An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways.

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY
Plant Genome Pub Date : 2025-03-01 DOI:10.1002/tpg2.20564
Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie
{"title":"An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways.","authors":"Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie","doi":"10.1002/tpg2.20564","DOIUrl":null,"url":null,"abstract":"<p><p>Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20564"},"PeriodicalIF":3.9000,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806286/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/tpg2.20564","RegionNum":2,"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

Abstract

Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.

姜黄的器官特异性转录组图谱:microrna, phasirna和代谢途径。
姜黄(Curcuma wenyujin yh Chen et c.c Ling)是一种广泛用于临床治疗的药用植物。在这项研究中,综合组学数据分析使我们能够在转录组范围内发现microRNAs (miRNAs)和阶段性小干扰rna (phasiRNAs)。共报道了186个成熟mirna和23个前体。此外,14个家族的31个mirna被器官特异性表达,其中13个mirna可以进行器官特异性靶标调控。超过80%的phasiRNA位点是器官特异性表达的,特别是在块茎中。在某些情况下,从高度重叠的区域产生了具有不同增量但具有一致器官特异性表达模式的phasiRNA,这表明不同的机制可能同步参与phasiRNA的加工。基于转录组组装,鉴定出28个和56个结核特异性基因分别参与生物碱和萜类代谢。对β-榄香烯生物合成途径的酶编码基因分析表明,下游基因具有结核特异性,而上游基因不具有结核特异性。我们假设在其他器官中产生的前体代谢物可能被传递到块茎中进行β-榄香烯生物合成的最后步骤。本研究提供了文玉金的器官特异性转录组图谱,为文玉金的器官发育和次生代谢的分子研究奠定了基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Plant Genome
Plant Genome PLANT SCIENCES-GENETICS & HEREDITY
CiteScore
6.00
自引率
4.80%
发文量
93
审稿时长
>12 weeks
期刊介绍: The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.
×
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:604180095
Book学术官方微信