohormones, environment stress, and photoresponsive elements. Transcriptomic data analysis shows that the expression levels of the tobacco and eggplant U-box genes in different tissues and various abiotic stress conditions. Using cultivar Hongda of tobacco and cultivar Yanzhi of eggplant as materials, qRT-PCR analysis has revealed that 15 selected NtU-box genes and 8 SmU-box may play important roles in response to pathogen Ras invasion both in tobacco and eggplant.
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Affiliation(s)
- Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Gang Gu
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | | | | | | | - Yan Zheng
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, China
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137
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Yang X, Wang S, Cai J, Zhang T, Yuan D, Li Y. Genome-wide identification, phylogeny and expression analysis of Hsf gene family in Verbena bonariensis under low-temperature stress. BMC Genomics 2024; 25:729. [PMID: 39075346 PMCID: PMC11285383 DOI: 10.1186/s12864-024-10612-8] [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: 12/14/2023] [Accepted: 07/10/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND The heat shock transcription factor (Hsf) is a crucial regulator of plant stress resistance, playing a key role in plant stress response, growth, and development regulation. RESULTS In this study, we utilized bioinformatics tools to screen 25 VbHsf members, which were named VbHsf1-VbHsf25. We used bioinformatics methods to analyze the sequence structure, physicochemical properties, conserved motifs, phylogenetic evolution, chromosome localization, promoter cis-acting elements, collinearity, and gene expression of Hsf heat shock transcription factor family members under low-temperature stress. The results revealed that the majority of the Hsf genes contained motif1, motif2, and motif3, signifying that these three motifs were highly conserved in the Hsf protein sequence of Verbena bonariensis. Although there were some variations in motif deletion among the members, the domain remained highly conserved. The theoretical isoelectric point ranged from 4.17 to 9.71, with 21 members being unstable proteins and the remainder being stable proteins. Subcellular localization predictions indicated that all members were located in the nucleus. Phylogenetic analysis of the Hsf gene family in V. bonariensis and Arabidopsis thaliana revealed that the Hsf gene family of V. bonariensis could be categorized into three groups, with group A comprising 17 members and group C having at least two members. Among the 25 Hsf members, there were 1-3 exons located on seven chromosome fragments, which were unevenly distributed. Collinearity analysis demonstrated the presence of seven pairs of homologous genes in the VbHsf gene family. The Ka/Ks ratios were less than one, indicating that the VbHsf gene underwent purification selection pressure. Additionally, nine genes in V. bonariensis were found to have collinearity with A. thaliana. Promoter analysis revealed that the promoters of all VbHsf genes contained various types of cis-acting elements related to hormones and stress. Based on RNA-seq data, qRT-PCR analysis of six highly expressed genes was performed, and it was found that VbHsf5, VbHsf14, VbHsf17, VbHsf18, VbHsf20 and VbHsf21 genes were highly expressed at 12 h of low-temperature treatment, and the expression decreased after 24 h, among which VbHsf14 was up-regulated at 12 h of low-temperature by 70-fold. CONCLUSIONS Our study may help reveal the important roles of Hsf in plant development and show insight for the further molecular breeding of V. bonariensis.
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Affiliation(s)
- Xiuliu Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Sisi Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ju Cai
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Tao Zhang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Dandan Yuan
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Yan Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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138
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Han S, Lin Y, Meng Y, Si C. Genome-Wide Identification and Analysis of SUS and AGPase Family Members in Sweet Potato: Response to Excessive Nitrogen Stress during Storage Root Formation. Int J Mol Sci 2024; 25:8236. [PMID: 39125807 PMCID: PMC11311812 DOI: 10.3390/ijms25158236] [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: 06/17/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
(1) The development of sweet potato storage roots is impacted by nitrogen (N) levels, with excessive nitrogen often impeding development. Starch synthesis enzymes such as sucrose synthase (SUS) and ADP-glucose pyrophosphorylase (AGPase) are pivotal in this context. Although the effects of excessive nitrogen on the formation of sweet potato storage roots are well documented, the specific responses of IbSUSs and IbAGPases have not been extensively reported on. (2) Pot experiments were conducted using the sweet potato cultivar "Pushu 32" at moderate (MN, 120 kg N ha-1) and excessive nitrogen levels (EN, 240 kg N ha-1). (3) Nine IbSUS and nine IbAGPase genes were categorized into three and two distinct subgroups based on phylogenetic analysis. Excessive nitrogen significantly (p < 0.05) suppressed the expression of IbAGPL1, IbAGPL2, IbAGPL4, IbAGPL5, IbAGPL6, IbAGPS1, and IbAGPS2 in fibrous roots and IbSUS2, IbSUS6, IbSUS7, IbSUS8, IbSUS9, IbAGPL2, and IbAGPL4 in storage roots, and then significantly (p < 0.05) decreased the SUS and AGPase activities and starch content of fibrous root and storage root, ultimately reducing the storage root formation of sweet potato. Excessive nitrogen extremely significantly (p < 0.01) enhanced the expression of IbAGPL3, which was strongly negatively correlated with the number and weight of storage roots per plant. (4) IbAGPL3 may be a key gene in the response to excessive nitrogen stress and modifying starch synthesis in sweet potato.
