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Lu L, Gu X, Wang Z, Gao J, Fan F, Song G, Zhong C, Zhang H. Functional characterization of AcWRKY94 in response to Pseudomonas syringae pv. actinidiae in kiwifruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108933. [PMID: 39033650 DOI: 10.1016/j.plaphy.2024.108933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
WRKY transcription factors are essential for coping with various biotic stresses. Pseudomonas syringae pv. actinidiae (Psa)-induced kiwifruit canker is a major problem restricting kiwifruit yield. Nevertheless, it's unclear how the kiwifruit WRKY genes respond to Psa. Through genome-wide identification, 112 WRKY members were found in 'Hongyang' genome in this work. Promoter analysis revealed that there were many cis-acting elements associated with stress responses in the AcWRKY gene's promoter region. According to transcriptomic analysis, 90 of the AcWRKY genes were differently expressed following Psa, salicylic acid (SA), or methyl jasmonate (MeJA) treatments. Almost all group III WRKYs were responsive to at least one of these treatments, with tissue-specific expression patterns. Quantitative RT-PCR study provided more evidence that Psa and SA treatments significantly induced the expression of the group III WRKY gene AcWRKY94, whereas MeJA treatment repressed it. AcWRKY94 was a transcriptionally active protein localized in the nucleus. Transient overexpression of AcWRKY94 in the leaves of 'Hongyang' enhanced the resistance of kiwifruit to Psa. Overexpression of AcWRKY94 in kiwifruit callus remarkably promoted the expression of PR and JAZ genes associated with SA and JA signals, respectively. These data imply that AcWRKY94 controls the signaling pathway dependent on SA and JA, thereby enhancing resistance to Psa. Taken together, this study establishes the basis for functional research on WRKY genes and provides important information for elucidating the resistance mechanism of kiwifruit canker disease.
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Affiliation(s)
- Linghong Lu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Xianbin Gu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Zupeng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Jing Gao
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Fei Fan
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Genhua Song
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Caihong Zhong
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China.
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2
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Wang Y, Li P, Zhu Y, Zhang F, Zhang S, He Y, Wu Y, Lin Y, Wang H, Ren W, Wang L, Yang Y, Wang R, Zheng P, Liu Y, Wang S, Yue J. Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400322. [PMID: 38757662 PMCID: PMC11267314 DOI: 10.1002/advs.202400322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.
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Affiliation(s)
- Yingzhen Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
- School of Forestry Science and TechnologyLishui Vocational and Technical CollegeLishui323000China
| | - Pengwei Li
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yanyan Zhu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Feng Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Sijia Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yan He
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Ying Wu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio‐resource and Eco‐environmentCollege of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610064China
| | - Hongtao Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Wangmei Ren
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Lihuan Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Ying Yang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Runze Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Pengpeng Zheng
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Yongsheng Liu
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
- Ministry of Education Key Laboratory for Bio‐resource and Eco‐environmentCollege of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610064China
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
| | - Junyang Yue
- Anhui Province Key Laboratory of Horticultural Crop Quality BiologySchool of HorticultureAnhui Agricultural UniversityHefei230036China
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3
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Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y, Fei Z, Zheng Y. HortGenome Search Engine, a universal genomic search engine for horticultural crops. HORTICULTURE RESEARCH 2024; 11:uhae100. [PMID: 38863996 PMCID: PMC11165154 DOI: 10.1093/hr/uhae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Abstract
Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.
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Affiliation(s)
- Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shangxiao Wei
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yuling Deng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shaoyuan Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hua Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yijian Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hui Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yiding Wang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Renlong Zhang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Lu Ning
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
- Library, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
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4
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Wang Y, Liu Y. Recent advances of kwifruit genome and genetic transformation. MOLECULAR HORTICULTURE 2024; 4:19. [PMID: 38725051 PMCID: PMC11084073 DOI: 10.1186/s43897-024-00096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Affiliation(s)
- Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, P. R. China.
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Cao Y, Zhang C, Liu F, Li D, Zhang A, Li L, Zhang X. Genome-Wide Identification and Expression Analysis of Kiwifruit Leucine-Rich Repeat Receptor-Like Proteins Reveal Their Roles in Biotic and Abiotic Stress Responses. Int J Mol Sci 2024; 25:4497. [PMID: 38674082 PMCID: PMC11050117 DOI: 10.3390/ijms25084497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Leucine-rich repeat receptor-like proteins (LRR-RLPs), a major group of receptor-like proteins in plants, have diverse functions in plant physiology, including growth, development, signal transduction, and stress responses. Despite their importance, the specific roles of kiwifruit LRR-RLPs in response to biotic and abiotic stresses remain poorly understood. In this study, we performed family identification, characterization, transcriptome data analysis, and differential gene expression analysis of kiwifruit LRR-RLPs. We identified totals of 101, 164, and 105 LRR-RLPs in Actinidia chinensis 'Hongyang', Actinidia eriantha 'Huate', and Actinidia chinensis 'Red5', respectively. Synteny analysis revealed that the expansion of kiwifruit LRR-RLPs was primarily attributed to segmental duplication events. Based on RNA-seq data from pathogen-infected kiwifruits, we identified specific LRR-RLP genes potentially involved in different stages of pathogen infection. Additionally, we observed the potential involvement of kiwifruit LRR-RLPs in abiotic stress responses, with upstream transcription factors possibly regulating their expression. Furthermore, protein interaction network analysis unveiled the participation of kiwifruit LRR-RLP in the regulatory network of abiotic stress responses. These findings highlight the crucial roles of LRR-RLPs in mediating both biotic and abiotic stress responses in kiwifruit, offering valuable insights for the breeding of stress-resistant kiwifruit varieties.
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Affiliation(s)
- Yingying Cao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congxiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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6
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Santos MG, Nunes da Silva M, Vasconcelos MW, Carvalho SMP. Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker. FRONTIERS IN PLANT SCIENCE 2024; 14:1306420. [PMID: 38273947 PMCID: PMC10808555 DOI: 10.3389/fpls.2023.1306420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.
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Affiliation(s)
- Miguel G. Santos
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
| | - Marta Nunes da Silva
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Susana M. P. Carvalho
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
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7
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Zhu L, Yin T, Zhang M, Yang X, Wu J, Cai H, Yang N, Li X, Wen K, Chen D, Zhang H, Liu X. Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress. BMC Genomics 2024; 25:12. [PMID: 38166720 PMCID: PMC10759511 DOI: 10.1186/s12864-023-09915-z] [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: 04/25/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. RESULTS In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. CONCLUSIONS These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.
