Multi-omics analysis reveals the regulatory mechanism of branching development in Quercus fabri

IF 2.8 2区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of proteomics Pub Date : 2025-01-06 DOI:10.1016/j.jprot.2024.105373

Shifa Xiong , Liwen Wu , Yicun Chen , Xiang Shi , Yangdong Wang

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引用次数: 0

Abstract

The ability of axillary meristems to form axillary buds and subsequently develop into branches is influenced by phytohormones, environmental conditions, and genetic factors. The main trunk of Quercus fabri is prone to branching, which not only impacts the appearance and density of the wood and significantly reduces the yield rate. This study conducted transcriptomic, proteomic, and metabolomic analyses on three stages of axillary bud development in Q. fabri. A total of 12,888 differentially expressed genes (DEGs), 8193 differentially accumulated proteins (DAPs), and 1788 differentially accumulated metabolites (DAMs) were identified through comparisons among the stages and subjected to multi-omics joint analysis. Conduct interaction network analysis on DEGs and DAPs to identify the significant transcription factor family (AP2/ERF) involved in the regulation of axillary bud development. Furthermore, KEGG enrichment analysis of DEGs, DAPs and DAMs indicated significant enrichment in plant hormone signaling pathways. The analysis of endogenous hormone levels and qRT-PCR results for pathway genes demonstrated that the expression levels of IAA and tZ significantly increased during late developmental stages, whereas the expression levels of ABA, ACC and JA significantly decreased. In summary, these findings contribute to a comprehensive understanding of the regulatory networks underlying the branching development of Q. fabri.

Significance

Q. fabri exhibits robust vegetative growth, and its primary trunk is prone to branching, significantly influencing the wood yield rate. Through a joint analysis of transcriptomics, proteomics, and metabolomics, we comprehensively examined the regulatory network governing the axillary bud development of Q. fabri. Our findings revealed the crucial roles of the AP2/ERF transcription factor family and plant hormone signal transduction pathways in branch development. These insights contribute to a deeper understanding of the mechanisms regulating branch development.

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多组学分析揭示了栓皮栎分枝发育的调控机制。

腋窝分生组织形成腋芽并发育成枝的能力受植物激素、环境条件和遗传因素的影响。柏树主干易发生分枝，不仅影响木材的外观和密度，而且显著降低了成材率。本研究对蚕豆腋芽发育的三个阶段进行了转录组学、蛋白质组学和代谢组学分析。通过阶段间比较和多组学联合分析，共鉴定出12888个差异表达基因（deg）、8193个差异积累蛋白（DAPs）和1788个差异积累代谢物（dam）。对DEGs和DAPs进行相互作用网络分析，确定参与腋芽发育调控的重要转录因子家族（AP2/ERF）。此外，对DEGs、DAPs和dam的KEGG富集分析表明，它们在植物激素信号通路中有显著富集。内源激素水平分析和通路基因qRT-PCR结果显示，IAA和tZ的表达水平在发育后期显著升高，ABA、ACC和JA的表达水平显著降低。综上所述，这些研究结果有助于全面了解紫茎甘蓝分支发育的调控网络。意义：蚕豆营养生长旺盛，主干易发生分枝，对木材产出率有显著影响。通过转录组学、蛋白质组学和代谢组学的联合分析，我们全面研究了蚕豆腋芽发育的调控网络。我们的研究结果揭示了AP2/ERF转录因子家族和植物激素信号转导途径在分支发育中的关键作用。这些见解有助于更深入地理解调控分支发展的机制。

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来源期刊

Journal of proteomics 生物-生化研究方法

CiteScore

7.10

自引率

3.00%

发文量

227

审稿时长

73 days

期刊介绍： Journal of Proteomics is aimed at protein scientists and analytical chemists in the field of proteomics, biomarker discovery, protein analytics, plant proteomics, microbial and animal proteomics, human studies, tissue imaging by mass spectrometry, non-conventional and non-model organism proteomics, and protein bioinformatics. The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics, pharmacoproteomics. Journal of Proteomics unifies both fundamental scientists and clinicians, and includes translational research. Suggestions for reviews, webinars and thematic issues are welcome.