Horticulture Research最新文献_第2页

Uncovering the genetic basis for enhanced mushroom flavor in Quercus fabri through genome sequencing and metabolic profiling 通过基因组测序和代谢谱分析揭示了栎香菇风味增强的遗传基础

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-09 DOI: 10.1093/hr/uhaf156

Liwen Wu, Yuqing Cai, Chenggang Jiang, Xiang Shi, Shifa Xiong, Yicun Chen, Yangdong Wang

{"title":"Uncovering the genetic basis for enhanced mushroom flavor in Quercus fabri through genome sequencing and metabolic profiling","authors":"Liwen Wu, Yuqing Cai, Chenggang Jiang, Xiang Shi, Shifa Xiong, Yicun Chen, Yangdong Wang","doi":"10.1093/hr/uhaf156","DOIUrl":"https://doi.org/10.1093/hr/uhaf156","url":null,"abstract":"Quercus fabri is a common timber oak tree species widely distributed in subtropical areas of China. In this study, we presented a chromosome-scale reference genome assembly of Q. fabri achieved by integrating PacBio Sequel II, DNBseqTM and Hi-C sequencing platforms, and the results indicated the Q. fabri genome has a size of 836.74 Mb. Through the analysis of significantly expanded gene families, we identified that many of the top-ranked KEGG pathways are associated with amino acid metabolism. Subsequently, we performed an amino acid metabolic profile analysis on Q. fabri and related species, including Q. aliena, Q. acutissima, and Q. variabilis. The findings revealed that the content of amino acids in Q. fabri was significantly higher than that in the other three oak species. Additionally, we found a significantly higher content of flavor amino acids, such as glutamic acid (Glu), aspartic acid (Asp), and glycine (Gly), in Q. fabri. Considering these results, we designed experiments to assess the nutrient content in mushrooms cultivated from the four oak trees. The results indicated that the total amino acid and protein content of mushrooms cultivated using Q. fabri as a substrate was significantly greater than that of mushrooms grown on the other three oak species. This characteristic may explain why Q. fabri wood is particularly effective as a substrate for cultivating more flavorful mushrooms. This study presents the complete genome and evolutionary information of Q. fabri, and integrates metabolic profiling to explore the underlying reasons for the enhanced flavor of mushrooms cultivated from it.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"4 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SlALKBH9B is involved in drought-induced flower drop by regulating ethylene production SlALKBH9B通过调节乙烯的产生参与干旱诱导的花落

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf173

Yue Cai, Lina Cheng, Xianfeng Liu, Ruizhen Li, Yang Liu, Siqi Ge, Sai Wang, Jing Liu, Changhua Tan, Sida Meng, Mingfang Qi, Cai-Zhong Jiang, Tianlai Li, Tao Xu

{"title":"SlALKBH9B is involved in drought-induced flower drop by regulating ethylene production","authors":"Yue Cai, Lina Cheng, Xianfeng Liu, Ruizhen Li, Yang Liu, Siqi Ge, Sai Wang, Jing Liu, Changhua Tan, Sida Meng, Mingfang Qi, Cai-Zhong Jiang, Tianlai Li, Tao Xu","doi":"10.1093/hr/uhaf173","DOIUrl":"https://doi.org/10.1093/hr/uhaf173","url":null,"abstract":"Drought induces tomato (Solanum lycopersicum) flowers and fruits drop, which causes serious yield and economic losses in agriculture. However, the mechanism of action remains unclear. N6-methyladenosine (m6A) methylation is a prevalent epigenetic change integral to the growth, development, and adaptation of plants to abiotic stress factors. However, whether it participates in drought-induced abscission remains to be further studied. Here, we report that tomato demethylase alpha-ketoglutarate-dependent dioxygenase B (AlkB) homolog 9B (SlALKBH9B) exerts a detrimental influence on the regulation of drought-induced flower drop by mediating ethylene production. We found that drought markedly reduced the expression of SlALKBH9B, and knockout of SlALKBH9B enhanced flower drop, while overexpression of SlALKBH9B delayed the flower drop. Under drought conditions, the ethylene production of Slalkbh9b exhibited a considerably greater yield than that of the wild type (WT), while SlALKBH9B overexpression plants had lower ethylene production. Application of ethylene could abolish the delayed abscission effect of overexpression of SlALKBH9B. Further studies showed that drought downregulated SlALKBH9B expression, which specifically enhanced the methylation level of the 3′ untranslated region (UTR) of tomato ethylene excess producer 1 (SlETO1), leading to a decrease in the stability of SlETO1 mRNA and its protein translation efficiency. The loss of SlETO1 resulted in the accumulation of tomato 1-aminocyclopropane-1-carboxylic acid synthase 3 (SlACS3) and SlACS8 in the abscission zone (AZ) and then boosted ethylene production to accelerate abscission. Our results show that SlALKBH9B is an important inhibitor for drought-induced abscission and reveal a new mechanism through which drought-enhanced ethylene production leads to flower drop.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"92 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CsCOI1 regulates plant growth and defense in citrus CsCOI1调控柑橘植物的生长和防御

