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Ma MM, Zhang HF, Tian Q, Wang HC, Zhang FY, Tian X, Zeng RF, Huang XM. MIKC type MADS-box transcription factor LcSVP2 is involved in dormancy regulation of the terminal buds in evergreen perennial litchi ( Litchi chinensis Sonn.). HORTICULTURE RESEARCH 2024; 11:uhae150. [PMID: 38988620 PMCID: PMC11233856 DOI: 10.1093/hr/uhae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/20/2024] [Indexed: 07/12/2024]
Abstract
SHORT VEGETATIVE PHASE (SVP), a member of the MADS-box transcription factor family, has been reported to regulate bud dormancy in deciduous perennial plants. Previously, three LcSVPs (LcSVP1, LcSVP2 and LcSVP3) were identified from litchi genome, and LcSVP2 was highly expressed in the terminal buds of litchi during growth cessation or dormancy stages and down-regulated during growth stages. In this study, the role of LcSVP2 in governing litchi bud dormancy was examined. LcSVP2 was highly expressed in the shoots, especially in the terminal buds at growth cessation stage, whereas low expression was showed in roots, female flowers and seeds. LcSVP2 was found to be located in the nucleus and have transcription inhibitory activity. Overexpression of LcSVP2 in Arabidopsis thaliana resulted in a later flowering phenotype compared to the wild-type control. Silencing LcSVP2 in growing litchi terminal buds delayed re-entry of dormancy, resulting in significantly lower dormancy rate. The treatment also significantly up-regulated litchi FLOWERING LOCUS T2 (LcFT2). Further study indicates that LcSVP2 interacts with an AP2-type transcription factor, SMALL ORGAN SIZE1 (LcSMOS1). Silencing LcSMOS1 promoted budbreak and delayed bud dormancy. Abscisic acid (200 mg/L), which enforced bud dormancy, induced a short-term increase in the expression of LcSVP2 and LcSMOS1. Our study reveals that LcSVP2 may play a crucial role, likely together with LcSMOS1, in dormancy onset of the terminal bud and may also serve as a flowering repressor in evergreen perennial litchi.
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Lei C, Dang Z, Zhu M, Zhang M, Wang H, Chen Y, Zhang H. Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae. Gene 2024; 912:148382. [PMID: 38493974 DOI: 10.1016/j.gene.2024.148382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.
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Affiliation(s)
- Chen Lei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Mengting Zhang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Huiliang Wang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China.
| | - He Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Wang Z, Song G, Zhang F, Shu X, Wang N. Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris. Int J Mol Sci 2023; 24:14464. [PMID: 37833913 PMCID: PMC10572147 DOI: 10.3390/ijms241914464] [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: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.
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Affiliation(s)
- Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Guowei Song
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybeans (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Zhang S, Zhu C, Zhang X, Liu M, Xue X, Lai C, Xuhan X, Chen Y, Zhang Z, Lai Z, Lin Y. Single-cell RNA sequencing analysis of the embryogenic callus clarifies the spatiotemporal developmental trajectories of the early somatic embryo in Dimocarpus longan. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1277-1297. [PMID: 37235696 DOI: 10.1111/tpj.16319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
Plant embryogenic calli (ECs) can undergo somatic embryogenesis to regenerate plants. This process is mediated by regulatory factors, such as transcription factors and specifically expressed genes, but the precise molecular mechanisms underlying somatic embryogenesis at the single-cell level remain unclear. In this study, we performed high-resolution single-cell RNA sequencing analysis to determine the cellular changes in the EC of the woody plant species Dimocarpus longan (longan) and clarify the continuous cell differentiation trajectories at the transcriptome level. The highly heterogeneous cells in the EC were divided into 12 putative clusters (e.g., proliferating, meristematic, vascular, and epidermal cell clusters). We determined cluster-enriched expression marker genes and found that overexpression of the epidermal cell marker gene GDSL ESTERASE/LIPASE-1 inhibited the hydrolysis of triacylglycerol. In addition, the stability of autophagy was critical for the somatic embryogenesis of longan. The pseudo-timeline analysis elucidated the continuous cell differentiation trajectories from early embryonic cell division to vascular and epidermal cell differentiation during the somatic embryogenesis of longan. Moreover, key transcriptional regulators associated with cell fates were revealed. We found that ETHYLENE RESPONSIVE FACTOR 6 was characterized as a heat-sensitive factor that negatively regulates longan somatic embryogenesis under high-temperature stress conditions. The results of this study provide new spatiotemporal insights into cell division and differentiation during longan somatic embryogenesis at single-cell resolution.
