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Wu C, Cai D, Li J, Lin Z, Wei W, Shan W, Chen J, Lu W, Su X, Kuang J. Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111. HORTICULTURE RESEARCH 2024; 11:uhae053. [PMID: 38706579 PMCID: PMC11069428 DOI: 10.1093/hr/uhae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024]
Abstract
Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.
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Affiliation(s)
- Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Danling Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zengxiang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xinguo Su
- Agronomy Dean, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Dai Y, Wang Y, Zeng L, Jia R, He L, Huang X, Zhao H, Liu D, Zhao H, Hu S, Gao L, Guo A, Xia W, Ji C. Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya. Int J Mol Sci 2023; 24:14039. [PMID: 37762345 PMCID: PMC10531014 DOI: 10.3390/ijms241814039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.
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Affiliation(s)
- Yunsu Dai
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Yu Wang
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Liwang Zeng
- Key Laboratory of Applied Research on Tropical Crop Information Technology of Hainan Province, Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Linwen He
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Xueying Huang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Difa Liu
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haixu Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Shuai Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Ling Gao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Anping Guo
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Wei Xia
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
| | - Changmian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
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Wang Z, Yao XM, Jia CH, Xu BY, Wang JY, Liu JH, Jin ZQ. Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana ( Musa acuminata L. AAA group, cv. Cavendish). FRONTIERS IN PLANT SCIENCE 2023; 14:1072086. [PMID: 37035063 PMCID: PMC10074854 DOI: 10.3389/fpls.2023.1072086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses. RESULTS In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in Musa acuminata genome and found the number of MaCOMT gene family was the largest, while MaC3Hs had only two members. MaPALs retained the original members, and the number of Ma4CLs in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for MaC3Hs, and tandem duplication was the main way to expand the number of MaCOMTs. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses. CONCLUSION This study systematically identified the lignin biosynthesis genes in the Musa acuminata genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Xiao-ming Yao
- Beijing Genomics Institute (BGI)-Sanya, Beijing Genomics Institute (BGI)-Shenzhen, Sanya, China
| | - Cai-hong Jia
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Bi-yu Xu
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jing-yi Wang
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ju-hua Liu
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhi-qiang Jin
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
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Zuo ZF, Lee HY, Kang HG. Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses. Int J Mol Sci 2023; 24:ijms24021419. [PMID: 36674933 PMCID: PMC9867082 DOI: 10.3390/ijms24021419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.
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Jia C, Wang Z, Wang J, Miao H, Zhang J, Xu B, Liu J, Jin Z, Liu J. Genome-Wide Analysis of the Banana WRKY Transcription Factor Gene Family Closely Related to Fruit Ripening and Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050662. [PMID: 35270130 PMCID: PMC8912484 DOI: 10.3390/plants11050662] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/14/2022] [Accepted: 02/24/2022] [Indexed: 05/11/2023]
Abstract
WRKY transcription factors (TFs) play an important role in plant responses to biotic and abiotic stress as well as in plant growth and development. In the present study, bioinformatics methods were used to identify members of the WRKY transcription factor family in the Musa acuminata (DH-Pahang) genome (version 2). A total of 164 MaWRKYs were identified and phylogenetic analysis showed that MaWRKYs could be categorized into three subfamilies. Overall, the 162 MaWRKYs were distributed on 11 chromosomes, and 2 genes were not located on the chromosome. There were 31 collinear genes from segmental duplication and 7 pairs of genes from tandem duplication. RNA-sequencing was used to analyze the expression profiles of MaWRKYs in different fruit development, ripening stages, under various abiotic and biotic stressors. Most of the MaWRKYs showed a variety of expression patterns in the banana fruit development and ripening stages. Some MaWRKYs responded to abiotic stress, such as low temperature, drought, and salt stress. Most differentially expressed MaWRKYs were downregulated during banana's response to Foc TR4 infection, which plays an important role in physiological regulation to stress. Our findings indicate that MaWRKY21 directly binds to the W-box of the MaICS promoter to decrease MaICS transcription and then reduce the enzyme activity. These studies have improved our understanding of the molecular basis for the development and stress resistance of an important banana variety.
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Affiliation(s)
- Caihong Jia
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (J.L.); (Z.J.); (J.L.)
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Z.W.); (J.W.); (H.M.); (J.Z.); (B.X.)
- Correspondence: (J.L.); (Z.J.); (J.L.)
| | - Jihong Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China;
- Correspondence: (J.L.); (Z.J.); (J.L.)