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf174

Gang Hu, Bing Liu, Kun Yang, Wei-Kang Zheng, Yi Zhang, Cai-Xia Teng, Duo-Yi Huang, Ruo-Hao Yan, Michitaka Notaguchi, Munenori Kitagawa, Zong-Cheng Lin, Qiang Xu

{"title":"CsCOI1 regulates plant growth and defense in citrus","authors":"Gang Hu, Bing Liu, Kun Yang, Wei-Kang Zheng, Yi Zhang, Cai-Xia Teng, Duo-Yi Huang, Ruo-Hao Yan, Michitaka Notaguchi, Munenori Kitagawa, Zong-Cheng Lin, Qiang Xu","doi":"10.1093/hr/uhaf174","DOIUrl":"https://doi.org/10.1093/hr/uhaf174","url":null,"abstract":"Jasmonates (JAs) play essential roles in plant development and defense. JA perception and responses remain elusive in citrus. Here, we identified core components for JA perception in citrus and elucidated transcriptional changes associated with JA signaling in growth and defense. We showed the F-box protein CORONATINE INSENSITIVE1 (COI1) in citrus is a JA receptor, as CsCOI1 mutants are insensitive to methyl jasmonate and CsCOI1 interacts with CsJAZs in the presence of JA-Ile. CsCOI1-mediated JA signaling represses shoot growth while enhancing resistance to insects. Consistently, CsCOI1 represses the expression of growth promoting genes such as PIF7, while upregulating genes related to defense metabolites in terpene and flavonoid pathways. Additionally, JA signaling antagonizes salicylic acid (SA) signaling at the transcriptional level and promotes susceptibility to citrus canker disease. This study highlights the role of JA signaling in balancing growth and resistance to biotic stress in citrus, revealing critical trade-offs for consideration in precision citrus breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The MaASR3-MaHDT1 module modulates high temperature-inhibited chlorophyll breakdown in banana fruit by suppressing the E3 ligase MaNIP1 MaASR3-MaHDT1模块通过抑制E3连接酶MaNIP1调节香蕉果实中高温抑制的叶绿素分解

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf172

Qi Luo, Wei Wei, Yu-mei Zhang, Jian-fei Kuang, Jian-ye Chen, Wang-jin Lu, Zhi-jun Cai, Wei Shan

