1
|
Wang X, Dong J, Hu Y, Huang Q, Lu X, Huang Y, Sheng M, Cao L, Xu B, Li Y, Zong Y, Guo W. Identification and Characterization of the Glutathione S-Transferase Gene Family in Blueberry ( Vaccinium corymbosum) and Their Potential Roles in Anthocyanin Intracellular Transportation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1316. [PMID: 38794388 PMCID: PMC11125127 DOI: 10.3390/plants13101316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
The glutathione S-transferases (GSTs, EC 2.5.1.18) constitute a versatile enzyme family with pivotal roles in plant stress responses and detoxification processes. Recent discoveries attributed the additional function of facilitating anthocyanin intracellular transportation in plants to GSTs. Our study identified 178 VcGST genes from 12 distinct subfamilies in the blueberry genome. An uneven distribution was observed among these genes across blueberry's chromosomes. Members within the same subfamily displayed homogeneity in gene structure and conserved protein motifs, whereas marked divergence was noted among subfamilies. Functional annotations revealed that VcGSTs were significantly enriched in several gene ontology and KEGG pathway categories. Promoter regions of VcGST genes predominantly contain light-responsive, MYB-binding, and stress-responsive elements. The majority of VcGST genes are subject to purifying selection, with whole-genome duplication or segmental duplication serving as key processes that drive the expansion of the VcGST gene family. Notably, during the ripening of the blueberry fruit, 100 VcGST genes were highly expressed, and the expression patterns of 24 of these genes demonstrated a strong correlation with the dynamic content of fruit anthocyanins. Further analysis identified VcGSTF8, VcGSTF20, and VcGSTF22 as prime candidates of VcGST genes involved in the anthocyanin intracellular transport. This study provides a reference for the exploration of anthocyanin intracellular transport mechanisms and paves the way for investigating the spectrum of GST functions in blueberries.
Collapse
Affiliation(s)
- Xuxiang Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Jiajia Dong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yiting Hu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Qiaoyu Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Xiaoying Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yilin Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Mingyang Sheng
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Lijun Cao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Buhuai Xu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
| | - Yongqiang Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Yu Zong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Weidong Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (X.W.); (J.D.); (Y.H.); (Q.H.); (X.L.); (Y.H.); (M.S.); (L.C.); (B.X.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
2
|
Begum K, Das A, Ahmed R, Akhtar S, Kulkarni R, Banu S. Genome-wide analysis of respiratory burst oxidase homolog ( Rboh) genes in Aquilaria species and insight into ROS-mediated metabolites biosynthesis and resin deposition. FRONTIERS IN PLANT SCIENCE 2024; 14:1326080. [PMID: 38405033 PMCID: PMC10893762 DOI: 10.3389/fpls.2023.1326080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/18/2023] [Indexed: 02/27/2024]
Abstract
Respiratory burst oxidase homolog (Rboh) generates reactive oxygen species (ROS) as a defense response during biotic and abiotic stress. In Aquilaria plants, wounding and fungal infection result in biosynthesis and deposition of secondary metabolites as defense responses, which later form constituents of fragrant resinous agarwood. During injury and fungal invasion, Aquilaria tree generates ROS species via the Rboh enzymes. Despite the implication of Rboh genes in agarwood formation, no comprehensive genomic-level study of the Rboh gene family in Aquilaria is present. A systematic illustration of their role during stress and involvement in initiating signal cascades for agarwood metabolite biosynthesis is missing. In this study, 14 Rboh genes were retrieved from genomes of two Aquilaria species, A. agallocha and A. sinensis, and were classified into five groups. The promoter regions of the genes had abundant of stress-responsive elements. Protein-protein network and in silico expression analysis suggested their functional association with MAPK proteins and transcription factors such as WRKY and MYC2. The study further explored the expression profiles of Rboh genes and found them to be differentially regulated in stress-induced callus and stem tissue, suggesting their involvement in ROS generation during stress in Aquilaria. Overall, the study provides in-depth insight into two Rboh genes, AaRbohC and AaRbohA, highlighting their role in defense against fungal and abiotic stress, and likely during initiation of agarwood formation through modulation of genes involved in secondary metabolites biosynthesis. The findings presented here offer valuable information about Rboh family members, which can be leveraged for further investigations into ROS-mediated regulation of agarwood formation in Aquilaria species.
Collapse
Affiliation(s)
- Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| |
Collapse
|
3
|
Wang J, Wang Y, Wu X, Wang B, Lu Z, Zhong L, Li G, Wu X. Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1128007. [PMID: 36874919 PMCID: PMC9981963 DOI: 10.3389/fpls.2022.1128007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.
Collapse
Affiliation(s)
- Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liping Zhong
- College of Horticulture Science, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
4
|
Feng X, Abubakar AS, Chen K, Yu C, Zhu A, Chen J, Gao G, Wang X, Mou P, Chen P. Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes. Front Genet 2023; 14:1080909. [PMID: 36896232 PMCID: PMC9989182 DOI: 10.3389/fgene.2023.1080909] [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: 10/26/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.
