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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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Wu A, Lian B, Hao P, Fu X, Zhang M, Lu J, Ma L, Yu S, Wei H, Wang H. GhMYB30-GhMUR3 affects fiber elongation and secondary wall thickening in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:694-712. [PMID: 37988560 DOI: 10.1111/tpj.16523] [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: 05/20/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Xyloglucan, an important hemicellulose, plays a crucial role in maintaining cell wall structure and cell elongation. However, the effects of xyloglucan on cotton fiber development are not well understood. GhMUR3 encodes a xyloglucan galactosyltransferase that is essential for xyloglucan synthesis and is highly expressed during fiber elongation. In this study, we report that GhMUR3 participates in cotton fiber development under the regulation of GhMYB30. Overexpression GhMUR3 affects the fiber elongation and cell wall thickening. Transcriptome showed that the expression of genes involved in secondary cell wall synthesis was prematurely activated in OE-MUR3 lines. In addition, GhMYB30 was identified as a key regulator of GhMUR3 by Y1H, Dual-Luc, and electrophoretic mobility shift assay (EMSA) assays. GhMYB30 directly bound the GhMUR3 promoter and activated GhMUR3 expression. Furthermore, DAP-seq of GhMYB30 was performed to identify its target genes in the whole genome. The results showed that many target genes were associated with fiber development, including cell wall synthesis-related genes, BR-related genes, reactive oxygen species pathway genes, and VLCFA synthesis genes. It was demonstrated that GhMYB30 may regulate fiber development through multiple pathways. Additionally, GhMYB46 was confirmed to be a target gene of GhMYB30 by EMSA, and GhMYB46 was significantly increased in GhMYB30-silenced lines, indicating that GhMYB30 inhibited GhMYB46 expression. Overall, these results revealed that GhMUR3 under the regulation of GhMYB30 and plays an essential role in cotton fiber elongation and secondary wall thickening. Additionally, GhMYB30 plays an important role in the regulation of fiber development and regulates fiber secondary wall synthesis by inhibiting the expression of GhMYB46.
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Affiliation(s)
- Aimin Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Boying Lian
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengbo Hao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaokang Fu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jianhua Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liang Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuxun Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hengling Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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Sharma P, Mishra S, Pandey B, Singh G. Genome-wide identification and expression analysis of the NHX gene family under salt stress in wheat ( Triticum aestivum L). FRONTIERS IN PLANT SCIENCE 2023; 14:1266699. [PMID: 38111881 PMCID: PMC10726055 DOI: 10.3389/fpls.2023.1266699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023]
Abstract
Salt stress affects plant growth and development, resulting in the loss of crop yield across the world, and sodium-proton antiporters (NHXs) are one of the genes known to promote salt tolerance in transgenic plants. In this study, we conducted a comprehensive genome-wide analysis and expression profile of NHX genes in wheat under salinity stress. We identified 30 TaNHX genes in wheat based on the Na+/H+ exchanger domain, with all genes containing an amiloride motif except one, a known for inhibiting Na+ ions in plants. Phylogenetic analysis classified these genes into three classes with subfamilies: 12 were localized in vacuoles, while 18 were in the endoplasmic reticulum and plasma membrane. Promoter analysis revealed stress-related cis-acting elements, indicating their potential role in abiotic stress tolerance. The non-synonymous (Ka)/synonymous (Ks) ratios highlighted that the majority of TaNHX genes experienced robust purifying selection throughout their evolutionary history. Transcriptomis data analysis and qRT-PCR demonstrated distinct expression patterns for TaNHX genes across various tissues when subjected to salt stress. Additionally, we predicted 20 different miRNA candidates targeting the identified TaNHX genes. Protein-protein interaction prediction revealed NHX6's involvement in the SOS1 pathway, while NHX1 gene exhibit proton antiporter activity. Molecular dynamics (MD) simulations were also conducted to examine the interactions of TaNHX1, TaNHX2, and TaNHX3. These results represent a significant advancement in our understanding of the molecular mechanisms governing Na+ transporters. This may also offer promising avenues for future studies aimed at unraveling the intricate details of their biological roles and applications.