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Affiliation(s)
- Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mengjie Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Jiexin Wu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Hanbing Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xulin Li
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Ke Wen
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Daming Chen
- Research Institute of Agriculture Ecological in Hot Areas, Yunnan Academy of Agricultural Science, Yuan Mou, Yunnan, 651300, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
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8
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Ling C, Liu Y, Yang Z, Xu J, Ouyang Z, Yang J, Wang S. Genome-Wide Identification of HSF Gene Family in Kiwifruit and the Function of AeHSFA2b in Salt Tolerance. Int J Mol Sci 2023; 24:15638. [PMID: 37958622 PMCID: PMC10649126 DOI: 10.3390/ijms242115638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Heat shock transcription factors (HSFs) play a crucial role in regulating plant growth and response to various abiotic stresses. In this study, we conducted a comprehensive analysis of the AeHSF gene family at genome-wide level in kiwifruit (Actinidia eriantha), focusing on their functions in the response to abiotic stresses. A total of 41 AeHSF genes were identified and categorized into three primary groups, namely, HSFA, HSFB, and HSFC. Further transcriptome analysis revealed that the expression of AeHSFA2b/2c and AeHSFB1c/1d/2c/3b was strongly induced by salt, which was confirmed by qRT-PCR assays. The overexpression of AeHSFA2b in Arabidopsis significantly improved the tolerance to salt stress by increasing AtRS5, AtGolS1 and AtGolS2 expression. Furthermore, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays demonstrated that AeHSFA2b could bind to the AeRFS4 promoter directly. Therefore, we speculated that AeHSFA2b may activate AeRFS4 expression by directly binding its promoter to enhance the kiwifruit's tolerance to salt stress. These results will provide a new insight into the evolutionary and functional mechanisms of AeHSF genes in kiwifruit.
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Affiliation(s)
| | | | | | | | | | - Jun Yang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agriculture University, Hefei 230036, China
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agriculture University, Hefei 230036, China
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9
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Tu J, Abid M, Luo J, Zhang Y, Yang E, Cai X, Gao P, Huang H, Wang Z. Genome-wide identification of the heat shock transcription factor gene family in two kiwifruit species. FRONTIERS IN PLANT SCIENCE 2023; 14:1075013. [PMID: 37799558 PMCID: PMC10548268 DOI: 10.3389/fpls.2023.1075013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/28/2023] [Indexed: 10/07/2023]
Abstract
High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 Hsf genes were identified in the A. chinensis (Ac) genome, while 41 Hsf genes were found in the A. eriantha (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit Hsfs into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the Hsf gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of Hsf genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of Arabidopsis protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of Hsf genes, especially AcHsfA2a, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of Hsfs in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.
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Affiliation(s)
- Jing Tu
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Muhammad Abid
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Juan Luo
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Yi Zhang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Endian Yang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Xinxia Cai
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Puxin Gao
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hongwen Huang
- College of Life Science, Nanchang University, Nanchang, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Zupeng Wang
- College of Life Science, Nanchang University, Nanchang, China
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10
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Guo D, Wang R, Fang J, Zhong Y, Qi X. Development of sex-linked markers for gender identification of Actinidia arguta. Sci Rep 2023; 13:12780. [PMID: 37550389 PMCID: PMC10406875 DOI: 10.1038/s41598-023-39561-0] [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: 09/08/2021] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
The fruit of the dioecious plant Actinidia arguta has become a great attraction recently. It has long been difficult to distinguish the genders of hybrid seedlings before flowering, therefore increasing the expenditures of breeding. To produce reliable molecular marker for gender identification, this research utilized whole-genome re-sequencing of 15 males and 15 females from an 8-year-old cross population to develop gender specific markers. P51 and P11 were identified as sex-linked markers after verification. Both of these markers, according to the PCR results, only amplified a single band in male samples. These two markers were tested in 97 hybrids (52 females and 45 males) and 31 wild individuals (13 females and 18 males), with an accuracy of 96.88% and 96.09%, correspondingly. This research also verified the universalities of the two markers in Actinidia chinensis samples, and it could be inferred from the PCR results that neither marker was applicable to A. chinensis samples. The BLAST results of the two markers demonstrated that the two markers were closely aligned with different parts of the Y male-specific region of A. chinensis genome, thus they were likely to be useful for the research on the mechanism of sex determination of A. arguta. The two male-linked makers, P51 and P11, have already been used in sex-identification of A. arguta seedlings.
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Affiliation(s)
- Dandan Guo
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Ran Wang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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11
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Tang X, Hou Y, Jiang F, Lang H, Li J, Cheng J, Wang L, Liu X, Zhang H. Genome-wide characterization of SINA E3 ubiquitin ligase family members and their expression profiles in response to various abiotic stresses and hormones in kiwifruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107891. [PMID: 37459805 DOI: 10.1016/j.plaphy.2023.107891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/27/2023] [Accepted: 07/08/2023] [Indexed: 08/13/2023]
Abstract
SINA (Seven in absentia) proteins in the subtype of E3 ubiquitin ligase family have important functions in regulating the growth and development as well as in response to abiotic and biotic stresses in plants. However, the characteristics and possible functions of SINA family proteins in kiwifruit are not studied. In this research, a total number of 11 AcSINA genes in the kiwifruit genome were identified. Chromosome location and multiple sequence alignment analyses indicated that they were unevenly distributed on 10 chromosomes and all contained the typical N-terminal RING domain and C-terminal SINA domain. Phylogenetic, gene structure and collinear relationship analyses revealed that they were highly conserved with the same gene structure, and have gone through segmental duplication events. Expression pattern analyses demonstrated that all AcSINAs were ubiquitously expressed in roots, stems and leaves, and were responsive to different abiotic and plant hormone treatments with overlapped but distinct expression patterns. Further yeast two-hybrid and Arabidopsis transformation analyses demonstrated most AcSINAs interacted with itself or other AcSINA members to form homo- or heterodimers, and ectopic expression of AcSINA2 in Arabidopsis led to hypersensitive growth phenotype of transgenic seedlings to ABA treatment. Our results reveal that AcSINAs take part in the response to various abiotic stresses and hormones, and provide important information for the functional elucidation of AcSINAs in vine fruit plants.
