白杨特化代谢物生物合成候选基因的代谢组学和转录组学资源。

IF 3.6 2区 生物学 Q1 PLANT SCIENCES
Sara M Rydman, Jenna Lihavainen, Kathryn M Robinson, Stefan Jansson, Benedicte R Albrectsen, Nathaniel R Street
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引用次数: 0

摘要

本研究旨在确定参与水杨科植物特化代谢产物水杨类酚苷(SPGs)生物合成的候选基因。虽然多组学数据的整合是将编码酶及其调控因子的基因与代谢物生物合成联系起来的有力途径,但合适的多组学数据资源很少。我们提出了一个全面的数据集,包括非靶向液相色谱-质谱(LC-MS)和mrna测序数据,这些数据来自欧洲白杨(Populus tremula L.)的各种器官和产生不同SPGs的基因型。我们提出了一种可重复的LC-MS数据分析管道,包括对潜在的新型SPGs的预测注释。我们通过鉴定与肉桂基片段的SPGs生物合成有关的候选基因来证明该资源的效用。通过整合基因和代谢物差异分析与基因共表达网络,我们确定了两个hxxxd型酰基转移酶基因和一个udp -葡萄糖基转移酶基因作为未来下游表征的候选基因。结合基因表达和代谢组学资源被整合到PlantGenIE.org中,以方便访问和数据挖掘。所有原始数据都可以在公共数据库中获得,所有数据和结果文件都可以在相关的Figshare存储库中获得。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula.

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography-mass spectrometry (LC-MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC-MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

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来源期刊
Physiologia plantarum
Physiologia plantarum 生物-植物科学
CiteScore
11.00
自引率
3.10%
发文量
224
审稿时长
3.9 months
期刊介绍: Physiologia Plantarum is an international journal committed to publishing the best full-length original research papers that advance our understanding of primary mechanisms of plant development, growth and productivity as well as plant interactions with the biotic and abiotic environment. All organisational levels of experimental plant biology – from molecular and cell biology, biochemistry and biophysics to ecophysiology and global change biology – fall within the scope of the journal. The content is distributed between 5 main subject areas supervised by Subject Editors specialised in the respective domain: (1) biochemistry and metabolism, (2) ecophysiology, stress and adaptation, (3) uptake, transport and assimilation, (4) development, growth and differentiation, (5) photobiology and photosynthesis.
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