Collapse
Affiliation(s)
- Xinkang Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Department of Agronomy, Bayero University, Kano, Nigeria
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Pan Mou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| |
Collapse
|
5
|
Sabir IA, Manzoor MA, Shah IH, Abbas F, Liu X, Fiaz S, Shah AN, Jiu S, Wang J, Abdullah M, Zhang C. Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes ( F. vesca, P. mume, and P. avium) Under Phytohormone Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:942969. [PMID: 35874024 PMCID: PMC9302438 DOI: 10.3389/fpls.2022.942969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus avium L., F. vesca, and P. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the PavGAox genes have a remarkably well-maintained exon-intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation, PavGAox genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in Prunus avium L., F. vesca, and P. mume revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of cis-regulatory elements in the upstream region of the 140 PavGAox members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the PavGAox genes display a variety of tissue expression patterns in diverse tissues, with most of the PavGAox genes displaying tissue-specific expression patterns. Furthermore, most of the PavGAox genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of PavGAox genes are responsible for maintaining the GA level in plant-like Pav co4017001.1 g010.1.br, Pav sc0000024.1 g340.1.br, and Pav sc0000024.1 g270.1.mk. The subcellular localization of PavGAox protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family's interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.
Collapse
Affiliation(s)
- Irfan Ali Sabir
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Farhat Abbas
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xunju Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Songtao Jiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Abdullah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
6
|
Identification and Characterization of the Core Region of ZmDi19-5 Promoter Activity and Its Upstream Regulatory Proteins. Int J Mol Sci 2022; 23:ijms23137390. [PMID: 35806396 PMCID: PMC9267117 DOI: 10.3390/ijms23137390] [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: 06/06/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
Drought-induced 19 (Di19) family genes play important roles in plant growth, development, and environmental stress responses. However, little is known about this family in maize. The upstream regulatory network of Di19 genes remains poorly understood in plant stress response, especially. In this study, seven ZmDi19 genes were identified, and sequence alignment, gene structure, and phylogenetic analysis was conducted. According to the phylogenetic analysis, the ZmDi19-5 promoter was cloned and multiple putative stress-responsive cis-acting elements (CAEs) were found in the promoter region. The transient transformation assay indicated that firefly luciferase (LUC)-expressed activity driven by the ZmDi19-5 promoter can be significantly induced by drought stress. A 450 bp core region of ZmDi19-5 promoter was identified, and 28 upstream regulatory proteins were screened using yeast one-hybird (Y1H) system. According to the functional annotation, some genes were related to photosynthesis, light response, and water transport, which may suggest the important roles of these genes in drought response. Particularly, five members that may be involved in drought response exhibited strong binding activity to the core region of the ZmDi19-5 promoter. This study laid an important foundation for further revealing the molecular mechanisms and regulatory network of Di19 genes in drought stress response.
Collapse
|
7
|
Zhou L, Yarra R. Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress. PROTOPLASMA 2022; 259:469-483. [PMID: 34212248 DOI: 10.1007/s00709-021-01666-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/07/2021] [Indexed: 06/13/2023]
Abstract
The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Phylogenetic analysis clustered all EgbZIPs into 12 clusters with Arabidopsis and rice bZIPs. EgbZIP gene structure analysis showed a distinct variation in the intron-exon organization among all EgbZIPs. Conserved motif analysis demonstrated the occurrence of ten additional conserved motifs besides having a common bZIP domain. All the identified 97 EgbZIPs were unevenly distributed on 16 chromosomes and exhibited tandem duplication in oil palm genome. Our results aslo demonstrated that tissue-specific expression patterns of EgbZIPs based on the available transcriptome data of six different tissue of oil palm. Stress-responsive expression analysis showed that 11EgbZIP transcription factors were highly expressed under cold, salinity, drought stress conditions. Taken together, our findings will provide insightful information on bZIP transcription factors as one of the stress-responsive regulators in oil palm.
Collapse
Affiliation(s)
- Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| |
Collapse
|
8
|
Zhou L, Yarra R, Jin L, Yang Y, Cao H, Zhao Z. Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm. BMC Genomics 2022; 23:11. [PMID: 34983381 PMCID: PMC8729141 DOI: 10.1186/s12864-021-08245-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background Oil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm. Results We reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. Conclusions A total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08245-2.
Collapse
Affiliation(s)
- Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Zhihao Zhao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| |
Collapse
|
9
|
Sabir IA, Manzoor MA, Shah IH, Liu X, Jiu S, Wang J, Alam P, Abdullah M, Zhang C. Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry ( Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:938800. [PMID: 35903236 PMCID: PMC9315441 DOI: 10.3389/fpls.2022.938800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/16/2022] [Indexed: 05/08/2023]
Abstract
Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not identified in sweet cherry (Prunus avium). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in P. avium genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that PavGST genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the PavGST genes had a relatively well-maintained exon-intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the PavGST genes showed a relatively well-maintained motif and exons-introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of PavGST gene family. Promoter regions of PavGST genes contain numerous cis-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry PavGSTs showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries.
