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

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.