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Affiliation(s)
- Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengyu Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, Toulouse, 31300, France
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Li S, Chen H, Hong J, Ye X, Wang J, Chen Y, Zhang L, Su Z, Yang Z. Chlorate-induced molecular floral transition revealed by transcriptomes. Open Life Sci 2023; 18:20220612. [PMID: 37528883 PMCID: PMC10389677 DOI: 10.1515/biol-2022-0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 08/03/2023] Open
Abstract
Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.
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Affiliation(s)
- Songgang Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Jiwang Hong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Jiabao Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Lei Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Zuanxian Su
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Ziqin Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
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Zhao Y, Liu G, Yang F, Liang Y, Gao Q, Xiang C, Li X, Yang R, Zhang G, Jiang H, Yu L, Yang S. Multilayered regulation of secondary metabolism in medicinal plants. MOLECULAR HORTICULTURE 2023; 3:11. [PMID: 37789448 PMCID: PMC10514987 DOI: 10.1186/s43897-023-00059-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/27/2023] [Indexed: 10/05/2023]
Abstract
Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanze Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
| | - Feng Yang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Liang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Run Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China.
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Li Z, Fu Z, Zhang S, Zhang X, Xue X, Chen Y, Zhang Z, Lai Z, Lin Y. Genome-wide analysis of the GLP gene family and overexpression of GLP1-5-1 to promote lignin accumulation during early somatic embryo development in Dimocarpus longan. BMC Genomics 2023; 24:138. [PMID: 36944911 PMCID: PMC10029309 DOI: 10.1186/s12864-023-09201-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree. Its fruit quality and yield are affected by embryo development. As a plant seed germination marker gene, the germin-like protein (GLP) gene plays an important role in embryo development. However, the mechanism underlying the role of the GLP gene in somatic embryos is still unclear. Therefore, we conducted genome-wide identification of the longan GLP (DlGLP) gene and preliminarily verified the function of DlGLP1-5-1. Thirty-five genes were identified as longan GLP genes and divided into 8 subfamilies. Based on transcriptome data and qRT‒PCR results, DlGLP genes exhibited the highest expression levels in the root, and the expression of most DlGLPs was upregulated during the early somatic embryogenesis (SE) in longan and responded to high temperature stress and 2,4-D treatment; eight DlGLP genes were upregulated under MeJA treatment, and four of them were downregulated under ABA treatment. Subcellular localization showed that DlGLP5-8-2 and DlGLP1-5-1 were located in the cytoplasm and extracellular stroma/chloroplast, respectively. Overexpression of DIGLP1-5-1 in the globular embryos (GEs) of longan promoted the accumulation of lignin and decreased the H2O2 content by regulating the activities of ROS-related enzymes. The results provide a reference for the functional analysis of DlGLPs and related research on improving lignin accumulation in the agricultural industry through genetic engineering.
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Affiliation(s)
- Zhuoyun Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuoran Fu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Zhao M, Li Y, Zhang X, You X, Yu H, Guo R, Zhao X. Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress. Int J Mol Sci 2022; 23:ijms232315225. [PMID: 36499551 PMCID: PMC9736363 DOI: 10.3390/ijms232315225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
Juglans mandshurica has strong freezing resistance, surviving temperatures as low as -40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT-PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.
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Affiliation(s)
- Minghui Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xinxin Zhang
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xiangling You
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Haiyang Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Ruixue Guo
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
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Jiang Q, Wang Z, Hu G, Yao X. Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha. BMC Genomics 2022; 23:650. [PMID: 36100898 PMCID: PMC9469511 DOI: 10.1186/s12864-022-08871-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis. RESULTS In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming. CONCLUSIONS We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.
