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Chang X, Chang X, Li L, Cheng X, Wang Y. Transcriptomic responses of 'Huping jujube' (Zizyphus jujuba mill. cv. Huping) fruit to combined treatment of acidic electrolyzed water and high-voltage electrostatic field. Food Res Int 2024; 191:114742. [PMID: 39059929 DOI: 10.1016/j.foodres.2024.114742] [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: 05/27/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
The molecular mechanism underlying the preserving superior quality attributes of postharvest Huping jujube fruit by combining acidic electrolyzed water and high-voltage electrostatic field (AH) treatment remained unclear. The high-throughput sequencing analysis revealed a total of 3590 common differentially expressed genes (DEGs) in the T-W-CK0 vs T-W-CK75 and T-W-CK75 vs T-W-AH75 groups. AH treatment down-regulated most genes associated with respiratory metabolism, as well as lignin and anthocyanin biosynthesis, thereby maintaining lower physiological activities, improving taste and color quality of mature-white jujube. Additionally, AH treatment downregulated the genes involved in reactive oxygen species (ROS) generation and disease resistance, while simultaneously upregulating the genes associated with ROS elimination. This suggested that AH treatment could inhibit pathogen infection to prevent the activation of plants' active defense and reduce the ROS-induced damage. In sum, the present study provided a comprehension explanation that AH treatment improved the storage quality attributes of jujube fruit at the genetic level.
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Affiliation(s)
- Xiaojie Chang
- College of Horticulture, Shanxi Agricultural University, Taigu 030800, China; Life Sciences Department, Shanxi Center of Technology Innovation for High Value Added echelon Utilization of Premium Agro-Products, Yuncheng University, Yuncheng 044000, China; Shanxi Center of Technology Innovation for Storage and Processing of Fruit and Vegetable, Taigu 030800, China.
| | - Xiaoyuan Chang
- Shenzhen Tobacco Industry Co., Ltd, Shenzhen 518000, China.
| | - Longzhen Li
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030800, China; Shanxi Center of Technology Innovation for Storage and Processing of Fruit and Vegetable, Taigu 030800, China.
| | - Xueling Cheng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030800, China; Shanxi Center of Technology Innovation for Storage and Processing of Fruit and Vegetable, Taigu 030800, China.
| | - Yu Wang
- College of Horticulture, Shanxi Agricultural University, Taigu 030800, China; College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030800, China; Shanxi Center of Technology Innovation for Storage and Processing of Fruit and Vegetable, Taigu 030800, China.
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Guan L, Liu J, Wang R, Mu Y, Sun T, Wang L, Zhao Y, Zhu N, Ji X, Lu Y, Wang Y. Metabolome and Transcriptome Analyses Reveal Flower Color Differentiation Mechanisms in Various Sophora japonica L. Petal Types. BIOLOGY 2023; 12:1466. [PMID: 38132292 PMCID: PMC10740404 DOI: 10.3390/biology12121466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Sophora japonica L. is an important landscaping and ornamental tree species throughout southern and northern parts of China. The most common color of S. japonica petals is yellow and white. In this study, S. japonica flower color mutants with yellow and white flag petals and light purple-red wing and keel petals were used for transcriptomics and metabolomics analyses. To investigate the underlying mechanisms of flower color variation in S. japonica 'AM' mutant, 36 anthocyanin metabolites were screened in the anthocyanin-targeting metabolome. The results demonstrated that cyanidins such as cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside in the 'AM' mutant were the key metabolites responsible for the red color of the wing and keel petals. Transcriptome sequencing and differentially expressed gene (DEG) analysis identified the key structural genes and transcription factors related to anthocyanin biosynthesis. Among these, F3'5'H, ANS, UFGT79B1, bHLH, and WRKY expression was significantly correlated with the cyanidin-type anthocyanins (key regulatory factors affecting anthocyanin biosynthesis) in the flag, wing, and keel petals in S. japonica at various flower development stages.