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Affiliation(s)
- Pradeep Sharma
- Crop Improvement division, ICAR-Indian Institute of Wheat and Barley Researh, Karnal, India
| | - Shefali Mishra
- Crop Improvement division, ICAR-Indian Institute of Wheat and Barley Researh, Karnal, India
| | - Bharati Pandey
- Division of AgriBioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- Crop Improvement division, ICAR-Indian Institute of Wheat and Barley Researh, Karnal, India
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Yang M, Umer MJ, Wang H, Han J, Han J, Liu Q, Zheng J, Cai X, Hou Y, Xu Y, Wang Y, Khan MKR, Ditta A, Liu F, Zhou Z. Decoding the guardians of cotton resilience: A comprehensive exploration of the βCA genes and its role in Verticillium dahliae resistance. PHYSIOLOGIA PLANTARUM 2023; 175:e14113. [PMID: 38148227 DOI: 10.1111/ppl.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 12/28/2023]
Abstract
Plant Carbonic anhydrases (Cas) have been shown to be stress-responsive enzymes that may play a role in adapting to adverse conditions. Cotton is a significant economic crop in China, with upland cotton (Gossypium hirsutum) being the most widely cultivated species. We conducted genome-wide identification of the βCA gene in six cotton species and preliminary analysis of the βCA gene in upland cotton. In total, 73 βCA genes from six cotton species were identified, with phylogenetic analysis dividing them into five subgroups. GHβCA proteins were predominantly localized in the chloroplast and cytoplasm. The genes exhibited conserved motifs, with motifs 1, 2, and 3 being prominent. GHβCA genes were unevenly distributed across chromosomes and were associated with stress-responsive cis-regulatory elements, including those responding to light, MeJA, salicylic acid, abscisic acid, cell cycle regulation, and defence/stress. Expression analysis indicated that GHβCA6, GHβCA7, GHβCA10, GHβCA15, and GHβCA16 were highly expressed under various abiotic stress conditions, whereas GHβCA3, GHβCA9, GHβCA10, and GHβCA18 had higher expression patterns under Verticillium dahliae infection at different time intervals. In Gossypium thurberi, GthβCA1, GthβCA2, and GthβCA4 showed elevated expression across stress conditions and tissues. Silencing GHβCA10 through VIGS increased Verticillium wilt severity and reduced lignin deposition compared to non-silenced plants. GHβCA10 is crucial for cotton's defense against Verticillium dahliae. Further research is needed to understand the underlying mechanisms and develop strategies to enhance resistance against Verticillium wilt.
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Affiliation(s)
- Mengying Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Heng Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Jiale Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangping Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qiankun Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Jie Zheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
| | - Yuqing Hou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Yanchao Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Yuhong Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | | | - Allah Ditta
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
| | - Zhongli Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
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Tang X, Hou Y, Jiang F, Lang H, Li J, Cheng J, Wang L, Liu X, Zhang H. Genome-wide characterization of SINA E3 ubiquitin ligase family members and their expression profiles in response to various abiotic stresses and hormones in kiwifruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107891. [PMID: 37459805 DOI: 10.1016/j.plaphy.2023.107891] [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: 02/26/2023] [Revised: 06/27/2023] [Accepted: 07/08/2023] [Indexed: 08/13/2023]
Abstract
SINA (Seven in absentia) proteins in the subtype of E3 ubiquitin ligase family have important functions in regulating the growth and development as well as in response to abiotic and biotic stresses in plants. However, the characteristics and possible functions of SINA family proteins in kiwifruit are not studied. In this research, a total number of 11 AcSINA genes in the kiwifruit genome were identified. Chromosome location and multiple sequence alignment analyses indicated that they were unevenly distributed on 10 chromosomes and all contained the typical N-terminal RING domain and C-terminal SINA domain. Phylogenetic, gene structure and collinear relationship analyses revealed that they were highly conserved with the same gene structure, and have gone through segmental duplication events. Expression pattern analyses demonstrated that all AcSINAs were ubiquitously expressed in roots, stems and leaves, and were responsive to different abiotic and plant hormone treatments with overlapped but distinct expression patterns. Further yeast two-hybrid and Arabidopsis transformation analyses demonstrated most AcSINAs interacted with itself or other AcSINA members to form homo- or heterodimers, and ectopic expression of AcSINA2 in Arabidopsis led to hypersensitive growth phenotype of transgenic seedlings to ABA treatment. Our results reveal that AcSINAs take part in the response to various abiotic stresses and hormones, and provide important information for the functional elucidation of AcSINAs in vine fruit plants.