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Cheng C, Liu F, Sun X, Wang B, Liu J, Ni X, Hu C, Deng G, Tong Z, Zhang Y, Lü P. Genome-wide identification of FAD gene family and their contributions to the temperature stresses and mutualistic and parasitic fungi colonization responses in banana. Int J Biol Macromol 2022; 204:661-676. [PMID: 35181326 DOI: 10.1016/j.ijbiomac.2022.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022]
Abstract
Fatty acid desaturase (FAD) plays important roles in plant growth and development and plant defense processes. In this study, we identified 27 MaFAD genes from the banana genome. According to the amino acid sequence similarities, their encoded proteins could be classified into five subfamilies. This classification is consistently supported by their gene and protein structures, conserved motifs and subcellular localizations. Segmental duplication events were found to play predominant roles in the MaFAD gene family expansion. Thirty miRNAs targeting MaFADs were identified and many hormone- and stress-responsive cis-acting elements and transcription factor binding sites (TFBSs) were identified in their promoters, indicating that the MaFADs expression regulation was very complicated. Gene expression analysis showed that some MaFADs showed significant differential expression in response to high and low temperature. FocTR4 influenced greatly the expression of several MaFADs and greatly induced the fatty acid (FA) accumulations in roots. Although S. indica showed no significant influence on the expression of most MaFADs, it could greatly alleviate the influence of FocTR4 on several MaFADs and FA biosynthesis. Our study revealed that MaFADs contributed greatly to the responses of high and low temperature stresses and mutualistic and parasitic fungi colonization in banana.
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Affiliation(s)
- Chunzhen Cheng
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Fan Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xueli Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Bin Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiapeng Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueting Ni
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zheng Tong
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongyan Zhang
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Wang J, Wang Z, Jia C, Miao H, Zhang J, Liu J, Xu B, Jin Z. Genome-Wide Identification and Transcript Analysis of TCP Gene Family in Banana (Musa acuminata L.). Biochem Genet 2021; 60:204-222. [PMID: 34156635 DOI: 10.1007/s10528-021-10100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) gene family has versatile functions in diverse aspects of plants. However, less research on banana TCPs was done comprehensively. Accordingly, 48 banana TCP genes were characterized on aspects of gene structure, conserved motifs, phylogenetic relationship, and expression patterns. Members of the MaTCP gene family were unevenly distributed among 11 chromosomes and purification selection was the driving force of the MaTCP gene family. Gene duplication analysis indicated that segmental duplication is the major contributor to family expansion. Promoter analysis showed that MaTCPs might be involved in banana growth, development, and abiotic stress responses. Further, the expression of 12 MaTCPs was analyzed by real-time quantitative RT-PCR, and the protein interaction analysis showed that MaPCF10 and MaPCF13 may have an important function in banana fruit development and ripening. These results lay the foundation for further study of the functions of TCP genes in banana.
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Affiliation(s)
- Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana. Sci Rep 2021; 11:9948. [PMID: 33976263 PMCID: PMC8113564 DOI: 10.1038/s41598-021-89211-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 01/19/2023] Open
Abstract
The LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.
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Iqbal Z, Shariq Iqbal M, Singh SP, Buaboocha T. Ca 2+/Calmodulin Complex Triggers CAMTA Transcriptional Machinery Under Stress in Plants: Signaling Cascade and Molecular Regulation. FRONTIERS IN PLANT SCIENCE 2020; 11:598327. [PMID: 33343600 PMCID: PMC7744605 DOI: 10.3389/fpls.2020.598327] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/30/2020] [Indexed: 05/21/2023]
Abstract
Calcium (Ca2+) ion is a critical ubiquitous intracellular second messenger, acting as a lead currency for several distinct signal transduction pathways. Transient perturbations in free cytosolic Ca2+ ([Ca2+]cyt) concentrations are indispensable for the translation of signals into adaptive biological responses. The transient increase in [Ca2+]cyt levels is sensed by an array of Ca2+ sensor relay proteins such as calmodulin (CaM), eventually leading to conformational changes and activation of CaM. CaM, in a Ca2+-dependent manner, regulates several transcription factors (TFs) that are implicated in various molecular, physiological, and biochemical functions in cells. CAMTA (calmodulin-binding transcription activator) is one such member of the Ca2+-loaded CaM-dependent family of TFs. The present review focuses on Ca2+ as a second messenger, its interaction with CaM, and Ca2+/CaM-mediated CAMTA transcriptional regulation in plants. The review recapitulates the molecular and physiological functions of CAMTA in model plants and various crops, confirming its probable involvement in stress signaling pathways and overall plant development. Studying Ca2+/CaM-mediated CAMTA TF will help in answering key questions concerning signaling cascades and molecular regulation under stress conditions and plant growth, thus improving our knowledge for crop improvement.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Mohammed Shariq Iqbal
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Pucker B, Reiher F, Schilbert HM. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1103. [PMID: 32867203 PMCID: PMC7570183 DOI: 10.3390/plants9091103] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
- Department of Plant Sciences, Evolution and Diversity, University of Cambridge, Cambridge CB2 3EA, UK
| | - Franziska Reiher
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
| | - Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
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