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Affiliation(s)
- Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guangming Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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10
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Chen X, Xu X, Zhang S, Munir N, Zhu C, Zhang Z, Chen Y, Xuhan X, Lin Y, Lai Z. Genome-wide circular RNA profiling and competing endogenous RNA regulatory network analysis provide new insights into the molecular mechanisms underlying early somatic embryogenesis in Dimocarpus longan Lour. TREE PHYSIOLOGY 2022; 42:1876-1898. [PMID: 35313353 DOI: 10.1093/treephys/tpac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Circular RNAs (circRNAs) are widely involved in plant growth and development. However, the function of circRNAs in plant somatic embryogenesis (SE) remains elusive. Here, by using high-throughput sequencing, a total of 5029 circRNAs were identified in the three stages of longan (Dimocarpus longan Lour.) early SE. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed (DE) circRNA host genes were enriched in the 'non-homologous end-joining' (NHEJ) and 'butanoate metabolism' pathways. In addition, the reactive oxygen species (ROS) content during longan early SE was determined. The results indicated that ROS-induced DNA double-strand breaks may not depend on the NHEJ repair pathway. Correlation analyses of the levels of related metabolites (glutamate, γ-aminobutyrate and pyruvate) and the expression levels of circRNAs and their host genes involved in butanoate metabolism were performed. The results suggested that circRNAs may act as regulators of the expression of cognate mRNAs, thereby affecting the accumulation of related compounds. A competing endogenous RNA (ceRNA) network of DE circRNAs, DE mRNAs, DE long noncoding RNAs (lncRNAs) and DE microRNAs (miRNAs) was constructed. The results showed that the putative targets of the noncoding RNA (ncRNAs) were significantly enriched in the KEGG pathways 'mitogen-activated protein kinase signaling' and 'nitrogen metabolism'. Furthermore, the expression patterns of the candidate circRNAs, lncRNAs, miRNAs and mRNAs confirmed the negative correlation between miRNAs and ceRNAs. In addition, two circRNA overexpression vectors were constructed to further verify the ceRNA network correlations in longan early SE. Our study revealed the potential role of circRNAs in longan early SE, providing new insights into the intricate regulatory mechanism underlying plant SE.
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Affiliation(s)
- Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
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11
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Wan R, Song J, Lv Z, Qi X, Han X, Guo Q, Wang S, Shi J, Jian Z, Hu Q, Chen Y. Genome-Wide Identification and Comprehensive Analysis of the AP2/ERF Gene Family in Pomegranate Fruit Development and Postharvest Preservation. Genes (Basel) 2022; 13:895. [PMID: 35627280 PMCID: PMC9141937 DOI: 10.3390/genes13050895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
Pomegranate (Punica granatum L.) is a kind of fruit with significant economic, ecological and health values. AP2/ERF transcription factors belong to a large group of factors mainly found in plants and play key roles in plant growth and development. However, AP2/ERF genes in pomegranate and their implication in development and postharvest preservation have been little described. In this study, 116 PgAP2/ERF genes in pomegranate were identified and renamed based on their chromosomal distributions. Phylogenetic relationship with genes from other species, structures, duplications, annotations, cis-elements in promoter sequences, and protein-protein interaction networks among PgAP2/ERF proteins were comprehensively explored. Expression analysis revealed several PgAP2/ERFs associated with the phenotypes of pomegranate seed hardness, including PgAP2/ERF5, PgAP2/ERF36, PgAP2/ERF58, and PgAP2/ERF86. Subsequent analysis indicated that many differentially expressed PgAP2/ERF genes are potentially important regulators of pomegranate fruit development. Furthermore, expression of more than one-half of PgAP2/ERFs was repressed in 'Tunisian soft seed' pomegranate fruit under low-temperature cold storage. The results showed that 1-MCP implicated in promoting postharvest preservation of 'Tunisian soft seed' pomegranate upregulated the PgAP2/ERF4, PgAP2/ERF15, PgAP2/ERF26, PgAP2/ERF30, PgAP2/ERF35 and PgAP2/ERF45 genes compared to those under low-temperature cold storage. This indicates that these genes are important candidate genes involved in pomegranate postharvest preservation. In summary, the findings of the present study provide an important basis for characterizing the PgAP2/ERF family genes and provide information on the candidate genes involved in pomegranate fruit development and postharvest preservation.
