RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

• DOI: 10.1101/gr.141424.112
• Publication Date: 2012-09-08T05:00:20Z
• Authors: Meng How Tan; Kin Fai Au; Arielle L. Yablon...; Andrea E. Wills; Jason Chuang; Julie C. Baker; Wing Hung Wong; Jin Billy Li
• Keywords: Ensembl; RNA-Seq

The Xenopus embryo has provided key insights into fate specification, the cell cycle, and other fundamental developmental cellular processes, yet a comprehensive understanding of its transcriptome is lacking. Here, we used paired end RNA sequencing (RNA-seq) to explore tropicalis in 23 distinct stages. We determined expression levels all genes annotated RefSeq Ensembl showed for first time on genome-wide scale that, despite general state transcriptional silence earliest stages development, approximately 150 are transcribed prior midblastula transition. In addition, our splicing analysis uncovered more than 10,000 novel splice junctions at each stage revealed that many known have additional unannotated isoforms. Furthermore, Cufflinks reconstruct transcripts from RNA-seq data found ∼13.5% final contigs derived regions, both within introns intergenic regions. then developed filtering pipeline separate protein-coding noncoding RNAs identified confident set 6686 3859 genomic loci. Since current reference genome, XenTro3, consists hundreds scaffolds instead full chromosomes, also performed de novo reconstruction using Trinity missing genome. Collectively, will not only aid completing assembly genome but serve as valuable resource gene discovery unraveling mechanisms vertebrate embryogenesis.