Transcriptomic Time-Series Analyses of Gene Expression Profile During Zygotic Embryo Development in Picea mongolica

Abstract

Zygotic embryogenesis is a critical process during seed development in gymnosperms. However, knowledge on the genome-wide transcriptional activation that guides this process in conifers is limited, especially in Picea mongolica. This tree species is endemic to semiarid habitats of Inner Mongolia in China. To extend what is known about the molecular events underpinning its zygotic embryogenesis, comparative transcriptomic analyses of gene expression in zygotic embryos were performed by RNA sequencing in P. mongolica. Our results showed that most changes in transcript levels occurred in the early embryonic pattering determination and formation of mature embryos. Transcripts related to embryogenic competence, cell division pattern, hormones, and stress response genes were identified during embryogenesis. Auxin is essential for early embryo patterning and pre-cotyledon embryonic formation. However, ABA is a major regulator of embryo maturation. Moreover, we found that methylation-related gene expression is associated with activation of early-stage embryos, late embryogenesis abundant proteins, and storage/energy-related genes with late and mature embryos. Furthermore, network analysis revealed stage-specific and multistage gene expression clusters during embryogenesis. WOX, MYB, AP2, and HLH transcription factors seem more relevant to embryogenesis in different stages. Our results provide large-scale and comprehensive transcriptome data for embryo development in P. mongolica. These data will lay a foundation for the protection and utilization of P. mongolica resources.

Transcriptome Landscape Analyses of the Regulatory Network for Zygotic Embryo Development in Paeonia ostii

“…AUX1 , LAX1 , and LAX2, which regulate IAA transport, were highly expressed in the early embryo development of Arabidopsis [ 22 , 61 ]. In P. mongolica , AUX1 and PIN3 were also highly expressed in early embryogenesis [ 41 ]. Our study found LAX3 and LAX5 specifically highly expressed and regulated IAA transport at the proembryo of P. ostii .…”

“…Transcriptome sequencing can comprehensively and quickly obtain transcripts of specific organs or tissues at a certain state, and it is an important technical way to reveal the gene expression profiling of cells and tissues [37][38][39][40]. Research showed that auxin was crucial for early embryo patterning and pre-cotyledon embryonic formation, while ABA was a major regulator of embryonic maturation by transcriptome, the key genes related to embryo development were obtained and used to improve the efficiency of the somatic embryo (SE) in Picea mongolica [41,42]. Transcription factors, hormone signals, and transduction-related and sugar-metabolism-related genes play a crucial role in barley grain development [3,43].…”

A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce

“…While gene expression during embryo development has been extensively studied in angiosperm model systems, efforts to analyse global transcript abundance during conifer embryo development have been hampered by a lack of reference genome assemblies due to the large genome sizes of gymnosperms, which average 200 times the size of the Arabidopsis genome (Mackay et al 2012). However, it has been demonstrated that gene families active during embryo development in angiosperms are also active in conifers, with differential expression (DE) of epigenetic regulators and transcription factors (TFs) implicated as developmental regulators in angiosperms being detected by microarray analysis in Zem of Pinus pinaster (de Vega- Bartol et al 2013), and RNA sequencing of Zem and FG respectively of Pinus sylvestris (Merino et al 2016) and whole seeds of Picea mongolica (Yan et al 2021). Efforts to analyse global transcript abundance during conifer embryo development have otherwise mainly focused on SE material due to the easy access of embryos at different developmental stages and the possibilities to analyse embryos under different growth conditions and from cell lines with varying degrees of developmental arrest (reviewed in Trontin et al 2016).…”

Time-Series Transcriptomic Analysis of Contrasting Rice Materials under Heat Stress Reveals a Faster Response in the Tolerant Cultivar

“…Furthermore, researchers have identified defense potential candidate genes in response to Fusarium udum infection by researching the characteristics of pigeon pea root tissue using this method [36]. The putative seed-dormancy gene AGL was identified based on the gene expression trends according to the juvenile olive-tree time-series transcriptome analysis [37]. Therefore, monitoring the time-series transcriptome would be conducive to better understanding the regulatory mechanism of biological processes.…”