{"title":"Michelia alba DC 的高质量单倍型基因组揭示了甲基化模式和花朵特征的差异。","authors":"Sirong Jiang, Meiling Zou, Chenji Zhang, Wanfeng Ma, Chengcai Xia, Zixuan Li, Long Zhao, Qi Liu, Fen Yu, Dongyi Huang, Zhiqiang Xia","doi":"10.1186/s43897-024-00098-z","DOIUrl":null,"url":null,"abstract":"<p><p>Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"4 1","pages":"23"},"PeriodicalIF":10.6000,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11134676/pdf/","citationCount":"0","resultStr":"{\"title\":\"A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics.\",\"authors\":\"Sirong Jiang, Meiling Zou, Chenji Zhang, Wanfeng Ma, Chengcai Xia, Zixuan Li, Long Zhao, Qi Liu, Fen Yu, Dongyi Huang, Zhiqiang Xia\",\"doi\":\"10.1186/s43897-024-00098-z\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.</p>\",\"PeriodicalId\":29970,\"journal\":{\"name\":\"Molecular Horticulture\",\"volume\":\"4 1\",\"pages\":\"23\"},\"PeriodicalIF\":10.6000,\"publicationDate\":\"2024-05-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11134676/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Horticulture\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1186/s43897-024-00098-z\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"HORTICULTURE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Horticulture","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/s43897-024-00098-z","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"HORTICULTURE","Score":null,"Total":0}
引用次数: 0
摘要
Michelia alba DC 是木兰科的一种非常珍贵的观赏植物。这种常绿热带树种通常生长在东南亚，因其芳香宜人而深受人们喜爱。我们的研究利用 Nanopore 超长读数、Pacbio Hifi 长读数和亲本二代数据组装了白千层单倍型基因组 MC 和 MM。此外，基于利用 Nanopore 数据获得的甲基化位点数据，构建了木兰科植物的首个甲基化图谱。从三个不同物种的花中生成了代谢组数据集，以评估色素和挥发性化合物积累的变化。最后，我们生成了转录组数据，将基因组、甲基化和形态学模式联系起来，以揭示白玉霓裳花及其亲本品系在花瓣颜色、花形和香味方面存在差异的原因。我们发现，AP1 和 AP2 基因对白千层花瓣的形成至关重要，而 4CL、PAL 和 C4H 基因则控制着花瓣的颜色。本研究获得的数据为今后白千层花的生理生化研究奠定了基础，有助于白千层花品种的定向改良，并为白千层花的分子研究提供了理论依据。
A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics.
Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.
期刊介绍：
Aims
Molecular Horticulture aims to publish research and review articles that significantly advance our knowledge in understanding how the horticultural crops or their parts operate mechanistically. Articles should have profound impacts not only in terms of high citation number or the like, but more importantly on the direction of the horticultural research field.
Scope
Molecular Horticulture publishes original Research Articles, Letters, and Reviews on novel discoveries on the following, but not limited to, aspects of horticultural plants (including medicinal plants):
▪ Developmental and evolutionary biology
▪ Physiology, biochemistry and cell biology
▪ Plant-microbe and plant-environment interactions
▪ Genetics and epigenetics
▪ Molecular breeding and biotechnology
▪ Secondary metabolism and synthetic biology
▪ Multi-omics dealing with data sets of genome, transcriptome, proteome, metabolome, epigenome and/or microbiome.
The journal also welcomes research articles using model plants that reveal mechanisms and/or principles readily applicable to horticultural plants, translational research articles involving application of basic knowledge (including those of model plants) to the horticultural crops, novel Methods and Resources of broad interest.
In addition, the journal publishes Editorial, News and View, and Commentary and Perspective on current, significant events and topics in global horticultural fields with international interests.
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