Horticulture Research最新文献_第3页

Litchi40K v1.0: a cost-effective, flexible and versatile liquid SNP chip for genetic analysis and digitalization of germplasm resources in litchi

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-10 DOI: 10.1093/hr/uhaf038

Lei Zhang, Pengfei Wang, Fang Li, Li Xu, Jietang Zhao, Jingxiao Fu, Jiabin Wang, Hui Zhang, Songang Li, Jiwang Hong, Jian Zheng, Xinping Luo, Huanling Li, Jiabao Wang

{"title":"Litchi40K v1.0: a cost-effective, flexible and versatile liquid SNP chip for genetic analysis and digitalization of germplasm resources in litchi","authors":"Lei Zhang, Pengfei Wang, Fang Li, Li Xu, Jietang Zhao, Jingxiao Fu, Jiabin Wang, Hui Zhang, Songang Li, Jiwang Hong, Jian Zheng, Xinping Luo, Huanling Li, Jiabao Wang","doi":"10.1093/hr/uhaf038","DOIUrl":"https://doi.org/10.1093/hr/uhaf038","url":null,"abstract":"Genetic breeding and molecular identification in varieties depend on high-performance genotyping tools. The high heterozygosity of the litchi genome contributes to increased resequencing costs and elevated error rates in hybridization-based genotyping methods. In this study, a liquid chip named Litchi4K v1.0 was developed with high-depth resequencing data from 875 litchi samples, and its efficacy was validated across three different populations. In the L. chinensis var. fulvosus population, three subpopulations characterized by spatial distribution, and a total of 1,110 genes were identified in the genomic regions with subpopulation differentiation. Additionally, a total of 30 significant signals associated with diverse agronomic traits were identified. The H002 haplotype of LITCHI02696, dominant in the Sub2 subgroup, significantly increased the soluble solid content in the L. chinensis var. fulvosus population. In a hybrid F1 population, a high-density genetic map was constructed and 79 dwarfing-related QTLs were identified with the liquid chip. A NAC transcription factor was identified as a candidate gene with a heterozygous frameshift variant in the male parent. To facilitate the digitization of germplasm resources, 384 SNPs were selected, and the DNA fingerprint map revealed clear genetic relationships and a total of 10 potential synonym groups or instances of bud mutations were identified in 164 main cultivated litchi varieties. This study provides cost-effective, flexible and versatile liquid chip for genetic analysis and digitalization of germplasm resources in litchi.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"63 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385425","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

Identification and functional characterization of genes associated with anthocyanin acylation in blueberry

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-10 DOI: 10.1093/hr/uhaf041

Molla F Mengist, Muhammad Ali Abid, Mary H Grace, Romit Seth, Nahla Bassil, Colin D Kay, Andrew P Dare, David Chagné, Richard V Espley, Andrew Neilson, Mary Ann Lila, Mario Ferruzzi, Massimo Iorizzo

{"title":"Identification and functional characterization of genes associated with anthocyanin acylation in blueberry","authors":"Molla F Mengist, Muhammad Ali Abid, Mary H Grace, Romit Seth, Nahla Bassil, Colin D Kay, Andrew P Dare, David Chagné, Richard V Espley, Andrew Neilson, Mary Ann Lila, Mario Ferruzzi, Massimo Iorizzo","doi":"10.1093/hr/uhaf041","DOIUrl":"https://doi.org/10.1093/hr/uhaf041","url":null,"abstract":"Blueberry is promoted as a super food with several health properties derived from chlorogenic acid and anthocyanin. Previous studies indicated that anthocyanin acylation and the content of chlorogenic acid could affect their level of absorption and biological activity. In this study, a genome-wide association study was performed to identify loci associated with anthocyanin and chlorogenic acid and characterize the candidate genes controlling anthocyanin acylation. Two stable loci controlling anthocyanin acylation and glucose specific glycosylation were confirmed on chromosomes 2 and 4, respectively, while no stable loci associated with chlorogenic acid were identified. Two acyl-CoA acyltransferases named VcBAHD-AT1 and VcBAHD-AT4, were identified as best candidate genes controlling anthocyanin acylation. Interestingly, the two genes clustered in acyl-CoA acyltransferases clade III, a clade that is not commonly associated with anthocyanin acylation. A Virus-induced gene silencing approach optimized for silencing VcBAHD-AT1 and VcBAHD-AT4 in the whole blueberry fruits, confirmed the role of these two genes in anthocyanin acylation. Overall, this study establishes the foundation to develop a molecular marker to select for higher acylated anthocyanin and delivered a method for rapid functional characterization of genes associated with other fruit related traits in blueberry. Also, the study adds evidence that during the evolution of acyl-CoA acyltransferases multiple routes led to the emergence and/or fixation of the anthocyanin acyltransferase activity. These outcomes advance knowledge about the genes controlling anthocyanin acylation in blueberries and that extend to other plants. Selecting new blueberry cultivars with higher acylated anthocyanin levels could potentially increase absorption of this health related bioactive.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"56 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385426","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