{"title":"The MaASR3-MaHDT1 module modulates high temperature-inhibited chlorophyll breakdown in banana fruit by suppressing the E3 ligase MaNIP1","authors":"Qi Luo, Wei Wei, Yu-mei Zhang, Jian-fei Kuang, Jian-ye Chen, Wang-jin Lu, Zhi-jun Cai, Wei Shan","doi":"10.1093/hr/uhaf172","DOIUrl":"https://doi.org/10.1093/hr/uhaf172","url":null,"abstract":"The ripening of banana fruit at high temperature (HT) exceeding 24 °C impedes developing yellow peels, causing green ripening, which considerably lowers its marketability. Our recent study found that HT induces E3 ubiquitin ligase MaNIP1 (NYC1 interacting protein 1)-mediated degradation of MaNYC1 (NON-YELLOW COLORING 1) to inhibit chlorophyll breakdown during banana fruit ripening, but MaNIP1's upstream regulatory mechanism is still unclear. Herein, the ASR transcription factor (TF) MaASR3, which is repressed in green-ripened fruit compared to yellow-ripened fruit, was identified as the potential binding protein for the MaNIP1 promoter. MaASR3 promoted chlorophyll degradation in banana fruit by repressing MaNIP1 expression. More importantly, the histone deacetylase MaHDT1 interacted with MaASR3 and enhanced MaASR3-mediated repression of MaNIP1. Overexpression of MaASR3 in banana fruit reduced the histone acetylation levels in the MaNIP1 promoter and repressed MaNIP1 expression, thereby weakening the HT-inhibited de-greening of banana fruit. Our study reveals an innovative regulatory cascade comprising the MaASR3-MaHDT1-MaNIP1 complex, which modulates HT-inhibited chlorophyll degradation. This explains the green ripening in bananas exposed to such conditions and enhances the comprehension of transcriptional and epigenetic regulations of fruit quality deterioration due to temperature stresses.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Warming temperature reduces the risk of pre-harvest freezing injury and modifies variety suitability in the main winegrape-growing regions of China 在中国主要的葡萄产区，温度升高降低了收获前冻害的风险，改变了品种的适宜性

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf176

Huiqing Bai, Jianqiang He, Cornelis Leeuwen, Rafiq Hamdi, Erna Blancquaert, Gregory V Jones, Zhanwu Dai

{"title":"Warming temperature reduces the risk of pre-harvest freezing injury and modifies variety suitability in the main winegrape-growing regions of China","authors":"Huiqing Bai, Jianqiang He, Cornelis Leeuwen, Rafiq Hamdi, Erna Blancquaert, Gregory V Jones, Zhanwu Dai","doi":"10.1093/hr/uhaf176","DOIUrl":"https://doi.org/10.1093/hr/uhaf176","url":null,"abstract":"Rising temperatures cause advanced phenology of grapevines and increased sugar concentration in berries, which ultimately modify variety suitability in a given region. Here, four bioclimatic indices and a refined Grapevine Sugar Ripeness (GSR) model were employed to assess the suitability of six winegrape varieties across six winegrape-growing regions of China under historical climate conditions (1961-2020). First, four indices were compared between two periods, one before (P1) and one after (P2) an abrupt climate change events identified during 1988-2002 in these regions. Results showed three temperature related indices increased in six regions while the first fall frost day (FFD) was delayed by 0-16 days in five out of the six regions during P2 compared with P1. Second, GSR model was applied to simulate target sugar concentrations as a proxy for grape harvest dates (GHDs). Direct utilization of original GSR model yielded unsatisfactory predictions with clear bias. Consequently, GSR model was recalibrated with local data to obtain an acceptable performance with R2 and NRMSE values of 0.83 and 2.8% as well as 0.83 and 3.1% for the calibration and validation datasets, respectively and further simulated GHDs of six varieties with advanced values of 6-30 days in six regions for P2 in comparison with P1. To provide a holistic view of freezing injury risk before harvest, comprehensive freezing injury index (CFI) was developed by integrating the frequency, duration, and severity of the freezing risk. CFI decreased (2%-60%) during P2 in all regions and the magnitudes of decrease was elevation dependent. These findings provide valuable insights for the selection of varieties that can more reliably achieve fully mature fruit, producing more balanced wines with greater typicity under warming climate.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"31 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoding Steroid-Derived Metabolite Engineering in Solanum 解读茄属植物类固醇衍生代谢物工程

