Study on somatic embryogenesis of cinnamomum camphora based on transcriptome sequencing

Abstract

In this study, non-embryogenic callus (NEC), embryogenic callus (EC), and somatic embryos (SE) sourced from various culture materials were employed to investigate somatic embryogenesis in Cinnamomum camphora. Utilizing RNA-Seq technology, we conducted transcriptome sequencing and analysis of C. camphora culture materials to elucidate the genes and metabolic pathways associated with somatic embryogenesis. Correlation analysis among the samples indicated substantial differences between the groups, confirming the representativeness of the three materials utilized. The analysis revealed three distinct databases of differentially expressed genes (DEGs) (SE vs EC, SE vs NEC, EC vs NEC) containing 10,449, 9,561, and 8,867 DEGs, respectively. Clustering analysis of DEGs unveiled significant separation among SE, EC, and NEC from different C. camphora materials. Notably, 21 genes were significantly up-regulated in SE and EC compared to NEC, predominantly comprising adversity stress-responsive genes, hormone-responsive genes, and zinc finger proteins. Of particular interest was the expression of the VACUOLAR IRON TRANSPORTER 1 (VIT1) gene, which was 78.33 and 3.05 times higher in SE than in NEC and EC, respectively. This suggests a potential crucial regulatory role for Fe²⁺ in C. camphora somatic embryogenesis. Further analysis of DEGs, in conjunction with Gene Ontology (GO) enrichment, unveiled a close association of C. camphora somatic embryogenesis with biological processes, transcriptional regulation, responses to salt stress and abscisic acid, cell nucleus activity, and DNA-binding transcription factors. Moreover, KEGG pathway analysis emphasized the significant enrichment of DEGs in plant hormone signal transduction, featuring 187 differential genes, highlighting the pivotal role of hormone signaling in C. camphora somatic embryogenesis. Most genes related to phytohormone synthesis, signal transduction, transcription factors, and stress responses were up-regulated, thereby promoting somatic embryogenesis in C. camphora. The findings of this study provide valuable insights into the molecular mechanisms underlying somatic embryogenesis in C. camphora and related species.