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Affiliation(s)
- Shaoxuan Han
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural, School of Rural Revitalization), Hainan University, Danzhou 571700, China; (S.H.); (Y.M.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Yanhui Lin
- Hainan Key Laboratory of Crop Genetics and Breeding, Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Yayi Meng
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural, School of Rural Revitalization), Hainan University, Danzhou 571700, China; (S.H.); (Y.M.)
| | - Chengcheng Si
- School of Tropical Agriculture and Forestry (School of Agricultural and Rural, School of Rural Revitalization), Hainan University, Danzhou 571700, China; (S.H.); (Y.M.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
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139
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Su Y, Fang J, Zeeshan Ul Haq M, Yang W, Yu J, Yang D, Liu Y, Wu Y. Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Peanut ( Arachis hypogea L.) Revealed Its Crucial Role in Growth and Multiple Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2077. [PMID: 39124195 PMCID: PMC11313903 DOI: 10.3390/plants13152077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Casparian strip membrane domain proteins (CASPs), regulating the formation of Casparian strips in plants, serve crucial functions in facilitating plant growth, development, and resilience to abiotic stress. However, little research has focused on the characteristics and functions of AhCASPs in cultivated peanuts. In this study, the genome-wide identification and expression analysis of the AhCASPs gene family was performed using bioinformatics and transcriptome data. Results showed that a total of 80 AhCASPs members on 20 chromosomes were identified and divided into three subclusters, which mainly localized to the cell membrane. Ka/Ks analysis revealed that most of the genes underwent purifying selection. Analysis of cis elements suggested the possible involvement of AhCASPs in hormonal and stress responses, including GA, MeJA, IAA, ABA, drought, and low temperature. Moreover, 20 different miRNAs for 37 different AhCASPs genes were identified by the psRNATarget service. Likewise, transcriptional analysis revealed key AhCASPs responding to various stresses, hormonal processing, and tissue types, including 33 genes in low temperature and drought stress and 41 genes in tissue-specific expression. These results provide an important theoretical basis for the functions of AhCASPs in growth, development, and multiple stress resistance in cultivated peanuts.
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Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jieyun Fang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Wanli Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Hainan University, Haikou 570228, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
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140
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Jia Z, Wang J, Meng X, Yang X, Tian Y, Wang B, Chen M, Yang J, Das D, Cao Y. Evolution and stress response potential of the plant splicing factor U1C. Sci Rep 2024; 14:17212. [PMID: 39060315 PMCID: PMC11282270 DOI: 10.1038/s41598-024-68190-4] [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: 06/27/2023] [Accepted: 07/22/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing is a crucial process in multicellular eukaryote, facilitated by the assembly of spliceosomal complexes comprising numerous small ribonucleoproteins. At an early stage, U1C is thought to be required for 5' splice site recognition and base pairing. However, a systematic analysis of the U1C gene family in response to developmental cues and stress conditions has not yet been conducted in plants. This study identified 114 U1C genes in 72 plant species using basic bioinformatics analyses. Phylogenetic analysis was used to compare gene and protein structures, promoter motifs, and tissue- and stress-specific expression levels, revealing their functional commonalities or diversity in response to developmental cues, such as embryonic expression, or stress treatments, including drought and heat. Fluorescence quantitative expression analysis showed that U1C gene expression changed under salt, low temperature, drought, and Cd stress in rice seedlings. However, gene expression in shoots and roots was not consistent under different stress conditions, suggesting a complex regulatory mechanism. This research provides foundational insights into the U1C gene family's role in plant development and stress responses, highlighting potential targets for future studies.
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Affiliation(s)
- Zichang Jia
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Junjie Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiangfeng Meng
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Xue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jingfang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65201, USA.
| | - Yunying Cao
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China.