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Affiliation(s)
- Xiaoli Tang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Yaqiong Hou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Fudong Jiang
- Yantai Academy of Agricultural Sciences, 26 West Gangcheng Avenue, Yantai, Shandong, 265559, China
| | - Hongshan Lang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jianzhao Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Jieshan Cheng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Limin Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China
| | - Xiaohua Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong Province, 264025, China; Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, 5 Qingdao Avenue, Yantai, 265503, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong Province, 265400, China.
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12
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Lin Y, Ye C, Li X, Chen Q, Wu Y, Zhang F, Pan R, Zhang S, Chen S, Wang X, Cao S, Wang Y, Yue Y, Liu Y, Yue J. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. HORTICULTURE RESEARCH 2023; 10:uhad127. [PMID: 37560017 PMCID: PMC10407605 DOI: 10.1093/hr/uhad127] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences, along with the emergence of a new 'telomere-to-telomere (T2T) assembly' era. However, the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited. Here, we developed a user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. First, AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome. Then, GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences. Finally, TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome. These four modules can be used alone or in combination with each other for T2T genome assembly and characterization. As a case study, by adopting the entire modular functions of quarTeT, we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0, which was assembled with the addition of manual handling. Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods. Collectively, quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.
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Affiliation(s)
- Yunzhi Lin
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chen Ye
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xingzhu Li
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qinyao Chen
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Feng Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Rui Pan
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Sijia Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shuxia Chen
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xu Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Shuo Cao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yi Yue
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yongsheng Liu
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
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13
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Miao T, Bao H, Ling H, Li P, Zhang Y, He Y, Hu X, Ling C, Liu Y, Tang W, Liu Y, Wang S. Comparative Transcriptomic Analysis Revealed the Suppression and Alternative Splicing of Kiwifruit ( Actinidia latifolia) NAP1 Gene Mediating Trichome Development. Int J Mol Sci 2023; 24:4481. [PMID: 36901911 PMCID: PMC10003061 DOI: 10.3390/ijms24054481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/26/2023] Open
Abstract
Kiwifruit (Actinidia chinensis) is commonly covered by fruit hairs (trichomes) that affect kiwifruit popularity in the commercial market. However, it remains largely unknown which gene mediates trichome development in kiwifruit. In this study, we analyzed two kiwifruit species, A. eriantha (Ae) with long, straight, and bushy trichomes and A. latifolia (Al) with short, distorted, and spare trichomes, by second- and third-generation RNA sequencing. Transcriptomic analysis indicated that the expression of the NAP1 gene, a positive regulator of trichome development, was suppressed in Al compared with that in Ae. Additionally, the alternative splicing of AlNAP1 produced two short transcripts (AlNAP1-AS1 and AlNAP1-AS2) lacking multiple exons, in addition to a full-length transcript of AlNAP1-FL. The defects of trichome development (short and distorted trichome) in Arabidopsis nap1 mutant were rescued by AlNAP1-FL but not by AlNAP1-AS1. AlNAP1-FL gene does not affect trichome density in nap1 mutant. The qRT-PCR analysis indicated that the alternative splicing further reduces the level of functional transcripts. These results indicated that the short and distorted trichomes in Al might be caused by the suppression and alternative splicing of AlNAP1. Together, we revealed that AlNAP1 mediates trichome development and is a good candidate target for genetic modification of trichome length in kiwifruit.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yajing Liu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Songhu Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
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14
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Wang Y, Dong M, Wu Y, Zhang F, Ren W, Lin Y, Chen Q, Zhang S, Yue J, Liu Y. Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha. MOLECULAR HORTICULTURE 2023; 3:4. [PMID: 37789444 PMCID: PMC10515003 DOI: 10.1186/s43897-023-00052-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/30/2023] [Indexed: 10/05/2023]
Abstract
Actinidia eriantha is a characteristic fruit tree featuring with great potential for its abundant vitamin C and strong disease resistance. It has been used in a wide range of breeding programs and functional genomics studies. Previously published genome assemblies of A. eriantha are quite fragmented and not highly contiguous. Using multiple sequencing strategies, we get the haplotype-resolved and gap-free genomes of an elite breeding line "Midao 31" (MD), termed MDHAPA and MDHAPB. The new assemblies anchored to 29 pseudochromosome pairs with a length of 619.3 Mb and 611.7 Mb, as well as resolved 27 and 28 gap-close chromosomes in a telomere-to-telomere (T2T) manner. Based on the haplotype-resolved genome, we found that most alleles experienced purifying selection and coordinately expressed. Owing to the high continuity of assemblies, we defined the centromeric regions of A. eriantha, and identified the major repeating monomer, which is designated as Ae-CEN153. This resource lays a solid foundation for further functional genomics study and horticultural traits improvement in kiwifruit.
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Affiliation(s)
- Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- School of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, 323000, China
| | - Minhui Dong
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Wangmei Ren
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Qinyao Chen
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Sijia Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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15
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Xia H, Deng H, Li M, Xie Y, Lin L, Zhang H, Luo X, Lv X, Wang J, Liang D. Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa). Sci Data 2023; 10:92. [PMID: 36788248 PMCID: PMC9929245 DOI: 10.1038/s41597-023-02006-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. 'Red5' and 'Hongyang' (11.1-27.7 mya) was more recent compared with the divergence time of them and Acd (19.9-41.2 mya), with the divergence time of A. eriantha cv. 'White' being the earliest (22.9-45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.
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Affiliation(s)
- Hui Xia
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhang Li
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Yue Xie
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huifen Zhang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xian Luo
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiulan Lv
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Wang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Liu Y, Lv G, Yang Y, Ma K, Ren X, Li M, Liu Z. Interaction of AcMADS68 with transcription factors regulates anthocyanin biosynthesis in red-fleshed kiwifruit. HORTICULTURE RESEARCH 2023; 10:uhac252. [PMID: 36751270 PMCID: PMC9896601 DOI: 10.1093/hr/uhac252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
In red-fleshed kiwifruit, anthocyanin pigmentation is a crucial commercial trait. The MYB-bHLH-WD40 (MBW) complex and other transcription factors regulate its accumulation. Herein, a new SEP gene, AcMADS68, was identified as a regulatory candidate for anthocyanin biosynthesis in the kiwifruit by transcriptome data and bioinformatic analyses. AcMADS68 alone could not induce the accumulation of anthocyanin both in Actinidia arguta fruit and tobacco leaves. However, in combination with AcMYBF110, AcMYB123, and AcbHLH1, AcMADS68 co-overexpression increased anthocyanin biosynthesis, whereas its silencing reduced anthocyanin accumulation. The results of the dual-luciferase reporter, firefly luciferase complementation, yeast two-hybrid and co-immunoprecipitation assays showed that AcMADS68 could interact with both AcMYBF110 and AcMYB123 but not with AcbHLH1, thereby co-regulating anthocyanin biosynthesis by promoting the activation of the target genes, including AcANS, AcF3GT1, and AcGST1. Moreover, AcMADS68 also could activate the promoter of AcbHLH1 surported by dual-luciferase reporter and yeast one-hybrid assays, thereby further amplifying the regulation signals from the MBW complex, thus resulting in enhanced anthocyanin accumulation in the kiwifruit. These findings may facilitate better elucidation of various regulatory mechanisms underlying anthocyanin accumulation and contribute to the quality enhancement of red-fleshed kiwifruit.