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf178

Farah Kanwal, Sana Ullah, Yingchen Hao, Shouchuang Wang

{"title":"Decoding Steroid-Derived Metabolite Engineering in Solanum","authors":"Farah Kanwal, Sana Ullah, Yingchen Hao, Shouchuang Wang","doi":"10.1093/hr/uhaf178","DOIUrl":"https://doi.org/10.1093/hr/uhaf178","url":null,"abstract":"Steroidal glycoalkaloids (SGAs) and steroidal saponins (STSs) play significant role in the plant defense against pests and offer various pharmaceuticals applications. SGAs and STSs generally share common biosynthetic pathways in Solanum, originating from a furostanol scaffold. Despite the discovery of multiple GLYCOALKALOID METABOLISM (GAME) genes involved in the biosynthesis of these compounds, previous attempts for the metabolic engineering of these pathways have remained unsuccessful. The GAME15 protein, with its dual enzymatic roles, has unlocked a mystery surrounding the intricate process of metabolizing cholesterol. This protein not only acts as a glucuronosyltransferase but also serves as a metabolic scaffold, organizing several proteins for the proper functioning. This mini review briefly describes the molecular mechanisms and functional dynamics of GAME genes, particularly focusing on GAME15 as a key game changer gene and its role in metabolite channeling, regulation of pathway, and ecological importance. We highlighted the potential of this discovery for advancing metabolic engineering in crop improvement and the pharmaceutical industry. This finding opens doors for designing crops that are resistant to pests. Additionally, we identify important future research directions, including the regulatory mechanisms of these pathways and uncovering structural aspects of pivotal enzymes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"2 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-omics analyses reveal the effects of layerage and grafting on flavonoid synthesis and accumulation in Citrus reticulata ‘Chachi’ 多组学分析揭示了分层和嫁接对‘茶柑’黄酮合成和积累的影响

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-07 DOI: 10.1093/hr/uhaf177

Jianmu Su, Mingmin Jiang, Huimin Pan, Weitao Zhou, Xueyan Cai, Yukun Wang, Wei Liu, Desen Wang, Mei Bai, Hong Wu

{"title":"Multi-omics analyses reveal the effects of layerage and grafting on flavonoid synthesis and accumulation in Citrus reticulata ‘Chachi’","authors":"Jianmu Su, Mingmin Jiang, Huimin Pan, Weitao Zhou, Xueyan Cai, Yukun Wang, Wei Liu, Desen Wang, Mei Bai, Hong Wu","doi":"10.1093/hr/uhaf177","DOIUrl":"https://doi.org/10.1093/hr/uhaf177","url":null,"abstract":"Guangdong Citri Reticulatae Pericarpium from the dry and mature peel of Citrus reticulata ‘Chachi’ (CRC) is a well-known medicinal and food materials in Asia. The main propagation methods of CRC are layerage and grafting. It is generally considered that the quality of CRC from layerage is superior to that obtained from plants propagated by grafting. Nevertheless, the effects of layerage and grafting on main bioactive ingredients flavonoid biosynthesis in peel of CRC keep unknown. Here, metabolomic analyses revealed the effects of layerage, self-grafting and heterografting (C. limonia as rootstock) on flavonoid biosynthesis in CRC from two main harvesting periods, CRCV (Citri Reticulatae Chachiensis Viride) and CRCR (Citri Reticulatae Chachiensis Reddish). Compared with CRCR, CRCV exhibited a higher content of flavonoids. Grafting CRC onto C. limonia exhibited a higher content of hesperidin, nobiletin, tangeretin, narirutin, demethylnobiletin and sinensetin, than layerage and self-grafting. This increase can be attributed to the upregulation of genes involved in flavonoid synthesis. Further, the transcription factor CrcMYBF1 was identified within the gene co-expression network and is confirmed to be significantly induced by methyl jasmonate (MeJA) and up-regulate the expression of Crc1,6RhaT through interacting with its promoter region, thereby boosting the biosynthesis and accumulation of hesperidin. In summary, our findings provide mechanistic insights into the coordinated regulation of hesperidin biosynthesis via MeJA inducing CrcMYBF1 in CRC. Our study is expected to provide a theoretical basis for CRC propagation and cultivation.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"81 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide association studies revealed partial genetic links between early vigor and precocity in macadamia 全基因组关联研究揭示了澳洲坚果早期活力和早熟之间的部分遗传联系

