RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
- Meng How Tan1,
- Kin Fai Au,
- Arielle Yablonovitch,
- Andrea Wills,
- Jason Chuang,
- Julie Baker,
- Wing Hung Wong and
- Jin Billy Li
- ↵* Corresponding author; email: menghow.tan{at}gmail.com
Abstract
The Xenopus embryo has provided key insights into fate specification, the cell cycle, and other fundamental developmental and cellular processes, yet a comprehensive understanding of its transcriptome is lacking. Here, we used paired end RNA sequencing (RNA-Seq) to explore the transcriptome of Xenopus tropicalis in 23 distinct developmental stages. We determined expression levels of all genes annotated in RefSeq and Ensembl and showed for the first time on a genome-wide scale that, despite a general state of transcriptional silence in the earliest stages of development, ~150 genes are transcribed prior to the midblastula transition. In addition, our splicing analysis uncovered more than 10,000 novel splice junctions at each stage and revealed that many known genes have additional unannotated isoforms. Furthermore, we used Cufflinks to reconstruct transcripts from our RNA-Seq data and found that ~13.5% of the final contigs are derived from novel transcribed regions, both within introns and in intergenic regions. We then developed a filtering pipeline to separate protein-coding transcripts from non-coding RNAs and identified a confident set of 6,686 non-coding transcripts in 3,859 genomic loci. Since the current reference genome, XenTro3, consists of hundreds of scaffolds instead of full chromosomes, we also performed de novo reconstruction of the transcriptome using Trinity and uncovered hundreds of transcripts that are missing from the genome. Collectively, our data will not only aid in completing the assembly of the Xenopus tropicalis genome but will also serve as a valuable resource for gene discovery and for unraveling the fundamental mechanisms of vertebrate embryogenesis.
- Received April 5, 2012.
- Accepted August 27, 2012.
- © 2012, Published by Cold Spring Harbor Laboratory Press
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