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Affiliation(s)
| | | | - Yaqi Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shannxi, China
| | - Kangxun Ma
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shannxi, China
| | - Xiaolin Ren
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shannxi, China
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17
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Yue J, Chen Q, Wang Y, Zhang L, Ye C, Wang X, Cao S, Lin Y, Huang W, Xian H, Qin H, Wang Y, Zhang S, Wu Y, Wang S, Yue Y, Liu Y. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. HORTICULTURE RESEARCH 2023; 10:uhac264. [PMID: 36778189 PMCID: PMC9909506 DOI: 10.1093/hr/uhac264] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/21/2022] [Indexed: 05/19/2023]
Abstract
Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions. Here, we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. 'Hongyang', named Hongyang v4.0, which is the first to achieve two de novo haploid-resolved haplotypes, HY4P and HY4A. HY4P and HY4A have a total length of 606.1 and 599.6 Mb, respectively, with almost the entire telomeres and centromeres assembled in each haplotype. In comparison with Hongyang v3.0, the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions, resulting in ~38.6-39.5 Mb extra sequences, which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A, respectively. Furthermore, our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres. Globally, centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer (Ach-CEN153) with different copy numbers among chromosomes. Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids, but also have genetic features for participation in the regulation of cell division. The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.
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Affiliation(s)
| | | | | | | | - Chen Ye
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xu Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Shuo Cao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulic and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Huang
- Department of Bioinformatics, Anhui Double Helix Gene Technology Corporation, Hefei, Anhui 230022, China
| | - He Xian
- Comprehensive Testing Ground, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830012, China
| | - Hongyan Qin
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, China
| | - Yanli Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, China
| | - Sijia Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Songhu Wang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yi Yue
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
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Choi D, Choi JH, Park KJ, Kim C, Lim JH, Kim DH. Transcriptomic analysis of effects of 1-methylcyclopropene (1-MCP) and ethylene treatment on kiwifruit ( Actinidia chinensis) ripening. FRONTIERS IN PLANT SCIENCE 2023; 13:1084997. [PMID: 36684730 PMCID: PMC9849763 DOI: 10.3389/fpls.2022.1084997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Ethylene (ET) is a gaseous phytohormone with a crucial role in the ripening of many fruits, including kiwifruit (Actinidia spp.). Meanwhile, treatment with 1-methylcyclopropene (1-MCP), an artificial ET inhibitor delays the ripening of kiwifruit. The objective of this study was to determine the effect of ET and 1-MCP application during time-course storage of kiwifruit. In addition, we aimed to elucidate the molecular details underlying ET-mediated ripening process in kiwifruit. For this purpose, we conducted a time-course transcriptomic analysis to determine target genes of the ET-mediated maturation process in kiwifruit during storage. Thousands of genes were identified to be dynamically changed during storage and clustered into 20 groups based on the similarity of their expression patterns. Gene ontology analysis using the list of differentially expressed genes (DEGs) in 1-MCP-treated kiwifruit revealed that the identified DEGs were significantly enriched in the processes of photosynthesis metabolism and cell wall composition throughout the ripening process. Meanwhile, ET treatment rapidly triggered secondary metabolisms related to the ripening process, phenylpropanoid (e.g. lignin) metabolism, and the biosynthesis of amino acids (e.g. Phe, Cys) in kiwifruit. It was demonstrated that ET biosynthesis and signaling genes were oppositely affected by ET and 1-MCP treatment during ripening. Furthermore, we identified a ET transcription factor, AcEIL (Acc32482) which is oppositely responsive by ET and 1-MCP treatment during early ripening, potentially one of key signaling factor of ET- or 1-MCP-mediated physiological changes. Therefore, this transcriptomic study unveiled the molecular targets of ET and its antagonist, 1-MCP, in kiwifruit during ripening. Our results provide a useful foundation for understanding the molecular details underlying the ripening process in kiwifruit.
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Affiliation(s)
- Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jeong Hee Choi
- Food safety and Distribution Research Group, Korea Food Research Institute, Wanju, Republic of Korea
| | - Kee-Jai Park
- Food safety and Distribution Research Group, Korea Food Research Institute, Wanju, Republic of Korea
| | - Changhyun Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Jeong-Ho Lim
- Food safety and Distribution Research Group, Korea Food Research Institute, Wanju, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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Li S, Xiao L, Chen M, Cao Q, Luo Z, Kang N, Jia M, Chen J, Xiang M. The involvement of the phenylpropanoid and jasmonate pathways in methyl jasmonate-induced soft rot resistance in kiwifruit ( Actinidia chinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:1097733. [PMID: 36589109 PMCID: PMC9800925 DOI: 10.3389/fpls.2022.1097733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Botryosphaeria dothidea is a major postharvest causal agent of soft rot in kiwifruit. Methyl jasmonate (MeJA) is an important plant hormone that participates as a plant defense against pathogens from a signal molecule. However, the impact and regulatory mechanism of MeJA on the attenuation of kiwifruit fungal decay remains unknown. This work investigated the effects of exogenous MeJA on the enzyme activity, metabolite content and gene expression of the phenylpropanoid and jasmonate pathways in kiwifruit. The results revealed that MeJA inhibited the expansion of B. dothidea lesion diameter in kiwifruit (Actinidia chinensis cv. 'Hongyang'), enhanced the activity of enzymes (phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate: coenzyme A ligase, cinnamyl alcohol dehydrogenase, peroxidase and polyphenol oxidase), and upregulated the expression of related genes (AcPAL, AcC4H, Ac4CL, and AcCAD). The accumulation of metabolites (total phenolics, flavonoids, chlorogenic acid, caffeic acid and lignin) with inhibitory effects on pathogens was promoted. Moreover, MeJA enhanced the expression of AcLOX, AcAOS, AcAOC, AcOPR3, AcJAR1, AcCOI1 and AcMYC2 and reduced the expression of AcJAZ. These results suggest that MeJA could display a better performance in enhancing the resistance of disease in kiwifruit by regulating the phenylpropanoid pathway and jasmonate pathway.