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Affiliation(s)
- Ran Wan
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Jinhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Zhenyang Lv
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Xingcheng Qi
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Xuemeng Han
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Qiang Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Sa Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Jiangli Shi
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Zaihai Jian
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Qingxia Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
| | - Yanhui Chen
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; (R.W.); (J.S.); (Z.L.); (X.Q.); (X.H.); (Q.G.); (S.W.); (J.S.); (Z.J.); (Y.C.)
- Henan Key Laboratory of Fruit and Cucurbit Biology, College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
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12
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Yu Y, Yu M, Zhang S, Song T, Zhang M, Zhou H, Wang Y, Xiang J, Zhang X. Transcriptomic Identification of Wheat AP2/ERF Transcription Factors and Functional Characterization of TaERF-6-3A in Response to Drought and Salinity Stresses. Int J Mol Sci 2022; 23:ijms23063272. [PMID: 35328693 PMCID: PMC8950334 DOI: 10.3390/ijms23063272] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022] Open
Abstract
AP2/ERF (APETALA2/ethylene responsive factor) is a family of plant-specific transcription factors whose members are widely involved in many biological processes, such as growth, development, and biotic and abiotic stress responses. Here, 20 AP2/ERF genes were identified based on wheat RNA-seq data before and after drought stress, and classified as AP2, ERF, DREB, and RAV. The analysis of gene structure revealed that about 85% of AP2/ERF family members had lost introns, which are presumed to have been lost during the formation and evolution of the wheat genome. The expression of 20 AP2/ERF family genes could be verified by qRT-PCR, which further supported the validity of the RNA-seq data. Subsequently, subcellular localization and transcriptional activity experiments showed that the ERF proteins were mainly located in the nucleus and were self-activating, which further supports their functions as transcription factors. Furthermore, we isolated a novel ERF gene induced by drought, salt, and cold stresses and named it TaERF-6-3A. TaERF-6-3A overexpression increased sensitivity to drought and salt stresses in Arabidopsis, which was supported by physiological and biochemical indices. Moreover, the expression of stress- and antioxidant-related genes was downregulated in TaERF-6-3A-overexpressing plants. Overall, these results contribute to the further understanding of the TaERF-6-3A gene function in wheat.
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Affiliation(s)
- Yang Yu
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Ming Yu
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Shuangxing Zhang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Tianqi Song
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Mingfei Zhang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China;
| | - Hongwei Zhou
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Yukun Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
| | - Jishan Xiang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China;
- Correspondence: (J.X.); (X.Z.)
| | - Xiaoke Zhang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.Y.); (M.Y.); (S.Z.); (T.S.); (H.Z.); (Y.W.)
- Correspondence: (J.X.); (X.Z.)