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Affiliation(s)
- Lingshan Guan
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Jinshi Liu
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Ruilong Wang
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
- College of Forestry, Shandong Agricultural University, Tai’an 271018, China
| | - Yanjuan Mu
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Tao Sun
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Lili Wang
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yunchao Zhao
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Nana Zhu
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
- State-Owned Yishan Forest Farm in Yishui County, Linyi 276400, China
| | - Xinyue Ji
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yizeng Lu
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yan Wang
- Key Laboratory of National Forestry and Grassland Administration on Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
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Zeng Z, Jia Y, Huang X, Chen Z, Xiang T, Han N, Bian H, Li C. Transcriptional and protein structural characterization of homogentisate phytyltransferase genes in barley, wheat, and oat. BMC PLANT BIOLOGY 2023; 23:528. [PMID: 37904113 PMCID: PMC10617047 DOI: 10.1186/s12870-023-04535-x] [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: 07/10/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Homogentisate phytyltransferase (HPT) is the critical enzyme for the biosynthesis of tocopherols (vitamin E), which are the major lipid-soluble antioxidants and help plants adapt to various stress conditions. HPT is generally strictly conserved in various plant genomes; however, a divergent lineage HPT2 was identified recently in some Triticeae species. The molecular function and transcriptional profiles of HPT2 remain to be characterized. RESULTS In this study, we performed comprehensive transcriptome data mining of HPT1 and HPT2 in different tissues and stages of barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa), followed by qRT-PCR experiments on HPT1 and HPT2 in different tissues of barley and wheat. We found that the common HPT1 genes (HvHPT1, TaHPT1s, and AsHPT1s) displayed a conserved transcriptional pattern in the three target species and were universally transcribed in various tissues, with a notable preference in leaf. In contrast, HPT2 genes (HvHPT2, TaHPT2, and AsHPT2) were specifically transcribed in spike (developmentally up-regulated) and shoot apex tissues, displaying a divergent tissue-specific pattern. Cis-regulatory elements prediction in the promoter region identified common factors related to light-, plant hormone-, low temperature-, drought- and defense- responses in both HPT1s and HPT2s. We observed the transcriptional up-regulation of HvHPT1 and HvHPT2 under various stress conditions, supporting their conserved function in environmental adaption. We detected a clear, relaxed selection pressure in the HPT2 lineage, consistent with the predicted evolution pattern following gene duplication. Protein structural modelling and substrate docking analyses identified putative catalytic amino acid residues for HvHPT1 and HvHPT2, which are strictly conserved and consistent with their function in vitamin E biosynthesis. CONCLUSIONS We confirmed the presence of two lineages of HPT in Triticeae and Aveninae, including hexaploid oat, and characterized their transcriptional profiles based on transcriptome and qRT-PCR data. HPT1s were ubiquitously transcribed in various tissues, whilst HPT2s were highly expressed in specific stages and tissue. The active transcription of HPT2s, together with its conserved cis-elements and protein structural features, support HPT2s' role in tocopherol production in Triticeae. This study is the first protein structural analysis on the membrane-bound plant HPTs and provides valuable insights into its catalytic mechanism.
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Affiliation(s)
- Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China
| | - Yong Jia
- Western Crops Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiaoping Huang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengdao Li
- Western Crops Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
- State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia.
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia.