Collapse
Affiliation(s)
- Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Iftikhar Hussain Shah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Caixi Zhang,
| |
Collapse
|
10
|
Manzoor MA, Li G, Abdullah M, Han W, Wenlong H, Yang Z, Xinya W, Yu Z, Xiaofeng F, Qing J, Shafique MS, Cai Y. Genome-wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri). PHYSIOLOGIA PLANTARUM 2021; 173:1163-1178. [PMID: 34363225 DOI: 10.1111/ppl.13511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/18/2021] [Accepted: 07/21/2021] [Indexed: 05/12/2023]
Abstract
The Multidrug and Toxic Compound Extrusion (MATE) protein belongs to a secondary transporter gene family, which plays a primary role in transporting many kinds of substrates such as organic compounds, secondary metabolites, and phytohormones. MATE protein members exist in both prokaryotes and eukaryotes. However, evolution and comprehensive analysis of the MATE genes has not been performed in Rosaceae species. In the present study, a total of 404 MATEs genes were identified from six Rosaceae genomes (Prunus avium, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Prunus mume, and Malus domestica) and classified into eight main subfamilies (I-VII) based on structural and phylogenetic analysis. Microcollinearity analysis showed that whole-genome duplication events might play a vital role in the expansion of the MATE genes family. The Ka/Ks analysis, chromosomal localization, subcellular localization, and molecular characteristics (length, weight, and pI) were performed using various bioinformatics tools. Furthermore, different subfamilies have different introns-exons structures, cis-acting elements, and conserved motifs analysis, indicating functional divergence in the MATE family. Subsequently, RNA-seq analysis and real-time qRT-PCR were conducted during Chinese pear fruit development. Moreover, PbMATE genes were significantly expressed under hormonal treatments of MeJA (methyl jasmonate), SA (salicylic acid), and ABA (abscisic acid). Overall, our results provide helpful insights into the functions, expansion complexity, and evolutions of the MATE genes in Chinese pear and five Rosaceae species.
Collapse
Affiliation(s)
| | - Guohui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wang Han
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Han Wenlong
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhang Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wang Xinya
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhao Yu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Feng Xiaofeng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jin Qing
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | | | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| |
Collapse
|
11
|
Liu J, Xu L, Shang J, Hu X, Yu H, Wu H, Lv W, Zhao Y. Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses. Genet Mol Biol 2021; 44:e20210035. [PMID: 34606562 PMCID: PMC8493800 DOI: 10.1590/1678-4685-gmb-2021-0035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
Superoxide dismutase proteins (SODs) are antioxidant enzymes with important roles in abiotic stress responses. The SOD gene family has been systematically analyzed in many plants; however, it is still poorly understood in maize. Here, a bioinformatics analysis of maize SOD gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, gene duplications, promoter cis-elements and GO annotations. In total, 13 SOD genes were identified in maize and five members were involved in segmental duplication. Phylogenetic analysis indicated that SODs from maize and other plants comprised two groups, which could be further classified into different subgroups, with most members in the same subgroup having the same subcellular localization. The ZmSOD promoters contained 2-10 stress-responsive cis-elements with different distributions. Heatmap analysis indicated that ZmSODs were expressed in most of the detected tissues and organs. The expression patterns of ZmSODs were investigated under drought and salt treatments by qRT-PCR, and most members were responsive to drought or salt stress, especially some ZmSODs with significant expression changes were identified, such as ZmCSD2 and ZmMSD2, suggesting the important roles of ZmSODs in abiotic stress responses. Our results provide an important basis for further functional study of ZmSODs in future study.
Collapse
Affiliation(s)
- Jing Liu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Lijuan Xu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Jian Shang
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Xiaolin Hu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Haitao Yu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Hongying Wu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Wenben Lv
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China
| | - Yang Zhao
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| |
Collapse
|
12
|
Han G, Ma H, Ren S, Gao X, He X, Zhu S, Deng R, Zhang S. Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor. Microbiologyopen 2020; 9:e1042. [PMID: 32529805 PMCID: PMC7424253 DOI: 10.1002/mbo3.1042] [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: 10/23/2019] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023] Open
Abstract
Fungal mycelia can eliminate almost all cocultured cyanobacterial cells within a short time. However, molecular mechanisms of algicidal fungi are poorly understood. In this study, a time‐course transcriptomic analysis of algicidal fungus Bjerkandera adusta T1 was applied to investigate gene expression and regulation. A total of 132, 300, 422, and 823 differentially expressed genes (DEGs) were identified at 6, 12, 24, and 48 hr, respectively. Most DEGs exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Many decomposition genes encoding endopeptidases were induced a little later in B. adusta T1 when compared with previously investigated algicidal fungus Trametes versicolor F21a. Besides, the accumulated expression of Polysaccharide lyases8 (PL8) gene with peptidoglycan and alginate decomposition abilities was greatly delayed in B. adusta T1 relative to T. versicolor F21a. It was implied that endopeptidases and enzymes of PL8 might be responsible for the strong algicidal ability of B. adusta T1 as well as T. versicolor F21a.
Collapse
Affiliation(s)
- Guomin Han
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Hui Ma
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shenrong Ren
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xueyan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaolong He
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Suwen Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Ruining Deng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shihua Zhang
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| |
Collapse
|