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13
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Chen H, Hu L, Wang L, Wang S, Cheng X. Genome-wide identification and expression profiles of AP2/ERF transcription factor family in mung bean (Vigna radiata L.). J Appl Genet 2022; 63:223-236. [PMID: 34989979 DOI: 10.1007/s13353-021-00675-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Mung bean (Vigna radiata L. Wilczek) is an economically important grain legume crop in Asia, with high nutritional quality and potential in other parts of the world particularly arid and semiarid regions. Considering the potential adverse effects of drought, high salt, and other abiotic stresses on crop yield, significant efforts have been made to understand the underlying molecular mechanisms of tolerance to these abiotic stresses in legumes. In this study, a total of 186 putative AP2/ERF genes were identified, which were named VrERF1-186. These VrERF genes were classified into four main subfamilies according to the number of AP2 domains and sequence similarity, including 24 AP2 gene members, 81 ERF gene members, 79 DREB gene members, and 2 RAV members. VrERF genes are scattered across all 11 chromosomes and form small gene clusters on chromosomes due to segmental or tandem duplication. Promoter analysis revealed various cis-acting elements related to light, hormones, and stress responsiveness processes. The expression profiles of the VrERF genes in tissues during development and in response to abiotic stresses were assessed by transcriptome sequencing, and the selected reference genes were validated by qRT-PCR. A total of 174 VrERF genes were expressed in at least one of five tissues, while others showed distinct expression patterns in different tissues or under specific abiotic stress treatments, which indicates that VrERF genes are involved in developmental and environmental stress responses in V. radiata. In conclusion, the genome localization, genome-wide characterization, gene duplication, phylogenetic relationships, and expression pattern of VrERF genes in V. radiata were analyzed, and these results will lay the foundation for further functional analysis of these genes and improve stress tolerance to adverse conditions in plants.
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Affiliation(s)
- Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Liangliang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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14
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Zhao M, Haxim Y, Liang Y, Qiao S, Gao B, Zhang D, Li X. Genome-wide investigation of AP2/ERF gene family in the desert legume Eremosparton songoricum: Identification, classification, evolution, and expression profiling under drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:885694. [PMID: 36035670 PMCID: PMC9413063 DOI: 10.3389/fpls.2022.885694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/22/2022] [Indexed: 05/05/2023]
Abstract
Eremosparton songoricum (Litv.) Vass. is a rare leafless legume shrub endemic to central Asia which grows on bare sand. It shows extreme drought tolerance and is being developed as a model organism for investigating morphological, physiological, and molecular adaptations to harsh desert environments. APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, our knowledge on the AP2/ERF family in legume species is limited, and no respective study was conducted so far on the desert shrubby legume E. songoricum. Here, 153 AP2/ERF genes were identified based on the E. songoricum genome data. EsAP2/ERFs covered AP2 (24 genes), DREB (59 genes), ERF (68 genes), and Soloist (2 genes) subfamilies, and lacked canonical RAV subfamily genes based on the widely used classification method. The DREB and ERF subfamilies were further divided into A1-A6 and B1-B6 groups, respectively. Protein motifs and exon-intron structures of EsAP2/ERFs were also examined, which matched the subfamily/group classification. Cis-acting element analysis suggested that EsAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Moreover, the gene numbers and the ratio of each subfamily and the intron-exon structures were systematically compared with other model plants ranging from algae to angiosperms, including ten legumes. Our results supported the view that AP2 and ERF evolved early and already existed in algae, whereas RAV and DREB began to appear in moss species. Almost all plant AP2 and Soloist genes contained introns, whereas most DREB and ERF genes did not. The majority of EsAP2/ERFs were induced by drought stress based on RNA-seq data, EsDREBs were highly induced and had the largest number of differentially expressed genes in response to drought. Eight out of twelve representative EsAP2/ERFs were significantly up-regulated as assessed by RT-qPCR. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of AP2/ERF genes in E. songoricum and lays a foundation for better understanding of drought stress tolerance mechanisms in legume plants. Moreover, candidate genes for drought-resistant plant breeding are proposed.