MADS-domain transcription factor AGAMOUS LIKE-9 participates in the gibberellin pathway to promote bud dormancy release of tree peony

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-10 DOI: 10.1093/hr/uhaf043

Niu Demei, Liu Fang, Gao Linqiang, Zhang Huailong, Liu Naibin, Zhang Lu, Yuan Yanchao, Liu Chunying, Gai Shupeng, Zhang Yuxi

{"title":"MADS-domain transcription factor AGAMOUS LIKE-9 participates in the gibberellin pathway to promote bud dormancy release of tree peony","authors":"Niu Demei, Liu Fang, Gao Linqiang, Zhang Huailong, Liu Naibin, Zhang Lu, Yuan Yanchao, Liu Chunying, Gai Shupeng, Zhang Yuxi","doi":"10.1093/hr/uhaf043","DOIUrl":"https://doi.org/10.1093/hr/uhaf043","url":null,"abstract":"Bud dormancy, which serves as a survival mechanism during winter, is crucial for determining the timing and quality of flowering in many perennial woody plants, including tree peony. The gibberellin (GA) signalling pathway participates in breaking bud dormancy in tree peony. Specifically, PsRGL1, a key DELLA protein, is a negative regulator in this process. MADS-box family members participate in plant growth and development regulation. In this study, a MADS-domain transcription factor, AGAMOUS-LIKE 9 (PsAGL9), was identified as a candidate interaction protein of PsRGL1 using a pull-down assay coupled with liquid chromatography-tandem mass spectrometry. PsAGL9 expression was induced by chilling and exogenous GA3. Yeast two-hybrid (Y2H), pull-down, and luciferase complementation assays (LCAs) confirmed that PsAGL9 interacted with PsRGL1. PsAGL9 overexpression significantly promoted dormancy break and upregulated the expression of marker genes such as PsBG6, PsBG9, PsEBB1, PsEBB3, and PsCYCD, suggesting a potential regulatory function of PsAGL9. Classical and non-classical CArG motifs were identified in the promoter regions of PsCYCD and PsEBB3, respectively. Yeast one-hybrid, electrophoretic mobility shift, and dual luciferase assays confirmed that PsAGL9 directly bound to and activated PsCYCD and PsEBB3 expression, and PsRGL1 abolished the DNA-binding activity of PsAGL9. Furthermore, interaction proteins of PsAGL9 were screened, and MADS-box members PsAGL9, PsAGL6, and PsPI were identified. Y2H, LCA, and pull-down assays confirmed that PsAGL9 formed both homodimers and heterodimers, and heterodimers further promoted target gene expression. This study provides an in-depth exploration of the GA pathway and elucidates a novel pathway, PsRGL1-PsAGL9-PsCYCD, involved in regulating dormancy break in tree peony.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"167 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385427","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

Wo interacts with SlTCP25 to regulate type I trichome branching in tomato

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-05 DOI: 10.1093/hr/uhaf032

Junqiang Wang, Shoujuan Yuan, Yihao Zhao, Xin Shu, Zhiling Liu, Taotao Wang, Zhibiao Ye, Changxian Yang