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Affiliation(s)
- Shucheng Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Liuhua Xiao
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Ming Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Qing Cao
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
- Scientific Research Division, Nanchang Institute of Technology, Nanchang, China
| | - Zhenyu Luo
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Naihui Kang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Mingshu Jia
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Jinyin Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
| | - Miaolian Xiang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Jiangxi Agricultural University, Nanchang, China
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Ye LX, Luo MM, Wang Z, Bai FX, Luo X, Gao L, Peng J, Chen QH, Zhang L. Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation. Front Genet 2022; 13:1043178. [PMID: 36468015 PMCID: PMC9714460 DOI: 10.3389/fgene.2022.1043178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.
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Affiliation(s)
- Li-Xia Ye
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Min-Min Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Zhi Wang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Fu-Xi Bai
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xuan Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Lei Gao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jue Peng
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qing-Hong Chen
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
| | - Lei Zhang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
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Wang P, Mo Y, Wang Y, Fei Y, Huang J, Ni J, Xu ZF. Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia. FRONTIERS IN PLANT SCIENCE 2022; 13:1007266. [PMID: 36388568 PMCID: PMC9646992 DOI: 10.3389/fpls.2022.1007266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
As an important nut crop species, macadamia continues to gain increased amounts of attention worldwide. Nevertheless, with the vast increase in macadamia omic data, it is becoming difficult for researchers to effectively process and utilize the information. In this work, we developed the first integrated germplasm and genomic database for macadamia (MacadamiaGGD), which includes five genomes of four species; three chloroplast and mitochondrial genomes; genome annotations; transcriptomic data for three macadamia varieties, germplasm data for four species and 262 main varieties; nine genetic linkage maps; and 35 single-nucleotide polymorphisms (SNPs). The database serves as a valuable collection of simple sequence repeat (SSR) markers, including both markers that are based on macadamia genomic sequences and developed in this study and markers developed previously. MacadamiaGGD is also integrated with multiple bioinformatic tools, such as search, JBrowse, BLAST, primer designer, sequence fetch, enrichment analysis, multiple sequence alignment, genome alignment, and gene homology annotation, which allows users to conveniently analyze their data of interest. MacadamiaGGD is freely available online (http://MacadamiaGGD.net). We believe that the database and additional information of the SSR markers can help scientists better understand the genomic sequence information of macadamia and further facilitate molecular breeding efforts of this species.
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Affiliation(s)
- Pan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Yuchong Fei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jianting Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Jun Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, China
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Transcriptome Analysis of Low-Temperature-Treated Tetraploid Yellow Actinidia chinensis Planch. Tissue Culture Plantlets. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101573. [PMID: 36295009 PMCID: PMC9604649 DOI: 10.3390/life12101573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Simple Summary Yellow kiwifruit (Actinidia chinensis Planch.) is popular in the market. However, it is highly susceptible to severe weather, including as low temperatures and frost, which may affect its production in the coming year. The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. To better understand cold-adaptive mechanisms, we grew plants under low-temperature conditions, which was followed by transcriptome analysis to discern the genes that play an active role in growth under low temperatures. The findings and dataset obtained in this study advance our knowledge of the cold-adaptive genes in regulatory networks and helps us to understand the cold-tolerance mechanisms in the tetraploid yellow kiwifruit. Abstract The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. In this study, to provide insight into the causes of differences in low-temperature tolerance and to better understand cold-adaptive mechanisms, we treated yellow tetraploid kiwifruit ‘SWFU03’ tissue culture plantlets at low temperatures, used these plantlets for transcriptome analysis, and validated the expression levels of ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. A number of 1630 differentially expressed genes (DEGs) were identified, of which 619 pathway genes were up-regulated, and 1011 were down-regulated in the cold treatment group. The DEGs enriched in the cold tolerance-related pathways mainly included the plant hormone signal transduction and the starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In this study, cold tolerance-related pathways (the plant hormone signal transduction and starch and sucrose metabolism pathway) and genes, e.g., CEY00_Acc03316 (abscisic acid receptor PYL), CEY00_Acc13130 (bZIP transcription factor), CEY00_Acc33627 (TIFY protein), CEY00_Acc26744 (alpha-trehalose-phosphate synthase), CEY00_Acc28966 (beta-amylase), CEY00_Acc16756 (trehalose phosphatase), and CEY00_Acc08918 (beta-amylase 4) were found.
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Liu W, Zhao C, Liu L, Huang D, Ma C, Li R, Huang L. Genome-wide identification of the TGA gene family in kiwifruit (Actinidia chinensis spp.) and revealing its roles in response to Pseudomonas syringae pv. actinidiae (Psa) infection. Int J Biol Macromol 2022; 222:101-113. [PMID: 36150565 DOI: 10.1016/j.ijbiomac.2022.09.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022]
Abstract
Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive disease of kiwifruit worldwide. Functional genes in response to Psa infection are needed, as they could be utilized to control disease. TGACG-binding transcription factor (TGA), as an essential regulator, involved in the process of plant against pathogens. However, the function of TGA regulators has not been reported in kiwifruit. It is unclear that whether TGA genes play a role in response to Psa infection. Here, we performed genome-wide screening and identified 13 TGA genes in kiwifruit. Phylogenetic analysis showed that 13 members of the AcTGA gene family could be divided into five groups. AcTGA proteins were mainly located in the nucleus, and significant differences were identified in their 3D structures. Segmental duplications promoted the expansion of the AcTGA family. Additionally, RNA-Seq and qRT-PCR revealed that four genes (AcTGA01/06/07/09) were tissue-specific and responsive to hormones at different levels. Subcellular localization showed that four proteins located in the nucleus, and among them, three (AcTGA01/06/07) had transcriptional activation activity. Lastly, transient overexpression proved that these three genes (AcTGA01/06/07) potentially played a role in the resistance to kiwifruit canker. These results provided a theoretical basis for revealing TGA involved in kiwifruit regulation against Psa.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Chao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Lu Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Chao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Rui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
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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] [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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08871-4.