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Affiliation(s)
- Mingqi Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Yuqing Liang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Siqi Qiao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Bei Gao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
| | - Xiaoshuang Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, China
- *Correspondence: Xiaoshuang Li,
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15
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Zhai Y, Fan Z, Cui Y, Gu X, Chen S, Ma H. APETALA2/ethylene responsive factor in fruit ripening: Roles, interactions and expression regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:979348. [PMID: 36061806 PMCID: PMC9434019 DOI: 10.3389/fpls.2022.979348] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 05/08/2023]
Abstract
Insects and animals are attracted to, and feed on ripe fruit, thereby promoting seed dispersal. As a vital vitamin and nutrient source, fruit make up an indispensable and enjoyable component of the human diet. Fruit ripening involves a series of physiological and biochemical changes in, among others, pigmentation, chlorophyll (Chl) degradation, texture, sugar accumulation, and flavor. Growing evidence indicates that the coordinated and ordered trait changes during fruit ripening depend on a complex regulatory network consisting of transcription factors, co-regulators, hormonal signals, and epigenetic modifications. As one of the predominant transcription factor families in plants and a downstream component of ethylene signaling, more and more studies are showing that APETALA2/ethylene responsive factor (AP2/ERF) family transcription factors act as critical regulators in fruit ripening. In this review, we focus on the regulatory mechanisms of AP2/ERFs in fruit ripening, and in particular the recent results on their target genes and co-regulators. We summarize and discuss the role of AP2/ERFs in the formation of key fruit-ripening attributes, the enactment of their regulatory mechanisms by interaction with other proteins, their role in the orchestration of phytohormone-signaling networks, and the epigenetic modifications associated with their gene expression. Our aim is to provide a multidimensional perspective on the regulatory mechanisms of AP2/ERFs in fruit ripening, and a reference for understanding and furthering research on the roles of AP2/ERF in fruit ripening.
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Affiliation(s)
- Yanlei Zhai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhiyi Fan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yuanyuan Cui
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaojiao Gu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shangwu Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, China
- *Correspondence: Huiqin Ma,
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Wang T, Gao X, Chen S, Li D, Chen S, Xie M, Xu Z, Yang G. Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia. PeerJ 2021; 9:e12429. [PMID: 34820183 PMCID: PMC8607932 DOI: 10.7717/peerj.12429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecular mechanism associated with walnut response to drought. In many plants, ethylene responsive factor (ERF) gene family plays important roles in response to biotic and abiotic stress, especial drought. Therefore, the identification and characterisation of walnut ERF genes will benefit walnut with regard to the clarification of drought response mechanism as well as the management, production, and quality of plantations. Methods ‘ERF’ was compared against the walnut transcriptome, and the JrERFs with a complete open reading frame (ORF) were identified by ORF Finder. The molecular weights, amino acid residues, and theoretical isoelectric point (pI) were predicted by ExPASy. The distribution of JrERFs in chromosome locations was determined based on walnut genome data from NCBI. The intron-exon structures and conserved domains were analysed using Gene Structure Display Server 2.0 and CD-Search, accordingly. Multi-sequence alignment and a phylogenetic tree were constructed by ClustalX2.1 and MEGA7, respectively. The conserved motifs were acquired using MEME. Total RNA was isolated using the cetyltrimethylammonium ammonium bromide (CTAB) method (Yang et al., 2018). Gene expression was determined by using real-time quantitative polymerase chain reaction (qRT-PCR) analysis and calculated according to the 2−ΔΔCT method (Livak & Schmittgen, 2001). Results A total of 44 JrERFs were identified from the walnut transcriptome, whose ORFs were 450–1,239 bp in length. The molecular weights of the JrERF proteins (consisting 149–412 amino acids) were 16.81–43.71 kDa, with pI ranging from 4.8 (JrERF11) to 9.89 (JrERF03). The JrERFs can be divided into six groups (B1–B6), and among the groups, B6 contained the most number of members. Each JrERF contained 1–6 motifs and each motif comprised 9–50 amino acids. Among the motifs, motif1, motif2, and motif3 were the most abundant. More than 40% of JrERFs were up-regulated continuously when subjected to ethephon (ETH), PEG6000, and PEG6000+ETH treatments. Of all the JrERFs, JrERF11 showed the highest expression. Therefore, we conclude that walnut ERF genes are highly conserved and involved in the regulation of drought response in the presence of ETH. JrERFs are possibly important candidate genes for molecular breeding; hence, the findings of this study provides the theoretical basis for further investigation of ERF genes in walnut and other species.
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Affiliation(s)
- Tianyu Wang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangqian Gao
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Sisi Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapei Li
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuwen Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Muhong Xie
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhenggang Xu
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
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Zong Y, Hao Z, Tu Z, Shen Y, Zhang C, Wen S, Yang L, Ma J, Li H. Genome-wide survey and identification of AP2/ERF genes involved in shoot and leaf development in Liriodendron chinense. BMC Genomics 2021; 22:807. [PMID: 34749659 PMCID: PMC8576965 DOI: 10.1186/s12864-021-08119-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/23/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses. RESULTS In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells. CONCLUSIONS Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.