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Jiang L, Gao Y, Han L, Zhang W, Fan P. Designing plant flavonoids: harnessing transcriptional regulation and enzyme variation to enhance yield and diversity. FRONTIERS IN PLANT SCIENCE 2023; 14:1220062. [PMID: 37575923 PMCID: PMC10420081 DOI: 10.3389/fpls.2023.1220062] [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: 05/11/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023]
Abstract
Plant synthetic biology has emerged as a powerful and promising approach to enhance the production of value-added metabolites in plants. Flavonoids, a class of plant secondary metabolites, offer numerous health benefits and have attracted attention for their potential use in plant-based products. However, achieving high yields of specific flavonoids remains challenging due to the complex and diverse metabolic pathways involved in their biosynthesis. In recent years, synthetic biology approaches leveraging transcription factors and enzyme diversity have demonstrated promise in enhancing flavonoid yields and expanding their production repertoire. This review delves into the latest research progress in flavonoid metabolic engineering, encompassing the identification and manipulation of transcription factors and enzymes involved in flavonoid biosynthesis, as well as the deployment of synthetic biology tools for designing metabolic pathways. This review underscores the importance of employing carefully-selected transcription factors to boost plant flavonoid production and harnessing enzyme promiscuity to broaden flavonoid diversity or streamline the biosynthetic steps required for effective metabolic engineering. By harnessing the power of synthetic biology and a deeper understanding of flavonoid biosynthesis, future researchers can potentially transform the landscape of plant-based product development across the food and beverage, pharmaceutical, and cosmetic industries, ultimately benefiting consumers worldwide.
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Affiliation(s)
- Lina Jiang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Yifei Gao
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Leiqin Han
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Wenxuan Zhang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Pengxiang Fan
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Hangzhou, China
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Yu H, Wang J, Shen Y, Sheng X, Shaw RK, Branca F, Gu H. A 43 Bp-Deletion in the F3'H Gene Reducing Anthocyanins Is Responsible for Keeping Buds Green at Low Temperatures in Broccoli. Int J Mol Sci 2023; 24:11391. [PMID: 37511150 PMCID: PMC10380335 DOI: 10.3390/ijms241411391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Most broccoli cultivars or accessions exhibit green buds under appropriate growth conditions, which turn purple at cold temperatures. However, certain cultivars consistently maintain green buds both during normal growth and at cold temperatures. In this study, we used BSA-seq (bulked segregation analysis-sequencing), along with fine mapping and transcriptome analysis to identify a candidate gene (flavonoid 3'-hydroxylase, F3'H) responsible for reducing anthocyanin accumulation in the mutant GS and HX-16 broccoli (Brassica oleracea L. var. italica), which could retain green buds even at low temperatures. A 43-bp deletion was detected in the coding sequence (CDS) of the F3'H gene in HX-16 and the mutant GS, which significantly decreased F3'H expression and the accumulation of cyanidin and delphinidin in the mutant GS. Furthermore, the expression of F3'H was upregulated at low temperatures in the wild line PS. Our results demonstrated the efficacy of utilizing the 43-bp InDel (Insertion-Deletion) in predicting whether buds in B. oleracea L. will turn purple or remain green at cold temperatures across forty-two germplasm materials. This study provides critical genetic and molecular insights for the molecular breeding of B. oleracea and sheds light on the molecular mechanisms underlying the effect of low temperatures on bud color in broccoli.
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Affiliation(s)
- Huifang Yu
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiansheng Wang
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yusen Shen
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoguang Sheng
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ranjan Kumar Shaw
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - Honghui Gu
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Fan S, Xu Y, Bai M, Luo F, Yu J, Yang G. Integrated Transcriptome and Metabolome Analysis Revealed the Causal Agent of Primary Bud Necrosis in 'Summer Black' Grape. Int J Mol Sci 2023; 24:10410. [PMID: 37373557 DOI: 10.3390/ijms241210410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Primary bud necrosis of grape buds is a physiological disorder that leads to decreased berry yield and has a catastrophic impact on the double cropping system in sub-tropical areas. The pathogenic mechanisms and potential solutions remain unknown. In this study, the progression and irreversibility patterns of primary bud necrosis in 'Summer Black' were examined via staining and transmission electron microscopy observation. Primary bud necrosis was initiated at 60 days after bud break and was characterized by plasmolysis, mitochondrial swelling, and severe damage to other organelles. To reveal the underlying regulatory networks, winter buds were collected during primary bud necrosis progression for integrated transcriptome and metabolome analysis. The accumulation of reactive oxygen species and subsequent signaling cascades disrupted the regulation systems for cellular protein quality. ROS cascade reactions were related to mitochondrial stress that can lead to mitochondrial dysfunction, lipid peroxidation causing damage to membrane structure, and endoplasmic reticulum stress leading to misfolded protein aggregates. All these factors ultimately resulted in primary bud necrosis. Visible tissue browning was associated with the oxidation and decreased levels of flavonoids during primary bud necrosis, while the products of polyunsaturated fatty acids and stilbenes exhibited an increasing trend, leading to a shift in carbon flow from flavonoids to stilbene. Increased ethylene may be closely related to primary bud necrosis, while auxin accelerated cell growth and alleviated necrosis by co-chaperone VvP23-regulated redistribution of auxin in meristem cells. Altogether, this study provides important clues for further study on primary bud necrosis.