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-04 DOI: 10.1093/hr/uhaf162

Pragya Dhakal Poudel, Joanne-De Faveri, Bruce Topp, Mobashwer Alam

{"title":"Genome-wide association studies revealed partial genetic links between early vigor and precocity in macadamia","authors":"Pragya Dhakal Poudel, Joanne-De Faveri, Bruce Topp, Mobashwer Alam","doi":"10.1093/hr/uhaf162","DOIUrl":"https://doi.org/10.1093/hr/uhaf162","url":null,"abstract":"Early vigor (EV) and precocity are important traits for orchard establishment and profitability in macadamia. EV determines tree growth and adaptation, while precocity facilitates early yield, offering economic benefits. Although, a positive relationship between these traits has been observed in other tree crops, their association in macadamia remains unclear. This study aimed to identify genetic links between EV and precocity by assessing genetic variability, heritability and correlations in a five-year-old macadamia breeding population. The population comprised 904 progenies planted across six sites in Queensland, Australia. Genome-wide association studies (GWAS) were conducted on a subset of 220 accessions genotyped with 7,401 SNP markers. A linear mixed model incorporating a kinship matrix and principal components to account for population structure was used to perform association analysis in TASSEL. Phenotypic analyses in ASReml-R revealed that precocity had higher broad- (H2 = 0.25-0.84) and narrow-sense (h2 = 0.10-0.77) heritability compared to EV (H2 = 0-0.61, h2 = 0-0.49). EV and precocity showed positive phenotypic (0.25-0.42) and genetic (0.21-0.31) correlations. GWAS identified 11 significant markers (FDR &lt;0.05), including two pleiotropic markers (Mint10079 and Mint4004) associated with both EV and precocity. Putative genes linked to these markers were involved in cell wall modelling, pathogen defence, abiotic stress tolerance, flowering, overall growth and development in other tree species. These significant markers, post-validation, hold substantial promise for utilization in marker-assisted selection (MAS). Integrating putative pleiotropic markers into MAS can enhance genetic gain by reducing the selection time for and enabling simultaneous selection for EV and precocity.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"50 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional characterization of key enzymes involved in the biosynthesis of distinctive flavonoids and stilbenoids in Morus notabilis 桑中黄酮类化合物和苯乙烯类化合物合成关键酶的功能研究

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-04 DOI: 10.1093/hr/uhaf171

Meng-Wen Hu, Jie Fu, Ying Lu, Xin-Yan Liu, Jiao-Zhen Zhang, Jiang-Nan Li, Dan-Dan Xu, Ya-Tong Li, Pei-Xi Hao, Ming-Xin Cui, Lin-Lin Zhi, Hong-Xiang Lou, Ai-Xia Cheng

