PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species.

IF 9.4 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Communications Pub Date : 2024-07-11 DOI:10.1016/j.xplc.2024.101038

Yue Hu, Yao Ruan, Xin-Le Zhao, Feng Jiang, Dongxu Liu, Qiang Zhu, Qing-Ye Zhang, Qing-Yong Yang

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引用次数: 0

Abstract

Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for intra- and cross-species comparison of metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a multilevel comparison database based on predicted metabolic profiles of 530 plant species. The PCMD serves as a platform for comparing metabolite characteristics at various levels, including species, metabolites, pathways, and biological taxonomy. The database also provides a number of user-friendly online tools, such as species comparison, metabolite enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. In addition, the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering. The PCMD is the most species-rich comparative plant metabolomics database currently available, and a case study demonstrates its ability to provide new insights into plant metabolic diversity.

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PCMD：530 个植物物种的种内和跨物种代谢图谱的多层次比较数据库。

比较代谢组学在研究基因功能、探索代谢物进化和加速作物遗传改良方面发挥着至关重要的作用。然而，目前还缺乏一个系统的平台来比较种内和种间代谢物。在此，我们报告了植物比较代谢组数据库（PCMD; http://yanglab.hzau.edu.cn/PCMD），这是一个基于 530 种植物的预测代谢谱的多级比较数据库。PCMD 可作为一个平台，从物种、代谢物、途径和生物分类学等不同层面比较代谢物的特征。该数据库还提供了一系列用户友好型在线工具，如物种比较、代谢物富集和 ID 转换等，使用户能够对不同物种的代谢物进行比较和富集分析。此外，PCMD 通过标准化代谢物编号，在现有代谢物相关数据库的基础上建立了一个统一的系统。PCMD 是目前物种最丰富的植物代谢组学比较数据库，一项案例研究证明了它能够为了解植物代谢多样性提供新的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant Communications Agricultural and Biological Sciences-Plant Science

CiteScore

15.70

自引率

5.70%

发文量

105

审稿时长

6 weeks

期刊介绍： Plant Communications is an open access publishing platform that supports the global plant science community. It publishes original research, review articles, technical advances, and research resources in various areas of plant sciences. The scope of topics includes evolution, ecology, physiology, biochemistry, development, reproduction, metabolism, molecular and cellular biology, genetics, genomics, environmental interactions, biotechnology, breeding of higher and lower plants, and their interactions with other organisms. The goal of Plant Communications is to provide a high-quality platform for the dissemination of plant science research.

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