NDLI: Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar

Content Provider	Springer Nature : BioMed Central
Author	Qu, Chunpu Zuo, Zhuang Cao, Lina Huang, Jiahuan Sun, Xue Zhang, Peng Yang, Chengjun Li, Lixin Xu, Zhiru Liu, Guanjun
Abstract	Background Seed germination, a complex, physiological–morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant. Results In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites. Conclusions Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
Related Links	https://bmcplantbiol.biomedcentral.com/counter/pdf/10.1186/s12870-019-1862-3.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712229
DOI	10.1186/s12870-019-1862-3
Journal	BMC Plant Biology
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2019-06-26
Access Restriction	Open
Subject Keyword	Plant Sciences Agriculture Tree Biology Poplar Seed germination and post-germination stages Transcriptomics Metabolomics Data integration Candidate genes
Content Type	Text
Resource Type	Article
Subject	Plant Science
Journal Impact Factor	4.3/2023
5-Year Journal Impact Factor	5.2/2023

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