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.
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Claims 7
Claim · model-written summary
Genes and metabolites differed significantly across germination and post germination stages.
- Organ / stage
- various stages of seed germination and post germinatione0
- Outcome
- significantly different genes and metabolitese0
PopulusOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
AP2/EREBP, DOF, and YABBY transcription factors were implicated in particular germination stages.
- Gene
- AP2/EREBP, DOF, and YABBYe0
- Outcome
- involved in specific seed germination and post-germination stagese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
Cell wall, amino acid metabolism, and transport pathways were significantly enriched in stages 3 and 5.
- Organ / stage
- stages 3 and 5e0
- Outcome
- cell wall, amino acid metabolism, and transport-related pathwayse0
- Direction
- enrichede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
Glycolysis and tricarboxylic acid cycle processes showed no significant enrichment.
- Outcome
- enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cyclee0
- Direction
- no significant enrichmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
Intermediate metabolites in those primary metabolic processes changed significantly.
- Outcome
- intermediate metabolites in these primary metabolic processese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“significant changes in intermediate metabolites in these primary metabolic processes”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
Correlation network analysis identified gene family members most relevant to changing metabolites.
- Outcome
- gene family members most relevant to these changing metabolitese0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites”
t0“seed germination and post-germination stages in poplar”
Claim · model-written summary
The targeted correlation network approach is proposed as a strategy for joint multiomics analyses.
- Outcome
- new strategy for joint multiomics analysese0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
t0“seed germination and post-germination stages in poplar”