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Affiliation(s)
- Shaogang Fan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Yanshuai Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Feixiong Luo
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jun Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Guoshun Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
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Zheng H, Jiao J, Niu Q, Zhu N, Huang Y, Ke L, Tang S, Liu H, Sun Y. Cloning and functional analysis of GhDFR1, a key gene of flavonoid synthesis pathway in naturally colored cotton. Mol Biol Rep 2023; 50:4865-4873. [PMID: 37052804 DOI: 10.1007/s11033-023-08420-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND The naturally colored brown cotton fiber is the most widely used environmentally friendly textile material, which primarily contains proanthocyanidins and their derivatives. Many structural genes in the flavonoid synthesis pathway are known to improve the genetic resources of naturally colored cotton. Among them, DFR is a crucial late enzyme to synthesis both anthocyanins and proanthocyanidins in the plant flavonoid pathway. METHODS The protein sequences of GhDFRs were analyzed using bioinformatic tools. The expression levels of GhDFRs in various tissues and organs of upland cotton Zongxu1 (ZX1), were analyzed by quantitative real-time PCR, and the expression pattern of GhDFR1 during fiber development of white cotton and brown cotton was analyzed further. The function of GhDFR1 in NCC ZX1 was preliminarily analyzed by virus induced gene silencing (VIGS) technology. RESULTS Bioinformatic analysis revealed that GhDFRs sequences in upland cotton genome were extremely conserved. Furthermore, evolutionary tree analysis revealed that the functions of GhDFR1 and GhDFR2, and GhDFR3 and GhDFR4, presented different and shared some similarities. Our study showed GhDFR1 and GhDFR2 were specifically expressed in fibers, while GhDFR3 and GhDFR4 were specifically expressed in petals. GhDFR1 was exclusively expressed in brown cotton fiber at various stages of development and progressively increased with the growth of fiber, but the trend of expression in white cotton was quite the opposite. We silenced GhDFR1 expression in brown cotton fiber using VIGS technology, and observed the VIGS-interference plants. After reducing the expression level of GhDFR1, the period for significant GhDFR1 expression in the developing fibers changed, reducing the content of anthocyanins, and lightening the color of mature cotton fibers. CONCLUSION GhDFR1 was preferentially expressed in brown cotton during fiber development. The timing of GhDFR1 expression for flavonoid synthesis altered, resulting in anthocyanin contents reduced and the fiber color of the GhDFR1i lines lightened. These findings showed the role of GhDFR1 in fiber coloration of NCC and provided a new candidate for NCC genetic improvement.