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Affiliation(s)
- Yaxian Zong
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyuan Hao
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhonghua Tu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Yufang Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Chengge Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Shaoying Wen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Lichun Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Jikai Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
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Cao D, Lin Z, Huang L, Damaris RN, Yang P. Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology. BMC Genomics 2021; 22:171. [PMID: 33750315 PMCID: PMC7945336 DOI: 10.1186/s12864-021-07473-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value. Results We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population. Conclusions In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07473-w.
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Affiliation(s)
- Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Longyu Huang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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19
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Zhang H, Pan X, Liu S, Lin W, Li Y, Zhang X. Genome-wide analysis of AP2/ERF transcription factors in pineapple reveals functional divergence during flowering induction mediated by ethylene and floral organ development. Genomics 2021; 113:474-489. [PMID: 33359830 DOI: 10.1016/j.ygeno.2020.10.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
The APETALA2/ethylene-responsive factor (AP2/ERF) has important roles in regulating developmental processes and hormone signaling transduction in plants. Pineapple demonstrates a special sensitivity to ethylene, and AP2/ERFs may contribute to this distinct sensitivity of pineapples to ethylene. However, little information is available on the AP2/ERF of pineapple. In this study, 97 AP2/ERF family members were identified from the pineapple genome. The AcAP2/ERF superfamily could be further divided into five subfamilies, and different subfamily existed functional divergence in multifarious biological processes. ERF and RAV subfamily genes might play important roles in the process of ethylene response of pineapple; ERF and DREB subfamily genes had particular functions in the floral organ development. This study is the first to provide detailed information on the features of AP2/ERFs in pineapple, provide new insights into the potential functional roles of the AP2/ERF superfamily members, and will facilitate a better understanding of the molecular mechanism of flower in pineapple.
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Affiliation(s)
- Hongna Zhang
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China; Hainan University, Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Tropical Crop New Variety Breeding Education Engineering Center, Haikou 570102, PR China
| | - Xiaolu Pan
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China; Hainan University, Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Tropical Crop New Variety Breeding Education Engineering Center, Haikou 570102, PR China
| | - Shenghui Liu
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Wenqiu Lin
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Yunhe Li
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Xiumei Zhang
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China.
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20
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Jiang Z, Tu L, Yang W, Zhang Y, Hu T, Ma B, Lu Y, Cui X, Gao J, Wu X, Tong Y, Zhou J, Song Y, Liu Y, Liu N, Huang L, Gao W. The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis. PLANT COMMUNICATIONS 2021; 2:100113. [PMID: 33511345 PMCID: PMC7816079 DOI: 10.1016/j.xplc.2020.100113] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 05/13/2023]
Abstract
Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb, produced with third-generation PacBio sequencing technology. This is the first chromosome-level genome assembly for the genus Panax. Through genome evolution analysis, we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis. We performed a detailed transcriptional analysis of P. notoginseng and explored gene-level mechanisms that regulate the formation of characteristic tubercles. Next, we studied the biosynthesis and regulation of saponins at temporal and spatial levels. We combined multi-omics data to identify genes that encode key enzymes in the P. notoginseng terpenoid biosynthetic pathway. Finally, we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P. notoginseng. The genetic information obtained in this study provides a resource for further exploration of the growth characteristics, cultivation, breeding, and saponin biosynthesis of P. notoginseng.