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Yang J, Ling C, Liu Y, Zhang H, Hussain Q, Lyu S, Wang S, Liu Y. Genome-Wide Expression Profiling Analysis of Kiwifruit GolS and RFS Genes and Identification of AcRFS4 Function in Raffinose Accumulation. Int J Mol Sci 2022; 23:ijms23168836. [PMID: 36012101 PMCID: PMC9408211 DOI: 10.3390/ijms23168836] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
The raffinose synthetase (RFS) and galactinol synthase (GolS) are two critical enzymes for raffinose biosynthesis, which play an important role in modulating plant growth and in response to a variety of biotic or abiotic stresses. Here, we comprehensively analyzed the RFS and GolS gene families and their involvement in abiotic and biotic stresses responses at the genome-wide scale in kiwifruit. A total of 22 GolS and 24 RFS genes were identified in Actinidia chinensis and Actinidia eriantha genomes. Phylogenetic analysis showed that the GolS and RFS genes were clustered into four and six groups, respectively. Transcriptomic analysis revealed that abiotic stresses strongly induced some crucial genes members including AcGolS1/2/4/8 and AcRFS2/4/8/11 and their expression levels were further confirmed by qRT-PCR. The GUS staining of AcRFS4Pro::GUS transgenic plants revealed that the transcriptionlevel of AcRFS4 was significantly increased by salt stress. Overexpression of AcRFS4 in Arabidopsis demonstrated that this gene enhanced the raffinose accumulation and the tolerance to salt stress. The co-expression networks analysis of hub transcription factors targeting key AcRFS4 genes indicated that there was a strong correlation between AcNAC30 and AcRFS4 expression under salt stress. Furthermore, the yeast one-hybrid assays showed that AcNAC30 could bind the AcRFS4 promoter directly. These results may provide insights into the evolutionary and functional mechanisms of GolS and RFS genes in kiwifruit.
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Affiliation(s)
- Jun Yang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Chengcheng Ling
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Yunyan Liu
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Huamin Zhang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Shiheng Lyu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Songhu Wang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
- Correspondence: (S.W.); (Y.L.)
| | - Yongsheng Liu
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
- Correspondence: (S.W.); (Y.L.)
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Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.). Genes (Basel) 2022; 13:genes13081379. [PMID: 36011289 PMCID: PMC9407107 DOI: 10.3390/genes13081379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H2PO3), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant–pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype.
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Yue C, Chen Q, Hu J, Li C, Luo L, Zeng L. Genome-Wide Identification and Characterization of GARP Transcription Factor Gene Family Members Reveal Their Diverse Functions in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:947072. [PMID: 35845671 PMCID: PMC9280663 DOI: 10.3389/fpls.2022.947072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Golden2, ARR-B, Psr1 (GARP) proteins are plant-specific transcription factors that play vital and diverse roles in plants. However, systematic research on the GARP gene family in plants, including tea plant (Camellia sinensis), is scarce. In this study, a total of 69 GARP genes were identified and characterized from the tea plant genome based on the B-motif sequence signature. The CsGARP genes were clustered into five subfamilies: PHR1/PHL1, KAN, NIGT1/HRS1/HHO, GLK and ARR-B subfamilies. The phylogenetic relationships, gene structures, chromosomal locations, conserved motifs and regulatory cis-acting elements of the CsGARP family members were comprehensively analyzed. The expansion of CsGARP genes occurred via whole-genome duplication/segmental duplication, proximal duplication, and dispersed duplication under purifying selective pressure. The expression patterns of the CsGARP genes were systematically explored from various perspectives: in different tissues during different seasons; in different leaf color stages of tea plant; under aluminum treatment and nitrogen treatment; and in response to abiotic stresses such as cold, drought and salt and to biotic stress caused by Acaphylla theae. The results demonstrate that CsGARP family genes are ubiquitously expressed and play crucial roles in the regulation of growth and development of tea plant and the responses to environmental stimuli. Collectively, these results not only provide valuable information for further functional investigations of CsGARPs in tea plant but also contribute to broadening our knowledge of the functional diversity of GARP family genes in plants.
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Affiliation(s)
- Chuan Yue
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Congcong Li
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liyong Luo
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Liang Zeng
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
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Abid M, Wang Z, Feng C, Luo J, Zhang Y, Tu J, Cai X, Gao P. Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11131633. [PMID: 35807582 PMCID: PMC9269249 DOI: 10.3390/plants11131633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 05/11/2023]
Abstract
Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. Although GRFs have been identified in various plants, there is no reported work available in Actinidia (commonly known as kiwifruit) so far. In the present study, we identified 22 GRF genes on A. chinensis (hereafter A. chinensis is referred to as Ac, and GRF genes in A. chinensis are referred to as AcGRF) distributed on 17 chromosomes and one contig, and 26 GRF genes in A. eriantha (hereafter A. eriantha is referred to as Ae, and GRF genes in A. eriantha are referred to as AeGRF) distributed on 21 chromosomes. Phylogenetic analysis showed that kiwifruit GRF proteins were clustered into five distinct groups. Additionally, kiwifruit GRFs showed motif composition and gene structure similarities within the same group. Synteny analysis showed that whole-genome duplication played a key role in the expansion of the GRF family in kiwifruit. The higher expression levels of kiwifruit GRFs in young tissues and under stress conditions indicated their regulatory role in kiwifruit growth and development. We observed two genes in Ae (AeGRF6.1, AeGRF 6.2) and two genes in Ac (AcGRF 6.1, AeGRF 6.2) significantly upregulated in different RNA-seq datasets. The presence of conserved protein structures and cis-regulatory elements caused functional divergence in duplicated gene pairs. The subcellular localization indicated the presence of kiwifruit GRFs in the nucleus of the plant cell. Protein-protein interaction analysis predicted AtGIF protein orthologs for AcGRFs and AeGRFs. Taken together, we systematically analyzed the characterization of kiwifruit GRF family members for their potential role in kiwifruit development and Pseudomonas syringae pv. actinidiae (Psa.) invasion response. Further functional studies of kiwifruit GRFs in plant growth, development, and stress response will provide valuable insights for kiwifruit breeders.
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Affiliation(s)
- Muhammad Abid
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
- Correspondence: (M.A.); (P.G.)
| | - Zupeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Chen Feng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
| | - Juan Luo
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
| | - Yi Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
| | - Jing Tu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
| | - Xinxia Cai
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
| | - Puxin Gao
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (C.F.); (J.L.); (Y.Z.); (J.T.); (X.C.)
- Correspondence: (M.A.); (P.G.)
