Abstract
Defining the dynamic transcriptome of the early embryo at high resolution would assist greatly in understanding vertebrate development. Here, we describe the dynamic transcription landscape of early chick embryo development using advanced single-molecule long-read isoform sequencing (Iso-Seq) and RNA-Seq technology. Our transcriptomic profiling reflected the time course of chicken embryonic development from day 1 to day 8 of incubation, a period encompassing gastrulation, somitogenesis, and organogenesis. This analysis identified transcriptional isoforms, alternative splicing (AS) events, fusion transcripts, alternative polyadenylation (APA) sites, and novel genes. Our results showed that intron retention (IR) represented the most abundant AS type and displayed distinct features and dynamic modulation during development. Moreover, we constructed a high-resolution expression profile across embryonic development. Our combined expression dataset correlates distinct gene clusters with specific morphological changes, and provides the first framework for the molecular basis of early chicken embryogenesis. Analysis of gene expression in the developing chicken embryo highlighted the dynamic nature and complexity of the chicken transcriptome and demonstrated that dramatically increased IR events are associated with distinct gene sets.
Highlights
The vertebrate embryo undergoes extensive morphological changes during the processes of gastrulation and organogenesis (Mitiku and Baker, 2007)
The transcriptome profiling of chicken embryos creates an opportunity to advance our understanding of the molecular regulation of embryo development
The initial 25 h of chicken embryonic development from a zygote to a blastoderm occurs in the oviduct
Summary
The vertebrate embryo undergoes extensive morphological changes during the processes of gastrulation and organogenesis (Mitiku and Baker, 2007). Analysis of the dynamic transcriptome during mouse gastrulation and organogenesis defined groups of genes that have distinct functions during development (Mitiku and Baker, 2007). These data represent a powerful resource for studying developmental gene regulation and reveal the functional potential of patterned genes during embryonic development
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