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Affiliation(s)
- Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | | | - Yifeng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Baowei Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jie Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yadi Song
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Nan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Corresponding author
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
- Corresponding author
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21
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Ge Y, Zang X, Yang Y, Wang T, Ma W. In-depth analysis of potential PaAP2/ERF transcription factor related to fatty acid accumulation in avocado (Persea americana Mill.) and functional characterization of two PaAP2/ERF genes in transgenic tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:308-320. [PMID: 33234384 DOI: 10.1016/j.plaphy.2020.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/13/2020] [Indexed: 05/24/2023]
Abstract
Fatty acids in avocado fruit are crucial components influencing taste as well as fruit quality and nutritional value. Changes to fatty acid contents and concentrations in avocado fruit are important because of the associated effects on sensory properties. Hence, plant physiologists and molecular biologists interested in elucidating the influence of transcription factors on fatty acid accumulation in avocado fruit. In this study, APETALA2/ethylene-responsive factor (AP2/ERF) family members in avocado (Persea americana Mill.) were systematically and comprehensively analyze to identify potential PaAP2/ERF genes related to fatty acid accumulation. The results of bioinformatics analysis and the expression profiles of the AP2/ERF members suggested that 10 highly expressed PaAP2/ERF genes may encode transcription factors with functions related to the fatty acid accumulation in the avocado mesocarp. Furthermore, PaWRI1 and PaWRI2, two AP2/ERF transcription factor genes in avocado, were functionally characterized regarding their effects on fatty acid accumulation. The transcriptome and biochemical analyses of PaWRI1-2-overexpressing transgenic tomato plants revealed the up-regulated expression of 17 unigenes related to fatty acid synthesis and triacylglycerol assembly as well as increased fatty acid contents relative to the corresponding levels in the wild-type plants. In contrast, the overexpression of PaWRI2 in transgenic tomato plants up-regulated the expression of only six unigenes associated with fatty acid synthesis and triacylglycerol assembly and negligibly affected fatty acid accumulation when compared with wild-type plants. This systematic analysis provides a foundation for future studies regarding AP2/ERF functions associated with fatty acid accumulation.
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Affiliation(s)
- Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China.
| | - Xiaoping Zang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China
| | - Ying Yang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China
| | - Tao Wang
- Institute of Vegetable, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, 110161, China
| | - Weihong Ma
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China.
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22
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Fang T, Peng Y, Rao Y, Li S, Zeng L. Genome-Wide Identification and Expression Analysis of Sugar Transporter (ST) Gene Family in Longan ( Dimocarpus longan L.). PLANTS 2020; 9:plants9030342. [PMID: 32182715 PMCID: PMC7154848 DOI: 10.3390/plants9030342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/16/2022]
Abstract
Carbohydrates are nutrients and important signal molecules in higher plants. Sugar transporters (ST) play important role not only in long-distance transport of sugar, but also in sugar accumulations in sink cells. Longan (Dimocarpus longan L.) is one of the most important commercial tropical/subtropical evergreen fruit species in Southeast Asia. In this study, a total of 52 longan sugar transporter (DlST) genes were identified and they were divided into eight clades according to phylogenetic analysis. Out of these 52 DlST genes, many plant hormones (e.g., MeJA and gibberellin), abiotic (e.g., cold and drought), and biotic stress responsive element exist in their promoter region. Gene structure analysis exhibited that each of the clades have closely associated gene architectural features based on similar number or length of exons. The numbers of DlSTs, which exhibited alternative splicing (AS) events, in flower bud is more than that in other tissues. Expression profile analysis revealed that ten DlST members may regulate longan flowerbud differentiation. In silico expression profiles in nine longan organs indicated that some DlST genes were tissue specificity and further qRT-PCR analysis suggested that the transcript level of seven DlSTs (DlINT3, DlpGlcT1, DlpGlcT2, DlPLT4, DlSTP1, DlVGT1 and DlVGT2) was consistent with sugar accumulation in fruit, indicating that they might be involved in sugar accumulations during longan fruit development. Our findings will contribute to a better understanding of sugar transporters in woody plant.
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Affiliation(s)
- Ting Fang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.F.); (Y.P.); (Y.R.); (S.L.)
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Peng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.F.); (Y.P.); (Y.R.); (S.L.)
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ya Rao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.F.); (Y.P.); (Y.R.); (S.L.)
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shenghao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.F.); (Y.P.); (Y.R.); (S.L.)
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.F.); (Y.P.); (Y.R.); (S.L.)
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel./Fax: 86-591-8378-9281
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