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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Mao S, Xiao J, Zhao Y, Hou J, Li L. Genome-Wide Analysis of DNA Demethylases in Land Plants and Their Expression Pattern in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:2068. [PMID: 39124186 PMCID: PMC11314353 DOI: 10.3390/plants13152068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
DNA demethylation is a very important biochemical pathway regulating a group of biological processes, such as embryo development, fruit ripening, and response to stress. Despite the essential role of DNA demethylases, their evolutionary relationship and detailed biological functions in different land plants remain unclear. In this study, 48 DNA demethylases in 12 land plants were identified and classified. A phylogenetic tree was constructed to demonstrate the evolutionary relationships among these DNA demethylases, indicating how they are related across different species. Conserved domain, protein motif, and gene structure analysis showed that these 48 DNA demethylases fell into the presently identified four classes of DNA demethylases. Amino acid alignment revealed conserved catalytic sites and a previously less-studied protein region (referred to as domain A) within the DNA demethylases. An analysis showed a conserved pattern of gene duplication for DNA demethylases throughout their evolutionary history, suggesting that these genes had been maintained due to their importance. The examination of promoter cis-elements displayed potential signaling and regulating pathways of DNA demethylases. Furthermore, the expression profile was analyzed to investigate the physiological role of rice DNA demethylase in different developmental stages, in tissues, and in response to stress and various phytohormone signals. The findings offer a deeper insight into the functional regions of DNA demethylases and their evolutionary relationships, which can guide future research directions. Understanding the role of DNA demethylases can lead to improved plant stress resistance and contribute to the development of better crop and fruit varieties.
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Affiliation(s)
| | | | | | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.M.); (J.X.)
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.M.); (J.X.)
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Zhang H, Zhang Y, Cui K, Liu C, Chen M, Fu Y, Li Z, Ma H, Zhang H, Qi B, Xu J. A Global Identification of Protein Disulfide Isomerases from 'duli' Pear ( Pyrus betulaefolia) and Their Expression Profiles under Salt Stress. Genes (Basel) 2024; 15:968. [PMID: 39202330 PMCID: PMC11353384 DOI: 10.3390/genes15080968] [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: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 09/03/2024] Open
Abstract
Protein disulfide isomerases (PDIs) and PDI-like proteins catalyze the oxidation and reduction in protein disulfide bonds, inhibit aggregation of misfolded proteins, and participate in isomerization and abiotic stress responses. The wild type 'duli' pear (Pyrus betulaefolia) is an important rootstock commonly used for commercial pear tree grafting in northern China. In this study, we identified 24 PDI genes, named PbPDIs, from the genome of 'duli' pear. With 12 homologous gene pairs, these 24 PbPDIs distribute on 12 of its 17 chromosomes. Phylogenetic analysis placed the 24 PbPDIs into four clades and eleven groups. Collinearity analysis of the PDIs between P. betulaefolia, Arabidopsis thaliana, and Oryza sativa revealed that the PbPDIs of 'duli' pear show a strong collinear relationship with those from Arabidopsis, a dicot; but a weak collinear relationship with those from rice, a monocot. Quantitative RT-PCR analysis showed that most of the PbPDIs were upregulated by salt stress. Identification and expression analysis of 'duli' pear PbPDIs under salt stress conditions could provide useful information for further research in order to generate salt-resistant rootstock for pear grafting in the future.
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Affiliation(s)
- Hao Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Yuyue Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Kexin Cui
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Chang Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Mengya Chen
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Yufan Fu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Zhenjie Li
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Hui Ma
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Haixia Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
| | - Baoxiu Qi
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK
| | - Jianfeng Xu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, China; (H.Z.); (Y.Z.); (K.C.); (C.L.); (M.C.); (Y.F.); (Z.L.); (H.M.); (H.Z.)
- Research Center for Pear Engineering and Technology of Hebei Province, Baoding 071001, China
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144
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Sultana F, Ghosh A. Exploring the evolutionary landscape and structural resonances of ferritin with insights into functional significance in plant. Biochimie 2024:S0300-9084(24)00173-1. [PMID: 39047810 DOI: 10.1016/j.biochi.2024.07.014] [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: 04/20/2024] [Revised: 07/04/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The mineral iron plays a crucial role in facilitating the optimal functioning of numerous biological processes within the cellular environment. These processes involve the transportation of oxygen, energy production, immune system functioning, cognitive abilities, and muscle function. However, it is crucial to note that excessive levels of iron can result in oxidative damage within cells, primarily through Fenton reactions. Iron availability and toxicity present significant challenges that have been addressed through evolution. Ferritin is an essential protein that stores iron and is divided into different subfamilies, including DNA-binding proteins under starvation (Dps), bacterioferritin, and classical ferritin. Ferritin plays a critical role in maintaining cellular balance and protecting against oxidative damage. This study delves into ferritin's evolutionary dynamics across diverse taxa, emphasizing structural features and regulatory mechanisms. Insights into ferritin's evolution and functional diversity are gained through phylogenetic and structural analysis in bacterial Dps, bacterioferritin, and classical ferritin proteins. Additionally, the involvement of ferritin in plant stress responses and development is explored. Analysis of ferritin gene expression across various developmental stages and stress conditions provides insights into its regulatory roles. This comprehensive exploration enhances our understanding of ferritin's significance in plant biology, offering insights into its evolutionary history, structural diversity, and protective mechanisms against oxidative stress.
