深层转录组和代谢组分析揭示雪莲(sausurea costus)未开发的特殊代谢空间动态。Lipsch

IF 3.9 4区 生物学 Q1 GENETICS & HEREDITY
Aasim Majeed, Romit Seth, Balraj Sharma, Amna Devi, Shikha Sharma, Mamta Masand, Mohammed Saba Rahim, Naveen Verma, Dinesh Kumar, Ram Kumar Sharma
{"title":"深层转录组和代谢组分析揭示雪莲(sausurea costus)未开发的特殊代谢空间动态。Lipsch","authors":"Aasim Majeed,&nbsp;Romit Seth,&nbsp;Balraj Sharma,&nbsp;Amna Devi,&nbsp;Shikha Sharma,&nbsp;Mamta Masand,&nbsp;Mohammed Saba Rahim,&nbsp;Naveen Verma,&nbsp;Dinesh Kumar,&nbsp;Ram Kumar Sharma","doi":"10.1007/s10142-025-01549-6","DOIUrl":null,"url":null,"abstract":"<div><p><i>Saussurea costus</i> (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in <i>S. costus</i>. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A <i>de novo</i> assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as ‘single gene families’. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in <i>S. costus</i>. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Deep transcriptome and metabolome analysis to dissect untapped spatial dynamics of specialized metabolism in Saussurea costus (Falc.) Lipsch\",\"authors\":\"Aasim Majeed,&nbsp;Romit Seth,&nbsp;Balraj Sharma,&nbsp;Amna Devi,&nbsp;Shikha Sharma,&nbsp;Mamta Masand,&nbsp;Mohammed Saba Rahim,&nbsp;Naveen Verma,&nbsp;Dinesh Kumar,&nbsp;Ram Kumar Sharma\",\"doi\":\"10.1007/s10142-025-01549-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><i>Saussurea costus</i> (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in <i>S. costus</i>. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A <i>de novo</i> assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as ‘single gene families’. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in <i>S. costus</i>. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.</p></div>\",\"PeriodicalId\":574,\"journal\":{\"name\":\"Functional & Integrative Genomics\",\"volume\":\"25 1\",\"pages\":\"\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-02-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Functional & Integrative Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s10142-025-01549-6\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Functional & Integrative Genomics","FirstCategoryId":"99","ListUrlMain":"https://link.springer.com/article/10.1007/s10142-025-01549-6","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

雪莲是一种濒危药用植物,具有多种具有临床意义的植物化学成分,用于治疗多种人类疾病。尽管富含植物化学物质的来源,但对木香树空间化代谢的分子见解知之甚少。本研究利用深度转录组测序和基于高通量UHPLC-QTOF的非靶向代谢组学分析研究了器官特异性次级代谢物的生物合成动力学。从高质量reads中重新组装得到59,725个转录本,其中非冗余转录本的结构注释(53.02%)和功能注释(66.13%)。在预测的7683个基因家族中,3211个被归类为“单基因家族”。有趣的是,在Asterids的4664个核心基因家族中,有4560个家族被捕获。器官特异性差异基因表达分析显示,叶与茎(23,102个转录本)、叶与根(30,590个转录本)和根与茎(21,759个转录本)之间存在显著差异。同样,在叶与根(250 pm)、叶与茎(350 pm)和根与茎(107 pm)中记录了推定代谢物(pm)的显著差异。综合转录组学和代谢组学分析确定了重要代谢物积累的器官特异性差异,包括木腥草素、薄荷呋喃、taraxerol、lupeol、乙酰丁香酚、东莨菪碱、木腥草内酯和脱氢木腥草内酯。此外,全球基因共表达网络(GCN)确定了控制次生代谢物途径关键靶基因表达的可能调控因子,包括萜类、苯丙类和类黄酮。这里创建的综合功能相关基因组资源为通过基因工程提高目标代谢物的生物合成提供了有益的见解,并加快了关联图谱的工作,以阐明控制特定生物活性代谢物的偶然遗传元件。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Deep transcriptome and metabolome analysis to dissect untapped spatial dynamics of specialized metabolism in Saussurea costus (Falc.) Lipsch

Saussurea costus (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in S. costus. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A de novo assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as ‘single gene families’. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in S. costus. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
3.50
自引率
3.40%
发文量
92
审稿时长
2 months
期刊介绍: Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信