Embryogenesis is a complex phase of conifer development involving hundreds of genes,
and a proper understanding of this process is critical not only to produce embryos with
different applied purposes but also for comparative studies with angiosperms. A global
view of transcriptome dynamics during pine somatic and zygotic embryogenesis is
currently missing. Here, we present a genome-wide transcriptome analysis of somatic
and zygotic embryos at three developmental stages to identify conserved biological
processes and gene functions during late embryogenesis. Most of the differences
became more significant as the developmental process progressed from early to
cotyledonary stages, and a higher number of genes were differentially expressed in
somatic than in zygotic embryos. Metabolic pathways substantially affected included
those involved in amino acid biosynthesis and utilization, and this difference was
already observable at early developmental stages. Overall, this effect was found to be
independent of the line (genotype) used to produce the somatic embryos. Additionally,
transcription factors differentially expressed in somatic versus zygotic embryos were
analyzed. Some potential hub regulatory genes were identified that can provide clues
as to what transcription factors are controlling the process and to how the observed
differences between somatic and zygotic embryogenesis in conifers could be regulated