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Affiliation(s)
- Fahmida Sultana
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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145
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Ping X, Ye Q, Yan M, Wang J, Zhang T, Chen S, Siddique KHM, Cowling WA, Li J, Liu L. Overexpression of BnaA10.WRKY75 Decreases Cadmium and Salt Tolerance via Increasing ROS Accumulation in Arabidopsis and Brassica napus L. Int J Mol Sci 2024; 25:8002. [PMID: 39063244 PMCID: PMC11276826 DOI: 10.3390/ijms25148002] [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: 07/04/2024] [Revised: 07/17/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024] Open
Abstract
Soil is indispensable for agricultural production but has been seriously polluted by cadmium and salt in recent years. Many crops are suffering from this, including rapeseed, the third largest global oilseed crop. However, genes simultaneously related to both cadmium and salt stress have not been extensively reported yet. In this study, BnaA10.WRKY75 was screened from previous RNA-seq data related to cadmium and salt stress and further analyses including sequence comparison, GUS staining, transformation and qRT-PCR were conducted to confirm its function. GUS staining and qRT-PCR results indicated BnaA10.WRKY75 was induced by CdCl2 and NaCl treatment. Sequence analysis suggested BnaA10.WRKY75 belongs to Group IIc of the WRKY gene family and transient expression assay showed it was a nuclear localized transcription factor. BnaA10.WRKY75-overexpressing Arabidopsis and rapeseed plants accumulated more H2O2 and O2- and were more sensitive to CdCl2 and NaCl treatment compared with untransformed plants, which may be caused by the downregulation of BnaC03.CAT2. Our study reported that BnaA10.WRKY75 increases sensitivity to cadmium and salt stress by disrupting the balance of reactive oxygen species both in Arabidopsis and rapeseed. The results support the further understanding of the mechanisms underlying cadmium and salt tolerance and provide BnaA10.WRKY75 as a valuable gene for rapeseed abiotic stress breeding.
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Affiliation(s)
- Xiaoke Ping
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Qianjun Ye
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Mei Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jia Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Taiyuan Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Sheng Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
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146
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Wang J, Liu Z, She H, Xu Z, Zhang H, Fang Z, Qian W. Genome-Wide Identification and Characterization of U-Box Gene Family Members and Analysis of Their Expression Patterns in Phaseolus vulgaris L. under Cold Stress. Int J Mol Sci 2024; 25:7968. [PMID: 39063210 PMCID: PMC11277347 DOI: 10.3390/ijms25147968] [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: 06/21/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.
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Affiliation(s)
- Jiawei Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
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147
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Huang P, Lin Z, Zhang Y, Gao Y, Tan S, Wang S, Cao X, Shi H, Sun C, Bai J, Ma X. Genome-Wide Identification and Expression Analysis of ADK Gene Family Members in Cotton under Abiotic Stress. Int J Mol Sci 2024; 25:7821. [PMID: 39063069 PMCID: PMC11277214 DOI: 10.3390/ijms25147821] [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: 06/04/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Adenosine kinase (ADK) is a key enzyme widely distributed in plants, playing an important role in maintaining cellular energy homeostasis and regulating plant growth, development, and responses to environmental stresses. However, research on ADK genes in cotton (Gossypium hirsutum), an economically significant crop, has been limited. This study identified 92 ADK genes from four cotton species (G. arboreum, G. raimondii, G. hirsutum, and G. barbadense) using HMMER and Local BLASTP methods and classified them into six groups. Chromosomal localization revealed a random distribution of ADK genes in G. hirsutum, with 13 genes located on the At subgenome and 14 genes on the Dt subgenome. Gene structure analysis showed consistency in exon-intron organization within subgroups, while conserved motif analysis identified subgroup-specific motifs, indicating functional diversity. Synteny and collinearity mapping analysis revealed that the primary expansion mechanisms of the ADK gene family in cotton are polyploidy and segmental duplication. Cis-regulatory elements in GhADK promoters were classified into light response, hormone response, developmental regulation, and stress response. We also analyzed the expression patterns of GhADK genes under a low temperature (4 °C) and drought conditions. Most GhADK genes responded to cold stress with different expression patterns, indicating their roles in rapid response and long-term cold adaptation. Under drought stress, expression patterns varied, with some genes showing sustained high expression levels. The qRT-PCR validation of transcriptomic data confirmed the stress-induced expression patterns of selected GhADK genes. Functional analysis through the VIGS silencing of GhADK25 demonstrated its importance in cold and drought stress responses, with silencing resulting in poor growth under stress, highlighting its significance in stress tolerance. This study provides a basis for further understanding the evolutionary relationships and functions of the cotton ADK gene family.