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Affiliation(s)
- Xiaoli Tang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Yaqiong Hou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Fudong Jiang
- Yantai Academy of Agricultural Sciences, 26 West Gangcheng Avenue, Yantai, Shandong, 265559, China
| | - Hongshan Lang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jianzhao Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jieshan Cheng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Limin Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Xiaohua Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, 5 Qingdao Avenue, Yantai, 265503, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
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Wang Z, Rehman A, Jia Y, Dai P, He S, Wang X, Li H, Wang L, Qayyum A, Peng Z, Du X. Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton. Gene 2023; 868:147374. [PMID: 36934785 DOI: 10.1016/j.gene.2023.147374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.
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Affiliation(s)
- Zhenzhen Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yinhua Jia
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Panhong Dai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Xiaoyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
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7
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Shuya M, Le L, Huiyun S, Yu G, Yujun L, Qanmber G. Genomic identification of cotton SAC genes branded ovule and stress-related key genes in Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2023; 14:1123745. [PMID: 36818879 PMCID: PMC9935941 DOI: 10.3389/fpls.2023.1123745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
SAC genes have been identified to play a variety of biological functions and responses to various stresses. Previously, SAC genes have been recognized in animals and Arabidopsis. For the very first time, we identified 157 SAC genes in eight cotton species including three diploids and five tetraploids with 23 SAC members in G. hirsutum. Evolutionary analysis classified all cotton SAC gene family members into five distinct groups. Cotton SAC genes showed conserved sequence logos and WGD or segmental duplication. Multiple synteny and collinearity analyses revealed gene family expansion and purifying selection pressure during evolution. G. hirsutum SAC genes showed uneven chromosomal distribution, multiple exons/introns, conserved protein motifs, and various growth and stress-related cis-elements. Expression pattern analysis revealed three GhSAC genes (GhSAC3, GhSAC14, and GhSAC20) preferentially expressed in flower, five genes (GhSAC1, GhSAC6, GhSAC9, GhSAC13, and GhSAC18) preferentially expressed in ovule and one gene (GhSAC5) preferentially expressed in fiber. Similarly, abiotic stress treatment verified that GhSAC5 was downregulated under all stresses, GhSAC6 and GhSAC9 were upregulated under NaCl treatment, and GhSAC9 and GhSAC18 were upregulated under PEG and heat treatment respectively. Overall, this study identified key genes related to flower, ovule, and fiber development and important genetic material for breeding cotton under abiotic stress conditions.