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Affiliation(s)
- Hongli Zheng
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- College of Textile Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Junye Jiao
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Qingqing Niu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ning Zhu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yinshuai Huang
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Liping Ke
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Shouwu Tang
- China Colored-Cotton (Group) Co., Ltd., Ürümqi, 830011, Xinjiang, People's Republic of China
| | - Haifeng Liu
- China Colored-Cotton (Group) Co., Ltd., Ürümqi, 830011, Xinjiang, People's Republic of China.
| | - Yuqiang Sun
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
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Stephen K, Aparna K, Beena R, Sah RP, Jha UC, Behera S. Identification of simple sequence repeat markers linked to heat tolerance in rice using bulked segregant analysis in F 2 population of NERICA-L 44 × Uma. FRONTIERS IN PLANT SCIENCE 2023; 14:1113838. [PMID: 37051081 PMCID: PMC10084929 DOI: 10.3389/fpls.2023.1113838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
The damage caused by high temperature is one of the most important abiotic stress affecting rice production. Reproductive stage of rice is highly susceptible to high temperature. The present investigation was undertaken to identify polymorphic microsatellite markers (SSR) associated with heat tolerance. The rice cultivars NERICA- L 44 (heat tolerant) and Uma (heat susceptible) were crossed to generate F1 and F2 populations. The F2 population was subjected to heat stress at >38°C and the 144 F2 plants were evaluated for their tolerance. The results note that the mean of the F2 population was influenced by the tolerant parent with regards to the traits of plant height, membrane stability index, photosynthetic rate, stomatal conductance, evapotranspiration rate, pollen viability, spikelet fertility and 1000 grain weight. Ten each of the extremely susceptible and tolerant plants were selected based on the spikelet fertility percentage. Their DNA was pooled into tolerant and susceptible bulks and Bulked Segregant Analysis (BSA) was carried out using 100 SSR markers to check for polymorphism. The survey revealed a polymorphism of 18% between the parents. RM337, RM10793, RM242, RM5749, RM6100, RM490, RM470, RM473, RM222 and RM556 are some of the prominent markers that were found to be polymorphic between the parents and the bulks. We performed gene annotation and enrichment analysis of identified polymorphic markers. Result revealed that the sequence specific site of that chromosome mostly enriched with biological processes like metabolic pathway, molecular mechanism, and subcellular function. Among that RM337 was newly reported marker for heat tolerance. Expression analysis of two genes corresponds to RM337 revealed that LOP1 (LOC_Os08g01330) was linked to high temperature tolerance in rice. The results demonstrate that BSA using SSR markers is useful in identifying genomic regions that contribute to thermotolerance.
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Affiliation(s)
- K. Stephen
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, India
| | - K. Aparna
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, India
| | - R. Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, India
| | - R. P. Sah
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute, Cuttack, India
| | - Uday Chand Jha
- Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, India
| | - Sasmita Behera
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute, Cuttack, India
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Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
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Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
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10
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Chromosomal-level genome and multi-omics dataset provides new insights into leaf pigmentation in Acer palmatum. Int J Biol Macromol 2023; 227:93-104. [PMID: 36470439 DOI: 10.1016/j.ijbiomac.2022.11.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022]
Abstract
Acer palmatum (A. palmatum), a deciduous shrub or small arbour which belongs to Acer of Aceraceae, is an excellent greening species as well as a beautiful ornamental plant. In this study, a high-quality chromosome-level reference genome for A. palmatum was constructed using Oxford Nanopore sequencing and Hi-C technology. The assembly genome was ∼745.78 Mb long with a contig N50 length of 3.20 Mb, and 95.30 % (710.71 Mb) of the assembly was anchored into 13 pseudochromosomes. A total of 28,559 protein-coding genes were obtained, ∼90.02 % (25,710) of which could be functionally annotated. The genomic evolutionary analysis revealed that A. palmatum is most closely related to A. yangbiense and A. truncatum, and underwent only an ancient gamma whole-genome duplication event. Despite lacking a recent independent WGD, 25,795 (90.32 %) genes of A. palmatum were duplicated, and the unique/expanded gene families were linked with genes involved in plant-pathogen interaction and several metabolic pathways, which might underpin adaptability. A combined genomic, transcriptomic, and metabolomic analysis related to the biosynthesis of anthocyanin in leaves during the different season were characterized. The results indicate that the dark-purple colouration of the leaves in spring was caused by a high amount of anthocyanins, especially delphinidin and its derivatives; and the red colouration of the leaves in autumn by a high amount of cyanidin 3-O-glucoside. In conclusion, these valuable multi-omic resources offer important foundations to explore the molecular regulation mechanism in leaf colouration and also provide a platform for the scientific and efficient utilization of A. palmatum.