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Affiliation(s)
- Peijun Huang
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (P.H.); (C.S.)
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Ziwei Lin
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Yuzhi Zhang
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Yu Gao
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Songjuan Tan
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Shuai Wang
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Xiaoyu Cao
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Hongyan Shi
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (P.H.); (C.S.)
| | - Jiangping Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (P.H.); (C.S.)
| | - Xiongfeng Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (P.H.); (C.S.)
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Z.L.); (Y.Z.); (Y.G.); (S.T.); (S.W.); (H.S.)
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
- College of Mechanical and Electrical Engineering, Shihezi University, Shihezi 518000, China
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148
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López-Virgen AG, Dautt-Castro M, Ulloa-Llanes LK, Casas-Flores S, Contreras-Vergara CA, Hernández-Oñate MA, Sotelo-Mundo RR, Vélez-de la Rocha R, Islas-Osuna MA. Genome-wide identification of gene families related to miRNA biogenesis in Mangifera indica L. and their possible role during heat stress. PeerJ 2024; 12:e17737. [PMID: 39035161 PMCID: PMC11260077 DOI: 10.7717/peerj.17737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/23/2024] [Indexed: 07/23/2024] Open
Abstract
Mango is a popular tropical fruit that requires quarantine hot water treatment (QHWT) for postharvest sanitation, which can cause abiotic stress. Plants have various defense mechanisms to cope with stress; miRNAs mainly regulate the expression of these defense responses. Proteins involved in the biogenesis of miRNAs include DICER-like (DCL), ARGONAUTE (AGO), HYPONASTIC LEAVES 1 (HYL1), SERRATE (SE), HUA ENHANCER1 (HEN1), HASTY (HST), and HEAT-SHOCK PROTEIN 90 (HSP90), among others. According to our analysis, the mango genome contains five DCL, thirteen AGO, six HYL, two SE, one HEN1, one HST, and five putative HSP90 genes. Gene structure prediction and domain identification indicate that sequences contain key domains for their respective gene families, including the RNase III domain in DCL and PAZ and PIWI domains for AGOs. In addition, phylogenetic analysis indicates the formation of clades that include the mango sequences and their respective orthologs in other flowering plant species, supporting the idea these are functional orthologs. The analysis of cis-regulatory elements of these genes allowed the identification of MYB, ABRE, GARE, MYC, and MeJA-responsive elements involved in stress responses. Gene expression analysis showed that most genes are induced between 3 to 6 h after QHWT, supporting the early role of miRNAs in stress response. Interestingly, our results suggest that mango rapidly induces the production of miRNAs after heat stress. This research will enable us to investigate further the regulation of gene expression and its effects on commercially cultivated fruits, such as mango, while maintaining sanitary standards.
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Affiliation(s)
- Andrés G. López-Virgen
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Mitzuko Dautt-Castro
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Lourdes K. Ulloa-Llanes
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosi, San Luis Potosi, México
| | | | | | - Rogerio R. Sotelo-Mundo
- CTAOA, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Rosabel Vélez-de la Rocha
- Unidad Culiacán, Centro de Investigación en Alimentación y Desarrollo, A.C., Culiacán, Sinaloa, México
| | - Maria A. Islas-Osuna
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
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149
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Huang X, Liu H, Wu F, Wei W, Zeng Z, Xu J, Chen C, Hao Y, Xia R, Liu Y. Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species. MOLECULAR HORTICULTURE 2024; 4:28. [PMID: 39010247 PMCID: PMC11251392 DOI: 10.1186/s43897-024-00104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Many species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position - 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.
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Affiliation(s)
- Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Hongsen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Wanchun Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Yanwei Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Hubei Wuhan, 430070, China.
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150
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Singh D, Tripathi A, Mitra R, Bhati J, Rani V, Taunk J, Singh D, Yadav RK, Siddiqui MH, Pal M. Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116558. [PMID: 38850702 DOI: 10.1016/j.ecoenv.2024.116558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Ankita Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Raktim Mitra
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Varsha Rani
- Department of Agriculture, Meerut Institute of Technology, Meerut 250103, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250103, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madan Pal
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
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