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Affiliation(s)
- Ma Shuya
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liu Le
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Shi Huiyun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Gu Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Li Yujun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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8
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Zhang P, Liu J, Jia N, Wang M, Lu Y, Wang D, Zhang J, Zhang H, Wang X. Genome-wide identification and characterization of the bZIP gene family and their function in starch accumulation in Chinese chestnut ( Castanea mollissima Blume). FRONTIERS IN PLANT SCIENCE 2023; 14:1166717. [PMID: 37077628 PMCID: PMC10106562 DOI: 10.3389/fpls.2023.1166717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
The transcription factors of basic leucine zipper (bZIP) family genes play significant roles in stress response as well as growth and development in plants. However, little is known about the bZIP gene family in Chinese chestnut (Castanea mollissima Blume). To better understand the characteristics of bZIPs in chestnut and their function in starch accumulation, a series of analyses were performed including phylogenetic, synteny, co-expression and yeast one-hybrid analyses. Totally, we identified 59 bZIP genes that were unevenly distributed in the chestnut genome and named them CmbZIP01 to CmbZIP59. These CmbZIPs were clustered into 13 clades with clade-specific motifs and structures. A synteny analysis revealed that segmental duplication was the major driving force of expansion of the CmbZIP gene family. A total of 41 CmbZIP genes had syntenic relationships with four other species. The results from the co-expression analyses indicated that seven CmbZIPs in three key modules may be important in regulating starch accumulation in chestnut seeds. Yeast one-hybrid assays showed that transcription factors CmbZIP13 and CmbZIP35 might participate in starch accumulation in the chestnut seed by binding to the promoters of CmISA2 and CmSBE1_2, respectively. Our study provided basic information on CmbZIP genes, which can be utilized in future functional analysis and breeding studies.
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Affiliation(s)
- Penglong Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
| | - Jing Liu
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
| | - Nan Jia
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Science, Changli, Hebei, China
| | - Meng Wang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
| | - Yi Lu
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
| | - Dongsheng Wang
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
| | - Jingzheng Zhang
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
| | - Haie Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
| | - Xuan Wang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Qinhuangdao, Hebei, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Changli, Hebei, China
- *Correspondence: Xuan Wang,
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Chowdhury AT, Hasan MN, Bhuiyan FH, Islam MQ, Nayon MRW, Rahaman MM, Hoque H, Jewel NA, Ashrafuzzaman M, Prodhan SH. Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions. PLoS One 2023; 18:e0273592. [PMID: 37163561 PMCID: PMC10171694 DOI: 10.1371/journal.pone.0273592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/27/2023] [Indexed: 05/12/2023] Open
Abstract
Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.
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Affiliation(s)
- Aniqua Tasnim Chowdhury
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Fahmid H Bhuiyan
- Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Md Qamrul Islam
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Rakib Wazed Nayon
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Mashiur Rahaman
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Ashrafuzzaman
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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10
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Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks. Genes (Basel) 2022; 13:genes13060954. [PMID: 35741716 PMCID: PMC9222338 DOI: 10.3390/genes13060954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.
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11
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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12
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Paul A, Chatterjee A, Subrahmanya S, Shen G, Mishra N. NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:777884. [PMID: 34987532 PMCID: PMC8720784 DOI: 10.3389/fpls.2021.777884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.
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Affiliation(s)
| | | | | | - Guoxin Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Neelam Mishra
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, India
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13
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Paul A, Srivastava AP, Subrahmanya S, Shen G, Mishra N. In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis. PLoS One 2021; 16:e0258657. [PMID: 34735479 PMCID: PMC8568164 DOI: 10.1371/journal.pone.0258657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022] Open
Abstract
Mitogen activated protein kinase kinase kinase (MAPKKK) form the upstream component of MAPK cascade. It is well characterized in several plants such as Arabidopsis and rice however the knowledge about MAPKKKs in tea plant is largely unknown. In the present study, MAPKKK genes of tea were obtained through a genome wide search using Arabidopsis thaliana as the reference genome. Among 59 candidate MAPKKK genes in tea, 17 genes were MEKK-like, 31 genes were Raf-like and 11 genes were ZIK- like. Additionally, phylogenetic relationships were established along with structural analysis, which includes gene structure, its location as well as conserved motifs, cis-acting regulatory elements and functional domain signatures that were systematically examined. Also, on the basis of one orthologous gene found between tea and Arabidopsis, functional interaction was carried out in C. sinensis based on an Arabidopsis association model. The expressional profiles indicated major involvement of MAPKKK genes from tea in response to various abiotic stress factors. Taken together, this study provides the targets for additional inclusive identification, functional study, and provides comprehensive knowledge for a better understanding of the MAPKKK cascade regulatory network in C. sinensis.