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11
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Liu Y, Li C, Yan R, Yu R, Ji M, Chen F, Fan S, Meng J, Liu F, Zhou G, Tang X. Metabolome and transcriptome analyses of the flavonoid biosynthetic pathway for the efficient accumulation of anthocyanins and other flavonoids in a new duckweed variety (68-red). JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153753. [PMID: 35760019 DOI: 10.1016/j.jplph.2022.153753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 05/21/2023]
Abstract
Duckweed is a kind of aquatic plant with the characteristics of high nutritional value and medicinal benefits. However, most researches focused on the natural germplasms. The underlying metabolic pathway remains to be systematically elaborated in duckweed. In our laboratory, one reddish-purple mutant with high-flavonoids was screened from a mutant library of Spirodela polyrhiza 6068, named 68-red. The content of anthocyanins and proanthocyanidins in 68-red mutant increased by 563.47% and 231.19%, respectively, compared to wild type. It is interesting that cynaroside and orientin content were significantly increased, in contrast, apigetrin and vitexin were decreased in 68-red mutant. Considering this, metabolome and transcriptome were employed to explore the flavonoids biosynthetic pathway. Here, a total of 734 metabolites were identified in the wild type and 68-red mutant. Among which, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside were significantly accumulated, which were positively correlated with deep reddish-purple of 68-red mutant. In addition, proanthocyanidins (B1, B2, B3, B4, C1, C2), flavonoid and its glycosides (11 luteolin and its glycosides, 14 quercetin and its glycosides, 14 kaempferol and its glycosides, 2 apigenin glycosides) were significantly accumulated, 2 apigenin glycosides were down-regulated in 68-red mutant. The transcriptome data and qRT-PCR indicated that 16 enzyme genes in flavonoids biosynthetic pathway (PAL, C4H, CHSs, F3H, ANS, ANR, F3'Hs, DFRs, LAR, GT1, BZ1) were significantly up-regulated in 68-red mutant. Correlation analysis found that three copies of F3'H gene play important roles in the synthesis of anthocyanins, luteolin and apigenin glycosides. In conclusion, the 68-red mutant is a high quality germplasm resources for food and medical industry. Metabolome and transcriptome provide new insight for exploring the enzyme genes and functional metabolites in duckweed.
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Affiliation(s)
- Yu Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Chuantong Li
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Ruiting Yan
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Ruikang Yu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Meijing Ji
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Fei Chen
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Shusheng Fan
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Jie Meng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Fumei Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
| | - Xianfeng Tang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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12
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Wang J, Zhang C, Li Y. Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds. Genes (Basel) 2022; 13:genes13030410. [PMID: 35327963 PMCID: PMC8951560 DOI: 10.3390/genes13030410] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022] Open
Abstract
Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.
