Transcriptomic time-series analyses of gene expression profile during zygotic embryo development in Taxodium distichum x Taxodium mucronatum

Key messageOur results from transcriptomics extend the understanding of the gene expression and major events associated with embryogenesis progression in Taxodium distichum x Taxodium mucronatum.AbstractZygotic embryogenesis is a critical process during seed development in which the plant body plan is established and the meristems responsible for all post-embryonic growth are determined. Taxodium 'Zhongshanshan' is a series of superior interspecies hybrids of T. distichum and T. mucronatum and has been widely planted in southeastern China. Understanding the molecular, cellular and metabolic processes of embryonic development will provide important information on the somatic embryogenesis of T. 'Zhongshanshan' and further developing zygotic embryogenesis research. In the present study, we sequenced the transcriptomes of zygotic T. distichum x T. mucronatum embryos at several developmental stages, covering most of embryogenesis. Total RNA samples from six zygotic embryo developmental stages were collected for high-throughput RNA sequencing. In total, 46,798 unigenes were identified, and 12,846 differentially expressed genes were annotated. Genes involved in carbohydrate metabolic, such as glycoside hydrolase-, alpha-xylosidase- and xyloglucan endotransglycosylase-encoding genes, were over-represented in early embryogenesis. Genes associated with auxin, gibberellin, and cytokinin signaling pathways and epigenetic genes related to chromatin remodeling, DNA methylation, and histone deacetylase showed significant differential expression during the embryo development process. Moreover, a number of transcription factors related to embryonic development were identified, among which WUSCHEL HOMEOBOX (WOX), NO APCAL MERISTEM (NAM), and LEAFY COTYLEDON1 (LEC1) being more relevant during early and mid-embryogenesis stages. Our results will provide a valuable resource for future studies and will be helpful to the research of T. 'Zhongshanshan' breeding programs.