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Affiliation(s)
- Abhirup Paul
- Department of Biochemistry, REVA University, Bangalore, Karnataka, India
| | - Anurag P. Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Shreya Subrahmanya
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
| | - Guoxin Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Neelam Mishra
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
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14
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Wu Y, Xia M, Zhang X, Li X, Zhang R, Yan Y, Lang F, Zheng Y, Wang M. Unraveling the metabolic network of organic acids in solid-state fermentation of Chinese cereal vinegar. Food Sci Nutr 2021; 9:4375-4384. [PMID: 34401086 PMCID: PMC8358386 DOI: 10.1002/fsn3.2409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/23/2021] [Accepted: 05/30/2021] [Indexed: 12/27/2022] Open
Abstract
Shanxi aged vinegar (SAV) is fermented by multispecies microorganism with solid-state fermentation (SSF) technology, which contains a variety of organic acids. However, the metabolic network of them in SSF is still unclear. In this study, metagenomics technology was used to reveal the microbial community and functional genes in SAV fermentation. The metabolic network of key organic acids with taste active value higher than 1 was reconstructed for the first time, including acetate, lactate, malate, citrate, succinate, and tartrate. The results show pyruvate is the core compound in the metabolic network of organic acids. Metabolic pathway of acetate plays a pivotal role in this network, and acetate has regulatory function on metabolism of other organic acids. Acetobacter and Lactobacillus are the predominant genera for organic acid metabolism in SSF of SAV. This is also the first report on metabolic network of organic acids in cereal vinegar, adding new knowledge on the flavor substance metabolism during multispecies fermentation of traditional fermented food.
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Affiliation(s)
- Yanfang Wu
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
| | - Menglei Xia
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
- Shanxi Province Key Laboratory of Vinegar Fermentation Science and EngineeringShanxi Zilin Vinegar Industry Co., Ltd.TaiyuanChina
| | - Xiaofeng Zhang
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
| | - Xiaowei Li
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
| | - Rongzhan Zhang
- Tianjin Tianli Duliu Mature Vinegar Co., Ltd.TianjinChina
| | - Yufeng Yan
- Shanxi Province Key Laboratory of Vinegar Fermentation Science and EngineeringShanxi Zilin Vinegar Industry Co., Ltd.TaiyuanChina
| | - Fanfan Lang
- Shanxi Province Key Laboratory of Vinegar Fermentation Science and EngineeringShanxi Zilin Vinegar Industry Co., Ltd.TaiyuanChina
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
- Shanxi Province Key Laboratory of Vinegar Fermentation Science and EngineeringShanxi Zilin Vinegar Industry Co., Ltd.TaiyuanChina
| | - Min Wang
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationCollege of BiotechnologyTianjin University of Science & TechnologyTianjinChina
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15
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Genome-wide identification and expression analysis of glycosyltransferase gene family 1 in Quercus robur L. J Appl Genet 2021; 62:559-570. [PMID: 34241817 DOI: 10.1007/s13353-021-00650-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022]
Abstract
Glycosyltransferase gene family 1, also known as uridine diphosphate glycosyltransferase (UGT), is the largest glycosyltransferase family in plants, playing a vital role in their growth and development. In this study, 244 UGT genes with conserved PSPG motifs were identified in the genome of Quercus robur L. The collinearity analysis results showed that tandem repeat was the main way of UGT genes expansion in Q. robur, with 21 groups of 55 tandem repeat genes. UGT genes were divided into 15 subgroups A-P; group K was lost, and the gene structure and conserved domain of the same subgroup were basically the same. Cis-element analysis showed that upstream 2,000 bp promoter sequence of UGT genes contained light response elements, plant hormone response elements, and stress-related cis-elements, which indicated that UGT genes of Q. robur might be regulated by various metabolic pathways. In particular, some UGTs in group L of Q. robur contained a conserved promoter structure. The expression pattern analysis results demonstrated that UGT genes of groups B, D, E, and I were differentially expressed under Tortrix viridana L. stress. The expression of UGTs in group E decreased under stress, the expression of group L increased, and that of genes in groups D and B were different. The functions of UGT genes in E and L groups are relatively conservative, and their functions may also conserve among species. The study results have a particular reference value for further research on the function of Q. robur UGT genes.