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13
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Yang F, Gao J, Wei Y, Ren R, Zhang G, Lu C, Jin J, Ai Y, Wang Y, Chen L, Ahmad S, Zhang D, Sun W, Tsai W, Liu Z, Zhu G. The genome of Cymbidium sinense revealed the evolution of orchid traits. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2501-2516. [PMID: 34342129 PMCID: PMC8633513 DOI: 10.1111/pbi.13676] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/08/2021] [Accepted: 07/23/2021] [Indexed: 05/04/2023]
Abstract
The Orchidaceae is of economic and ecological importance and constitutes ˜10% of all seed plant species. Here, we report a genome physical map for Cymbidium sinense, a well-known species belonging to genus Cymbidium that has thousands of natural variation varieties of flower organs, flower and leaf colours and also referred as the King of Fragrance, which make it arose into a unique cultural symbol in China. The high-quality chromosome-scale genome assembly was 3.52 Gb in size, 29 638 protein-coding genes were predicted, and evidence for whole-genome duplication shared with other orchids was provided. Marked amplification of cytochrome- and photosystem-related genes was observed, which was consistent with the shade tolerance and dark green leaves of C. sinense. Extensive duplication of MADS-box genes, and the resulting subfunctional and expressional differentiation, was associated with regulation of species-specific flower traits, including wild-type and mutant-type floral patterning, seasonal flowering and ecological adaption. CsSEP4 was originally found to positively regulate gynostemium development. The CsSVP genes and their interaction proteins CsAP1 and CsSOC1 were significantly expanded and involved in the regulation of low-temperature-dependent flowering. Important genetic clues to the colourful leaf traits, purple-black flowers and volatile trait in C. sinense were also found. The results provide new insights into the molecular mechanisms of important phenotypic traits of Cymbidium and its evolution and serve as a powerful platform for future evolutionary studies and molecular breeding of orchids.
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Affiliation(s)
- Feng‐Xi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Yong‐Lu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Rui Ren
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Guo‐Qiang Zhang
- Laboratory for Orchid Conservation and UtilizationThe Orchid Conservation and Research Center of ShenzhenThe National Orchid Conservation Center of ChinaShenzhenChina
| | - Chu‐Qiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Jian‐Peng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Ye Ai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ya‐Qin Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant DevelopmentSchool of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Li‐Jun Chen
- Laboratory for Orchid Conservation and UtilizationThe Orchid Conservation and Research Center of ShenzhenThe National Orchid Conservation Center of ChinaShenzhenChina
| | - Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Di‐Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wei‐Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wen‐Chieh Tsai
- Orchid Research and Development CenterNational Cheng Kung UniversityTainanTaiwan
- Institute of Tropical Plant Sciences and MicrobiologyNational Cheng Kung UniversityTainanTaiwan
| | - Zhong‐Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Gen‐Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental HorticultureGuangdong Academy of Agricultural SciencesGuangzhouChina
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14
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Xiao Y, Wen J, Meng R, Meng Y, Zhou Q, Nie ZL. The expansion and diversity of the CYP75 gene family in Vitaceae. PeerJ 2021; 9:e12174. [PMID: 34616623 PMCID: PMC8449539 DOI: 10.7717/peerj.12174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms.
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Affiliation(s)
- Yang Xiao
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., U.S.A
| | - Ran Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Qiang Zhou
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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15
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do Nascimento CD, de Paula ACCFF, de Oliveira Júnior AH, Mendonça HDOP, Reina LDCB, Augusti R, Figueiredo-Ribeiro RDCL, Melo JOF. Paper Spray Mass Spectrometry on the Analysis of Phenolic Compounds in Rhynchelytrum repens: A Tropical Grass with Hypoglycemic Activity. PLANTS (BASEL, SWITZERLAND) 2021; 10:1617. [PMID: 34451661 PMCID: PMC8398573 DOI: 10.3390/plants10081617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022]
Abstract
The characterization of plant compounds with pharmacological activity is a field of great relevance in research and development. As such, identification techniques with the goal of developing new drugs or even validating the bioactive properties of extracts must be explored in order to further expand the knowledge of plant extract composition. Most works in this field employ HPLC, when exploring non-structural and cell wall carbohydrates from Rhynchelytrum repens. Phenolic compounds were studied by classical chromatography techniques and UV-vis spectrophotometry, with C-glycosylated flavonoids being detected but with no further details regarding the chemical structure of these compounds. In this work we employ paper spray ionization mass spectrometry (PS-MS) for the evaluation of the chemical profile of R. repens methanol extract. Positive ionization mode identified 15 compounds, belonging to flavonoids, fatty acids, and other classes of compounds; negative mode ionization was able to identify 20 compounds comprising the classes of quinic acids, stilbenes and flavonoids. PS-MS proved effective for the evaluation of R. repens extracts, making it possible to identify a total of thirty-five compounds. The bioactive properties attributed to R. repens were confirmed by the identification and characterization of compounds identified by PS-MS.