{"title":"Wo interacts with SlTCP25 to regulate type I trichome branching in tomato","authors":"Junqiang Wang, Shoujuan Yuan, Yihao Zhao, Xin Shu, Zhiling Liu, Taotao Wang, Zhibiao Ye, Changxian Yang","doi":"10.1093/hr/uhaf032","DOIUrl":"https://doi.org/10.1093/hr/uhaf032","url":null,"abstract":"Plant trichomes serve as a protective barrier against various stresses. Although the molecular mechanisms governing the initiation of trichomes have been extensively studied, the regulatory pathways underlying the trichome branching in tomato remain elusive. Here, we found that Woolly (Wo) mutant and its overexpression transgenic plants displayed branched type I trichomes. The expression level of SlTCP25, a transcription factor of type TB1 of the TCP subfamily, was obviously decreased in Wo mutant and Wo overexpressing lines. Knockout of SlTCP25 resulted in the formation of type I trichome branches on the hypocotyls. Genetic evidence showed that SlTCP25 is epistatic to Wo in the branched trichome formation. Biochemical data further indicated that Wo can directly bind to the L1-box cis-element in the SlTCP25 promoter and repress its transcription. We further determined that SlTCP25 interacts with Wo to weaken Wo-regulated the expression of SlCycB2, a trichome branching inhibitor. In addition, the number of trichome branches was significantly increased in Sltcp25Slcycb2 double mutant, suggesting that SlTCP25 and SlCycB2 coordinately repress trichome branching in wild type. In conclusion, we elucidate a molecular network governing the morphogenesis of multicellular trichomes in tomato.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"31 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143125112","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

Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-05 DOI: 10.1093/hr/uhaf037

Wan-ling Song, Bao-zheng Chen, Lei Feng, Geng Chen, Si-mei He, Bing Hao, Guang-hui Zhang, Yang Dong, Sheng-chao Yang

{"title":"Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis","authors":"Wan-ling Song, Bao-zheng Chen, Lei Feng, Geng Chen, Si-mei He, Bing Hao, Guang-hui Zhang, Yang Dong, Sheng-chao Yang","doi":"10.1093/hr/uhaf037","DOIUrl":"https://doi.org/10.1093/hr/uhaf037","url":null,"abstract":"Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside, which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a telomere-to-telomere (T2T) C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb of repetitive sequences and 25,200 protein-coding genes. Comparative genomic analyses revealed that C. asiatica as early diverging genus within the Apiaceae family with a single whole-genome duplication (WGD, Apiaceae-ω) event following the ancient γ-triplication, contrasting with Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω). We further constructed 3D chromatin structures, A/B compartments and topologically associated domains (TAD) in C. asiatica leaves, elucidating the influence of chromatin organization on expression WGD-derived genes. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene co-expression network analysis (WGCNA) further highlighted the pathways modulated in response to MeJA, offering insights into the regulatory networks governing saponin biosynthesis. This work not only provides a valuable genomic resource for C. asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"50 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143367548","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

Citrus genomes: Past, present and future

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-04 DOI: 10.1093/hr/uhaf033

Upuli Nakandala, Agnelo Furtado, Robert J Henry

{"title":"Citrus genomes: Past, present and future","authors":"Upuli Nakandala, Agnelo Furtado, Robert J Henry","doi":"10.1093/hr/uhaf033","DOIUrl":"https://doi.org/10.1093/hr/uhaf033","url":null,"abstract":"Over the past decade, genome sequencing, and assembly approaches have been greatly improved resulting in the assembly of many genomes for citrus including wild, domesticated and citrus related genomes. Improvements in technologies have led to assembled genomes with higher completeness, contiguity, quality and accuracy that have greatly facilitated annotation and analysis. This review summarizes the evolution of the sequencing, assembly and annotation technologies leading to citrus genomes over the past 11 years, a comprehensive evaluation of their quality, contiguity, and completeness, and their major findings and applications. Of the 50 genomes now available, 35 have been assembled to chromosome level, 15 to draft level, and 14 were haplotype-resolved assemblies. To date there have been four pangenome wide studies for citrus. The very recent genomes assembled with long read sequencing have achieved more than 99% and more than 98% assembly and annotation completeness (BUSCO) respectively. However, some early genomes are not of the same high quality as more recently sequenced genomes and would benefit from re-sequencing. A more comprehensive pan genome based upon of a larger set of species and genotypes at assembled at the haplotype level would allow genomics to deliver the maximum benefits for citrus improvement and research.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"12 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083773","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 China national GeneBank sequence archive (CNSA) 2024 update