{"title":"Functional characterization of key enzymes involved in the biosynthesis of distinctive flavonoids and stilbenoids in Morus notabilis","authors":"Meng-Wen Hu, Jie Fu, Ying Lu, Xin-Yan Liu, Jiao-Zhen Zhang, Jiang-Nan Li, Dan-Dan Xu, Ya-Tong Li, Pei-Xi Hao, Ming-Xin Cui, Lin-Lin Zhi, Hong-Xiang Lou, Ai-Xia Cheng","doi":"10.1093/hr/uhaf171","DOIUrl":"https://doi.org/10.1093/hr/uhaf171","url":null,"abstract":"The mulberry (Morus notabilis) is a medicinal and edible plant and contains diverse flavonoids and stilbenoids with significant medicinal benefits. The biosynthesis of these compounds has only been partially elucidated. In the present investigation, we identified and characterized two 4-coumarate: coenzyme A ligases (Mn4CL1 and Mn4CL2), two polyketide synthases (MnCHS and MnSTS), three chalcone reductases (MnCHR1-3) and two 2-oxoglutarate-dependent dioxygenases (MnFLS and MnF3H) involved in flavonoids and stilbenoids biosynthesis. MnCHS converts p-coumaroyl-CoA into naringenin and facilitates the novel conversion of 2,4-dihydroxycinnamoyl-CoA to steppogenin, which features hydroxyl groups at the 4' and 6' positions on the B ring. MnSTS could convert p-coumaroyl-CoA and 2,4-dihydroxycinnamoyl-CoA into resveratrol and oxyresveratrol, respectively. Furthermore, MnCHR1 was firstly identified in mulberry and collaborated with MnCHS to produce isoliquiritigenin and 2,4,2',4'-tetrahydroxychalcone. A co-expression system of Mn4CL1, MnCHS and MnCHR1 enabled the fermentation production of steppogenin and 2,4,2',4'-tetrahydroxychalcone in engineered Escherichia coli. The in vitro enzymatic assays confirmed that MnFLS showed both FLS and F3H activities, whereas transgenic experiments revealed its predominant FLS function in vivo; MnF3H was confirmed as a bona fide F3H. These findings provide new insights into the flavonoids and stilbenoids biosynthesis pathway in mulberry and suggest a potential parallel pathway for 4',6'-dihydroxylated flavonoids biosynthesis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"103 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mango Pangenome Reveals Dramatic Impacts of Reference Bias on Genomic Analyses 芒果泛基因组揭示了参考偏差对基因组分析的巨大影响

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-07-01 DOI: 10.1093/hr/uhaf166

Bilal Ahmad, Ying Su, Yani Hao, Tayyaba Razzaq, Rida Arshad, Yi Zhang, Yingchun Zhang, Xingyi Wang, Guizhou Huang, Xiangnian Su, Ting Hou, Chaochao Li, Xuanwen Yang, Chuanning Li, Zhenzhou Chu, Qiuyan Wang, Yu Zhang, Zhongxin Jin, Qi Xu, Xiaodong Xu, Yanling Peng, Guiqi Bi, Chengjie Chen, Yeyuan Chen, Hua Xiao, Jianfeng Huang, Yongfeng Zhou, Xinmin Tian

{"title":"Mango Pangenome Reveals Dramatic Impacts of Reference Bias on Genomic Analyses","authors":"Bilal Ahmad, Ying Su, Yani Hao, Tayyaba Razzaq, Rida Arshad, Yi Zhang, Yingchun Zhang, Xingyi Wang, Guizhou Huang, Xiangnian Su, Ting Hou, Chaochao Li, Xuanwen Yang, Chuanning Li, Zhenzhou Chu, Qiuyan Wang, Yu Zhang, Zhongxin Jin, Qi Xu, Xiaodong Xu, Yanling Peng, Guiqi Bi, Chengjie Chen, Yeyuan Chen, Hua Xiao, Jianfeng Huang, Yongfeng Zhou, Xinmin Tian","doi":"10.1093/hr/uhaf166","DOIUrl":"https://doi.org/10.1093/hr/uhaf166","url":null,"abstract":"Most genomics studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias and methods to reduce it have gained limited attention. This study compared genomic analyses using four different reference genomes of mango (Mangifera indica), including the two haploid assemblies of haplotype-resolved telomere-to-telomere (T2T) genome assembly, a pangenome, and an older version of the reference genome available on NCBI. The choice of reference genome dramatically impacted the mapping efficiency and resulted in notable differences in calling the genetic variants, particularly structural variations (SVs). Phylogenetic analysis was more sensitive to the reference genome compared to genetic differentiation. Population genomic analyses of artificial selection in domestication and SV hotspot regions varied across reference genomes. Notably, the gene enrichment analyses showed significant differences in the top enriched biological processes depending on the reference genome used. Overall, the mango pangenome outperformed the other reference genomes across various metrics, followed by T2T reference genomes, as they captured greater diversity and effectively reduced reference bias. Our findings highlight the role of the mango pangenome in reducing reference bias and underscore the critical role of reference genome selection, suggesting that it is one of the most important factors in genomic studies.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"77 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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