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Affiliation(s)
- Cezar D. do Nascimento
- Department of Agrarian Sciences (DCA), Federal Institute of Education, Science and Technology of Minas Gerais (IFMG), Campus Bambuí, Rodovia Bambuí/Medeiros, km 05, Bambuí 38900-000, Brazil;
| | - Ana C. C. F. F. de Paula
- Department of Agrarian Sciences (DCA), Federal Institute of Education, Science and Technology of Minas Gerais (IFMG), Campus Bambuí, Rodovia Bambuí/Medeiros, km 05, Bambuí 38900-000, Brazil;
| | - Afonso H. de Oliveira Júnior
- Department of Exact and Biological Sciences (DECEB), Federal University of São João del-Rei (UFSJ), MG 424, km 47, Sete Lagoas 35701-970, Brazil; (A.H.d.O.J.); (H.d.O.P.M.)
| | - Henrique de O. P. Mendonça
- Department of Exact and Biological Sciences (DECEB), Federal University of São João del-Rei (UFSJ), MG 424, km 47, Sete Lagoas 35701-970, Brazil; (A.H.d.O.J.); (H.d.O.P.M.)
| | - Luisa del C. B. Reina
- Campus Sinop, Federal University of Mato Grosso, Av. Alexandre Ferronato, 1200—Res. Cidade Jardim, Sinop 78550-728, Brazil;
| | - Rodinei Augusti
- Department of Chemistry, Federal University of Minas Gerais (UFMG), Av. Pres. Antônio Carlos, 6627—Pampulha, Belo Horizonte 31270-901, Brazil;
| | - Rita de C. L. Figueiredo-Ribeiro
- Physiology and Biochemistry Section of Plants, Botanic Institute of São Paulo, Av. Miguel Stéfano, 3687—Agua Funda, São Paulo CEP 04301-902, Brazil;
| | - Júlio O. F. Melo
- Department of Exact and Biological Sciences (DECEB), Federal University of São João del-Rei (UFSJ), MG 424, km 47, Sete Lagoas 35701-970, Brazil; (A.H.d.O.J.); (H.d.O.P.M.)
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16
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Pucker B, Reiher F, Schilbert HM. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1103. [PMID: 32867203 PMCID: PMC7570183 DOI: 10.3390/plants9091103] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
- Department of Plant Sciences, Evolution and Diversity, University of Cambridge, Cambridge CB2 3EA, UK
| | - Franziska Reiher
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
| | - Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
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17
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Jia Y, Selva C, Zhang Y, Li B, McFawn LA, Broughton S, Zhang X, Westcott S, Wang P, Tan C, Angessa T, Xu Y, Whitford R, Li C. Uncovering the evolutionary origin of blue anthocyanins in cereal grains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1057-1074. [PMID: 31571294 DOI: 10.1111/tpj.14557] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/16/2019] [Accepted: 09/24/2019] [Indexed: 05/23/2023]
Abstract
Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.
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Affiliation(s)
- Yong Jia
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Caterina Selva
- School of Agriculture, Food and Wine, Adelaide University, Adelaide, SA, 5064, Australia
| | - Yujuan Zhang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Bo Li
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Lee A McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Xiaoqi Zhang
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Sharon Westcott
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Penghao Wang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Cong Tan
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Tefera Angessa
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Ryan Whitford
- School of Agriculture, Food and Wine, Adelaide University, Adelaide, SA, 5064, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
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