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-04 DOI: 10.1093/hr/uhaf036

Weiwen Wang, Cong Tan, Ling Li, Xia Li, Lei Zhang, Xiaoqiang Li, Jieyu Wang, Ziyi He, Tao Yang, Kailong Ma, Qingjiang Hu, Wenzhen Yang, Zhiyong Li, Mingwen Zhang, Wensi Du, Fan Yang, Zhicheng Xu, Xizheng Ma, Jiawei Tong, Jia Cai, Cong Hua, Fengzhen Chen, Lijin You, Liang Li, Wenjun Zeng, Bo Wang, Xun Xu, Xiaofeng Wei

{"title":"The China national GeneBank sequence archive (CNSA) 2024 update","authors":"Weiwen Wang, Cong Tan, Ling Li, Xia Li, Lei Zhang, Xiaoqiang Li, Jieyu Wang, Ziyi He, Tao Yang, Kailong Ma, Qingjiang Hu, Wenzhen Yang, Zhiyong Li, Mingwen Zhang, Wensi Du, Fan Yang, Zhicheng Xu, Xizheng Ma, Jiawei Tong, Jia Cai, Cong Hua, Fengzhen Chen, Lijin You, Liang Li, Wenjun Zeng, Bo Wang, Xun Xu, Xiaofeng Wei","doi":"10.1093/hr/uhaf036","DOIUrl":"https://doi.org/10.1093/hr/uhaf036","url":null,"abstract":"The China National GeneBank Sequence Archive (CNSA) is an open and freely accessible curated data repository built for archiving, sharing, and re-utilizing of multi-omics data. The remarkable advancement in sequencing technologies has triggered a paradigm shift in life science research. However, it also poses tremendous challenges for the research community in data manage and reusability. With the dramatic advance of sequencing technologies like spatial transcriptome sequencing, it brings an unprecedented explosion in sequence data and new requirements for data archiving. CNSA was established in 2017 as one of the fundamental infrastructures to offer multi-omics data archiving for the worldwide research community. Here, we present the state-of-the-art enhancements of CNSA encompassing the dramatical increase of varied types of data, the latest features and services implemented in CNSA as well as consistent efforts supporting global cooperation in biodiversity preservation and utilization. CNSA provides public archiving and open-sharing services for sequencing data and relevant metadata including genome, transcriptome, metabolism, and proteome from single-cell (also spatial resolved) level to individual and population level, as well as further analyzed results. As of 2024, CNSA has archived over 16.3 petabytes of data and provided the data curation, preservation, and open-share service for over 1,581 publications from over 560 institutions. It plays a pivotal role in supporting global scientific projects such as the 10,000 Plant Genomes Project. So far, CNSA has been recommended by various academic publishers such as Cell, Elsevier, and Oxford University Press. CNSA is accessible at https://db.cngb.org/cnsa/.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"55 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258320","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

Genetic architecture of cherry leaf spot (Blumeriella jaapii) resistance in sour cherry (P. Cerasus L.) uncovered by QTL analyses in a biparental population genotyped with the 6+9K SNP array

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-03 DOI: 10.1093/hr/uhaf035

Ofere Francis Emeriewen, Thomas Wolfgang Wöhner, Vincent Braun, Susan Schröpfer, Mirko Schuster, Andreas Peil, Henryk Flachowsky

