A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure. Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development

为解析发育过程中编码与非编码转录本的动态变化及多样性，我们覆盖6个发育阶段采集聚腺苷酸化信使RNA（polyadenylated mRNA）与去除核糖体RNA的总RNA（ribosomal RNA-depleted total RNA）样本，并开展高通量测序。母源加载的转录组具有高度多样性，同时包含聚腺苷酸化与去腺苷酸化的转录本。众多母源基因的表达峰值出现在卵母细胞阶段，其中包含已知的卵母细胞成熟、受精等关键事件的调控基因。在囊胚早期至幼虫阶段丰度上调的全部转录本中，约30%的胚胎基因在囊胚晚期时表达量较初始上调4倍及以上，另有35%的胚胎基因于原肠晚期完成该幅度的上调。我们通过基因模型验证与发现流程，鉴定出大量新型转录本，其中绝大多数在编码潜力与基因结构层面均具备长链非编码RNA（long non-coding RNAs）的典型特征。本数据集涵盖热带爪蟾（Xenopus tropicalis）早期发育过程中，聚腺苷酸化信使RNA（6个发育阶段）与去除核糖体RNA的总RNA（3个发育阶段）的表达谱数据。