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Tian M, Wu A, Zhang M, Zhang J, Wei H, Yang X, Ma L, Lu J, Fu X, Wang H, Yu S. Genome-Wide Identification of the Early Flowering 4 ( ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance. Front Genet 2021; 12:686852. [PMID: 34326861 PMCID: PMC8315153 DOI: 10.3389/fgene.2021.686852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock's regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.
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Affiliation(s)
- Miaomiao Tian
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Fu X, Yang Y, Kang M, Wei H, Lian B, Wang B, Ma L, Hao P, Lu J, Yu S, Wang H. Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:801239. [PMID: 35111180 PMCID: PMC8802827 DOI: 10.3389/fpls.2021.801239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/23/2021] [Indexed: 05/17/2023]
Abstract
The caleosin (CLO) protein family displays calcium-binding properties and plays an important role in the abiotic stress response. Here, a total of 107 CLO genes were identified in 15 plant species, while no CLO genes were detected in two green algal species. Evolutionary analysis revealed that the CLO gene family may have evolved mainly in terrestrial plants and that biological functional differentiation between species and functional expansion within species have occurred. Of these, 56 CLO genes were identified in four cotton species. Collinearity analysis showed that CLO gene family expansion mainly occurred through segmental duplication and whole-genome duplication in cotton. Sequence alignment and phylogenetic analysis showed that the CLO proteins of the four cotton species were mainly divided into two types: H-caleosins (class I) and L-caleosins (class II). Cis-acting element analysis and quantitative RT-PCR (qRT-PCR) suggested that GhCLOs might be regulated by abscisic acid (ABA) and methyl jasmonate (MeJA). Moreover, transcriptome data and qRT-PCR results revealed that GhCLO genes responded to salt and drought stresses. Under salt stress, gene-silenced plants (TRV: GhCLO06) showed obvious yellowing and wilting, higher malondialdehyde (MDA) content accumulation, and significantly lower activities of superoxide dismutase (SOD) and peroxidase (POD), indicating that GhCLO06 plays a positive regulatory role in cotton salt tolerance. In gene-silenced plants (TRV: GhCLO06), ABA-related genes (GhABF2, GhABI5, and GhNAC4) were significantly upregulated after salt stress, suggesting that the regulation of salt tolerance may be related to the ABA signaling pathway. This research provides an important reference for further understanding and analyzing the molecular regulatory mechanism of CLOs for salt tolerance.
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Affiliation(s)
- Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Yonglin Yang
- Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Meng Kang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Boying Lian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Baoquan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
- *Correspondence: Shuxun Yu,
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China
- Hantao Wang,
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Bettaieb I, Hamdi J, Bouktila D. Genome-wide analysis of HSP90 gene family in the Mediterranean olive ( Olea europaea subsp. europaea) provides insight into structural patterns, evolution and functional diversity. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2301-2318. [PMID: 33268931 PMCID: PMC7688888 DOI: 10.1007/s12298-020-00888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 05/09/2023]
Abstract
Plants regularly experience multiple abiotic and biotic pressures affecting their normal development. The 90-kDa heat shock protein (HSP90) plays a dynamic role in countering abiotic and biotic stresses via a plethora of functional mechanisms. The HSP90 has been investigated in many plant species. However, there is little information available about this gene family in the cultivated Mediterranean olive tree, Olea europaea subsp. europaea var. europaea. In the current study, we systematically performed genome-wide identification and characterization of the HSP90 gene family in O. europaea var. europaea (OeHSP90s). Twelve regular OeHSP90s were identified, which were phylogenetically grouped into two major clusters and four sub-clusters, showing five paralogous gene pairs evolving under purifying selection. All of the 12 proteins contained a Histidine kinase-like ATPase (HATPase_c) domain, justifying the role played by HSP90 proteins in ATP binding and hydrolysis. The predicted 3D structure of OeHSP90 proteins provided information to understand their functions at the biochemical level. Consistent with their phylogenetic relationships, OeHSP90 members were predicted to be localized in different cellular compartments, suggesting their involvement in various subcellular processes. In consonance with their spatial organization, olive HSP90 family members were found to share similar motif arrangements and similar number of exons. We found that OeHSP90 promoters contained various cis-acting elements associated with light responsiveness, hormone signaling pathways and reaction to various stress conditions. In addition, expression sequence tags (ESTs) analysis offered a view of OeHSP90 tissue- and developmental stage specific pattern of expression. Proteins interacting with OeHSP90s were predicted and their potential roles were discussed. Overall, our results offer premises for further investigation of the implication of HSP90 genes in the physiological processes of the olive and its adaptation to stresses.
