Integrative Analysis of the Transcriptome and Metabolome Reveals the Mechanism of Chinese Fir Seed Germination

Abstract

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important plantation tree species in China, and seed germination is a key step in forest tree cultivation. To reveal the gene expression network and molecular mechanisms in the germination of Chinese fir seeds, physiological indexes were measured and transcriptome and metabolome analyses were performed on Chinese fir seeds in four stages of germination (imbibition stage, preliminary stage, emergence stage, and germination stage). All six physiological indicators had significant differences at different developmental stages. In transcriptome and metabolome analysis, we identified a large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). Gene Ontology (GO) analysis showed a large number of DEGs associated with cell growth, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEGs were significantly enriched in the flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. The KEGG enrichment results of DAMs were similar to those of DEGs. The joint analysis of DEGs and DAMs indicated that flavonoid biosynthesis and phenylpropanoid biosynthesis were the key pathways of Chinese fir seed germination. Our study revealed a number of key genes and key metabolites, laying the foundation for further studies on the gene regulatory network of Chinese fir seed germination.

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

“…In our study, KEGG pathway analysis indicated that 13 DEGs were significantly enriched in the phenylpropanoid biosynthesis pathway and 6 DEGs in the flavonoid biosynthesis pathway ( Figure 5 ), implying that phenylpropanoid biosynthesis and flavonoid biosynthesis are the key pathways during GA 3 -induced dormancy release. A similar result was also described by Chen et al. (2023) , who found that the phenylpropanoid biosynthesis and flavonoid biosynthesis pathways had important roles in the seed germination of Chinese fir [ Cunninghamia lanceolat (Lamb.)…”

Combined Analysis of Untargeted Metabolomics and Transcriptomics Revealed Seed Germination and Seedling Establishment in Zelkova schneideriana

“…Similarly, in Cinnamomum migao, genes related to carbohydrate and lipid metabolism were predominantly activated after seed coat rupture [64]. Additionally, there was a decrease in total starch and crude oil content during seed germination of Phyllostachys edulis, whereas genes involved in starch metabolism and lipid body degradation pathways were consistently upregulated [65]. These findings align with our own results; however, unlike these studies, we inferred a relationship between starch and lipid release based on our results.…”

Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress

“…In the present study, the length of the roots of mulberry plants decreased significantly with increasing salt concentration, while the decrease in fresh weight was not significant. In addition, seed germination is one of the most important growth and developmental processes in plants; it is extremely sensitive to salt stress and is subjected to the coordinated interactions of multiple genes and metabolites [ 43 ]. Mulberry plants are rich in flavonoids and other secondary metabolites, which play a wide range of roles in defense against biotic and abiotic stresses [ 18 ].…”