Data_Sheet_1_Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine.xlsx

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.

胚胎发生（embryogenesis）是针叶树（conifer）发育进程中的复杂阶段，涉及数百个基因的协同调控。对这一过程的透彻认知，不仅是培育具备不同应用目标胚胎的核心前提，同时也为被子植物（angiosperms）的比较研究奠定了关键基础。目前学界仍缺乏松树（pine）体细胞胚胎发生（somatic embryogenesis）与合子胚胎发生（zygotic embryogenesis）过程中转录组（transcriptome）动态变化的全局视角。本研究针对三个发育阶段的体细胞与合子胚胎开展全基因组转录组分析，旨在鉴定晚期胚胎发生过程中保守的生物学过程与基因功能。随着发育进程从早期向子叶期（cotyledonary stages）推进，两类胚胎间的表达差异愈发显著；且体细胞胚胎中差异表达基因（differentially expressed genes）的数量显著多于合子胚胎。受到显著影响的代谢通路（metabolic pathways）涵盖氨基酸生物合成与代谢途径，且该差异在发育早期即可被观测到。整体而言，该差异效应与用于制备体细胞胚胎的株系（line），即基因型（genotype）无关。此外，本研究还分析了体细胞与合子胚胎间差异表达的转录因子（transcription factors）。本研究鉴定出若干潜在的核心调控基因（hub regulatory genes），可为解析调控该过程的转录因子，以及针叶树体细胞与合子胚胎发生间差异的调控机制提供重要线索。