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Yao X, Wang S, Wang Z, Li D, Jiang Q, Zhang Q, Gao L, Zhong C, Huang H, Liu Y. The genome sequencing and comparative analysis of a wild kiwifruit Actinidia eriantha. MOLECULAR HORTICULTURE 2022; 2:13. [PMID: 37789488 PMCID: PMC10515239 DOI: 10.1186/s43897-022-00034-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/18/2022] [Indexed: 10/05/2023]
Abstract
The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis (Ac) which may bring risks such as canker disease. Introgression of desired traits from wild relatives is an important method for improving kiwifruit cultivars. Actinidia eriantha (Ae) is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits. Here, we assembled a chromosome-scale high-quality genome of a Ae sample which was directly collected from its wild populations. Our analysis revealed that 41.3% of the genome consists of repetitive elements, comparable to the percentage in Ac and Ae cultivar "White" genomes. The genomic structural variation, including the presence/absence-variation (PAV) of genes, is distinct between Ae and Ac, despite both sharing the same two kiwifruit-specific whole genome duplication (WGD) events. This suggests that a post-WGD divergence mechanism occurred during their evolution. We further investigated genes involved in ascorbic acid biosynthesis and disease-resistance of Ae, and we found introgressive genome could contribute to the complex relationship between Ae and other representative kiwifruit taxa. Collectively, the Ae genome offers valuable genetic resource to accelerate kiwifruit breeding applications.
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Affiliation(s)
- Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shuaibin Wang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zupeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Quan Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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Yue J, Liu Y. SSR2Marker: an integrated pipeline for identification of SSR markers within any two given genome-scale sequences. MOLECULAR HORTICULTURE 2022; 2:11. [PMID: 37789487 PMCID: PMC10515269 DOI: 10.1186/s43897-022-00033-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/11/2022] [Indexed: 10/05/2023]
Affiliation(s)
- Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
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Yang J, Yan H, Liu Y, Da L, Xiao Q, Xu W, Su Z. GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. Front Genet 2022; 13:823966. [PMID: 35495163 PMCID: PMC9039005 DOI: 10.3389/fgene.2022.823966] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
Glycyrrhiza uralensis (Licorice), which belongs to Leguminosae, is famous for the function of pharmacologic action and natural sweetener with its dried roots and rhizomes. In recent years, the whole-genome sequence of G. uralensis has been completed, which will help to lay the foundation for the study of gene function. Here, we integrated the available genomic and transcriptomic data of G. uralensis and constructed the G. uralensis gene co-expression network. We then annotated gene functions of G. uralensis via aligning with public databases. Furthermore, gene families of G. uralensis were predicted by tools including iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid, and PfamScan. Finally, we constructed a platform for gene function analysis in G. uralensis (GURFAP, www.gzybioinfoormatics.cn/GURFAP). For analyzed and predicted gene function, we introduced various tools including BLAST (Basic local alignment search tool), GSEA (Gene set enrichment analysis), Motif, Heatmap, and JBrowse. Our analysis based on this platform indicated that the biosynthesis of glycyrrhizin might be regulated by MYB and bHLH. We also took CYP88D6, CYP72A154, and bAS gene in the synthesis pathway of glycyrrhizin as examples to demonstrate the reliability and availability of our platform. Our platform GURFAP will provide convenience for researchers to mine the gene function of G. uralensis and thus discover more key genes involved in the biosynthetic pathway of active ingredients.
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Affiliation(s)
- Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hengyu Yan
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Lingling Da
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Qiaoqiao Xiao
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
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Tao J, Jia H, Wu M, Zhong W, Jia D, Wang Z, Huang C. Genome-wide identification and characterization of the TIFY gene family in kiwifruit. BMC Genomics 2022; 23:179. [PMID: 35247966 PMCID: PMC8897921 DOI: 10.1186/s12864-022-08398-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/17/2022] [Indexed: 12/25/2022] Open
Abstract
Background The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well characterized in kiwifruit, a popular fruit with important nutritional and economic value. Results A total of 27 and 21 TIFY genes were identified in the genomes of Actinidia eriantha and A. chinensis, respectively. Phylogenetic analyses showed that kiwifruit TIFY genes could be classified into four major groups, JAZ, ZML, TIFY and PPD, and the JAZ group could be further clustered into six subgroups (JAZ I to JAZ VI). Members within the same group or subgroup have similar exon-intron structures and conserved motif compositions. The kiwifruit TIFY genes are unevenly distributed on the chromosomes, and the segmental duplication events played a vital role in the expansion of the TIFY genes in kiwifruit. Syntenic analyses of TIFY genes between kiwifruit and other five plant species (including Arabidopsis thaliana, Camellia sinensis, Oryza sativa, Solanum lycopersicum and Vitis vinifera) and between the two kiwifruit species provided valuable clues for understanding the potential evolution of the kiwifruit TIFY family. Molecular evolutionary analysis showed that the evolution of kiwifruit TIFY genes was primarily constrained by intense purifying selection. Promoter cis-element analysis showed that most kiwifruit TIFY genes possess multiple cis-elements related to stress-response, phytohormone signal transduction and plant growth and development. The expression pattern analyses indicated that TIFY genes might play a role in different kiwifruit tissues, including fruit at specific development stages. In addition, several TIFY genes with high expression levels during Psa (Pseudomonas syringae pv. actinidiae) infection were identified, suggesting a role in the process of Pas infection. Conclusions In this study, the kiwifruit TIFY genes were identified from two assembled kiwifruit genomes. In addition, their basic physiochemical properties, chromosomal localization, phylogeny, gene structures and conserved motifs, synteny analyses, promoter cis-elements and expression patters were systematically examined. The results laid a foundation for further understanding the function of TIFY genes in kiwifruit, and provided a new potential approach for the prevention and treatment of Psa infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08398-8.
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Abstract
Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries.