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Affiliation(s)
- Inchirah Bettaieb
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Jihen Hamdi
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Dhia Bouktila
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
- Institut Supérieur de Biotechnologie de Béja, Université de Jendouba, Béja, Tunisia
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Zhang J, Wu A, Wei H, Hao P, Zhang Q, Tian M, Yang X, Cheng S, Fu X, Ma L, Wang H, Yu S. Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton. BMC Genomics 2020; 21:643. [PMID: 32948145 PMCID: PMC7501681 DOI: 10.1186/s12864-020-07069-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/14/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. RESULTS In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. CONCLUSIONS Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
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Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Miaomiao Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Fu X, Lu Z, Wei H, Zhang J, Yang X, Wu A, Ma L, Kang M, Lu J, Wang H, Yu S. Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton. Front Genet 2020; 11:964. [PMID: 32973884 PMCID: PMC7461838 DOI: 10.3389/fgene.2020.00964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/31/2020] [Indexed: 01/17/2023] Open
Abstract
The sodium/hydrogen antiporter (NHX) gene family with the Na+/H+ exchange protein domain is a transporter of sodium and hydrogen ions and plays an important role in the response of plants to salt stress. Studying the response of cotton to salt stress through comprehensive identification and analysis of NHX genes in several species and their roles in salt tolerance mechanisms is of great significance. In this study, 23, 24, 12, and 12 NHX genes were identified from Gossypium hirsutum (Gh), G. barbadense, G. arboreum and G. raimondii, respectively. Phylogenetic analysis showed that these genes were mainly divided into three clades with significant subcellular localization, namely, endosome (Endo-class), plasma membrane (PM-class) and vacuole (Vac-class). By analyzing the structure of NHX genes and proteins, each branch of the NHX gene family was found to be structurally conserved, and collinearity analysis showed that NHX genes were mainly expressed through whole genome and segmental duplication. The non-synonymous (Ka)/synonymous (Ks) values showed that the NHX gene family experienced strong purifying selection during long-term evolution. Cis-acting element analysis showed that the NHX gene family may be related to the regulation of abscisic acid (ABA) and methyl jasmonate (MeJA) hormones. Additionally, transcriptomic data analysis and qRT-PCR showed that GhNHXs exhibited different expression patterns in each tissue and under different salinities. These results provide an important reference for us to further understand and analyze the molecular regulation mechanism of cotton NHX genes.
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Affiliation(s)
- Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meng Kang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Wan Y, Wang Z, Xia J, Shen S, Guan M, Zhu M, Qiao C, Sun F, Liang Y, Li J, Lu K, Qu C. Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance. Int J Mol Sci 2020; 21:E2209. [PMID: 32210032 PMCID: PMC7139346 DOI: 10.3390/ijms21062209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022] Open
Abstract
Phosphorus transporter (PHT) genes encode H2PO4-/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1-PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.
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Affiliation(s)
- Yuanyuan Wan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zhen Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jichun Xia
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Shulin Shen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Meichen Zhu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cailin Qiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Fujun Sun
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Ying Liang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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