{"title":"Genetic architecture of cherry leaf spot (Blumeriella jaapii) resistance in sour cherry (P. Cerasus L.) uncovered by QTL analyses in a biparental population genotyped with the 6+9K SNP array","authors":"Ofere Francis Emeriewen, Thomas Wolfgang Wöhner, Vincent Braun, Susan Schröpfer, Mirko Schuster, Andreas Peil, Henryk Flachowsky","doi":"10.1093/hr/uhaf035","DOIUrl":"https://doi.org/10.1093/hr/uhaf035","url":null,"abstract":"Sour cherry (Prunus cerasus L.) is an economically significant species in the Rosaceae family. Hitherto, there had been limited genetic and genomic resources to elucidate important horticultural traits in this species mainly because of the complex polyploid nature of its genome, a hybrid between Prunus avium and Prunus fruticosa. An important trait that has not been well studied in sour cherry is resistance to cherry leaf spot (CLS), caused by the fungus Blumeriella jaapii. This work took advantage of the RosBREED 6+9K SNP array to study the genetic basis of CLS resistance and inheritance in sour cherry. We established an F1 segregating population by crossing two cultivars, ‘Schattenmorelle’ and ‘Pc 2’ and genotyped both parents and the progeny with the cherry 6+9K SNP array and SSR markers. We evaluated both parents and progeny for resistance and susceptibility to CLS under field conditions. The applied marker systems facilitated the development of parental genetic maps, and the identification of two stable QTLs associated with CLS resistance, CLSR_1f in ‘Pc 2’ and susceptibility, CLSS_1f, in ‘Schattenmorelle’ explaining 40.9% and 21.5%, respectively of the phenotypic variation within the population. The mechanism of resistance in sour cherry appears to be independent of the CLS resistance QTL, CLSR_G4, previously identified in P. canescens, as the CLSR_G4-QTL and associated allele were not identified. Based on our findings, we propose a two-gene model for CLS resistance in sour cherry involving a susceptibility QTL, which might explain why some CLSR_G4-resistant plants in previous studies were susceptible.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"32 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083774","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

Haplotype-resolved genome of Agastache rugosa (Huo Xiang) provides insight into monoterpenoid biosynthesis and gene cluster evolution

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-01 DOI: 10.1093/hr/uhaf034

Chanchan Liu, DiShuai Li, Jingjie Dang, Juan Shu, Samuel J Smit, QiNan Wu, Benjamin R Lichman

{"title":"Haplotype-resolved genome of Agastache rugosa (Huo Xiang) provides insight into monoterpenoid biosynthesis and gene cluster evolution","authors":"Chanchan Liu, DiShuai Li, Jingjie Dang, Juan Shu, Samuel J Smit, QiNan Wu, Benjamin R Lichman","doi":"10.1093/hr/uhaf034","DOIUrl":"https://doi.org/10.1093/hr/uhaf034","url":null,"abstract":"Monoterpenoids are small volatile molecules produced by many plants that have applications in consumer products and healthcare. Plants from the mint family (Lamiaceae) are prodigious producers of monoterpenoids, including a chemotype of Agastache rugosa (Huo Xiang), which produces pulegone and isomenthone. We sequenced, assembled and annotated a haplotype-resolved chromosome-scale genome assembly of A. rugosa with a monoterpene chemotype. This genome assembly revealed that pulegone biosynthesis genes are in a biosynthetic gene cluster, which shares a common origin with the pulegone gene cluster in Schizonepeta tenuifolia. Using phylogenetics and synteny analysis, we describe how the clusters in these two species diverged through inversions and duplications. Using Hi-C analysis, we identified tentative evidence of contact between the pulegone gene cluster and an array of pulegone reductases, with both regions also enriched in retrotransposons. This genome and its analysis add valuable and novel insights to the organization and evolution of terpenoid biosynthesis in Lamiaceae.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"22 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072558","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

Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-01-29 DOI: 10.1093/hr/uhaf030

Hanwen Yu, Haixia Wang, Xiao Liang, Juan Liu, Chao Jiang, Xiulian Chi, Nannan Zhi, Ping Su, Liangping Zha, Shuangying Gui

{"title":"Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus","authors":"Hanwen Yu, Haixia Wang, Xiao Liang, Juan Liu, Chao Jiang, Xiulian Chi, Nannan Zhi, Ping Su, Liangping Zha, Shuangying Gui","doi":"10.1093/hr/uhaf030","DOIUrl":"https://doi.org/10.1093/hr/uhaf030","url":null,"abstract":"Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, provides a foundation for the complete elucidation of the platycodins biosynthetic pathway, consequently leading to heterologous bioproduction, and a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"39 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072665","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