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Wang X, Li Y, Liu Y, Zhang D, Ni M, Jia B, Heng W, Fang Z, Zhu LW, Liu P. Transcriptomic and Proteomic Profiling Reveal the Key Role of AcMYB16 in the Response of Pseudomonas syringae pv. actinidiae in Kiwifruit. FRONTIERS IN PLANT SCIENCE 2021; 12:756330. [PMID: 34868148 PMCID: PMC8632638 DOI: 10.3389/fpls.2021.756330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 06/01/2023]
Abstract
Kiwifruit bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa), is an important disease of kiwifruit (Actinidia Lind.). Plant hormones may induce various secondary metabolites to resist pathogens via modulation of hormone-responsive transcription factors (TFs), as reported in past studies. In this study, we showed that JA accumulated in the susceptible cultivar Actinidia chinensis 'Hongyang' but decreased in the resistant cultivar of A. chinensis var. deliciosa 'Jinkui' in response to Psa. Integrated transcriptomic and proteomic analyses were carried out using the resistant cultivar 'Jinkui'. A total of 5,045 differentially expressed genes (DEGs) and 1,681 differentially expressed proteins (DEPs) were identified after Psa infection. Two pathways, 'plant hormone signal transduction' and 'phenylpropanoid biosynthesis,' were activated at the protein and transcript levels. In addition, a total of 27 R2R3-MYB transcription factors (TFs) were involved in the response to Psa of 'Jinkui,' including the R2R3-MYB TF subgroup 4 gene AcMYB16, which was downregulated in 'Jinkui' but upregulated in 'Hongyang.' The promoter region of AcMYB16 has a MeJA responsiveness cis-acting regulatory element (CRE). Transient expression of the AcMYB16 gene in the leaves of 'Jinkui' induced Psa infection. Together, these data suggest that AcMYB16 acts as a repressor to regulate the response of kiwifruit to Psa infection. Our work will help to unravel the processes of kiwifruit resistance to pathogens and will facilitate the development of varieties with resistance against bacterial pathogens.
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Affiliation(s)
- Xiaojie Wang
- School of Horticulture, Anhui Agricultural University, Hefei, China
- School of Life Sciences, Anhui University, Hefei, China
| | - Yawei Li
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Yuanyuan Liu
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Dongle Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Min Ni
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Bing Jia
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Wei Heng
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, China
| | - Li-wu Zhu
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Pu Liu
- School of Horticulture, Anhui Agricultural University, Hefei, China
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Wang Y, Chen F, Ma Y, Zhang T, Sun P, Lan M, Li F, Fang W. An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis). HORTICULTURE RESEARCH 2021; 8:176. [PMID: 34333548 PMCID: PMC8325681 DOI: 10.1038/s41438-021-00613-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 05/14/2023]
Abstract
Tea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.
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Affiliation(s)
- Ya Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Taikui Zhang
- College of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Meifang Lan
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063099, China
| | - Fang Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Gan Z, Yuan X, Shan N, Wan C, Chen C, Xu Y, Xu Q, Chen J. AcWRKY40 mediates ethylene biosynthesis during postharvest ripening in kiwifruit. PLANT SCIENCE 2021; 309:110948. [PMID: 34134847 DOI: 10.1016/j.plantsci.2021.110948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
WRKY transcription factors belong to a superfamily that is involved in many important biological processes, including plant development and senescence. However, little is known about the transcriptional regulation mechanisms of WRKY genes involved in kiwifruit postharvest ripening. Here, we isolated a WRKY gene from the kiwifruit genome and named it AcWRKY40. AcWRKY40 is a nucleus-localized protein that possesses transcriptional activation activity. The expression of AcWRKY40 was detected, and the gene responded to ethylene treatment during kiwifruit postharvest ripening, indicating its involvement in this process at the transcriptional level. We found multiple cis-acting elements related to maturation and senescence in the AcWRKY40 promoter. GUS activity analysis showed that its promoter activity was induced by exogenous ethylene. Yeast one-hybrid and dual-luciferase assays demonstrated that AcWRKY40 binds to the promoters of AcSAM2, AcACS1, and AcACS2 to activate them. In addition, transient transformations showed that AcWRKY40 enhances the expression of AcSAM2, AcACS1, and AcACS2. Taken together, these results suggest that AcWRKY40 is involved in kiwifruit postharvest ripening, possibly by regulating the expression of genes related to ethylene biosynthesis, thus deepening our understanding of the regulatory mechanisms of WRKY transcription factors in fruit ripening.
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Affiliation(s)
- Zengyu Gan
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xin Yuan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nan Shan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chunpeng Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuying Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yunhe Xu
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qin Xu
- Agriculture and Rural Bureau of Gongcheng Yao Autonomous County, Guilin, 542500, China
| | - Jinyin Chen
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang, 330075, China.
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Staton M, Cannon E, Sanderson LA, Wegrzyn J, Anderson T, Buehler S, Cobo-Simón I, Faaberg K, Grau E, Guignon V, Gunoskey J, Inderski B, Jung S, Lager K, Main D, Poelchau M, Ramnath R, Richter P, West J, Ficklin S. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Brief Bioinform 2021; 22:6318561. [PMID: 34251419 PMCID: PMC8574961 DOI: 10.1093/bib/bbab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/01/2022] Open
Abstract
Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
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Affiliation(s)
| | - Ethalinda Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA USA
| | | | | | | | | | | | - Kay Faaberg
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Emily Grau
- University of Connecticut, Storrs, CT USA
| | | | | | | | - Sook Jung
- Washington State University, Pullman, WA USA
| | - Kelly Lager
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Dorrie Main
- Washington State University, Pullman, WA USA
| | - Monica Poelchau
- USDA-ARS, National Agricultural Library, Beltsville, MD, USA
| | | | | | - Joe West
- University of Tennessee, Knoxville, TN USA
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Lin M, Sun S, Fang J, Qi X, Sun L, Zhong Y, Sun Y, Hong G, Wang R, Li Y. BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. BMC Genomics 2021; 22:72. [PMID: 33482717 PMCID: PMC7821520 DOI: 10.1186/s12864-021-07369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/05/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia arguta has excellent cold resistance, but knowledge relevant to molecular mechanisms is still limited. Understanding the mechanism underlying cold resistance in kiwifruit is important for breeding cold resistance. RESULTS In our study, a population resulting from the cross of A. arguta 'Ruby-3' × 'Kuilv' male was generated for kiwifruit hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to their LT50. Then, we performed bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes that provide cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold-tolerant population than in the cold-sensitive population. Upon - 30 °C low-temperature treatment, 126 differentially expressed genes were identify; the expression of 59 genes was up-regulated and that of 67 genes was down-regulated between the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs were primarily related to starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Ten major key enzyme-encoding genes and two regulatory genes were up-regulated in the tolerant pool, and regulatory genes of the CBF pathway were found to be differentially expressed. In particular, a 14-3-3 gene was down-regulated and an EBF gene was up-regulated. To validate the BSR-Seq results, 24 DEGs were assessed via qRT-PCR, and the results were consistent with those obtained by BSR-Seq. CONCLUSION Our research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit.
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Affiliation(s)
- Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shihang Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yanxiang Sun
- Langfang Normal University, Langfang, 065000, China
| | - Gu Hong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Ran Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
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