The Zebrafish transcriptome during early development

Background: Zebrafish (Danio rerio) is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA_Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped to the zebrafish genome and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA-Seq results, and to further investigate the developmental expression of specific genes, the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card (TLDA). Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels, with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre-MBT were similar when comparing highly expressed genes, whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions.