The fetal sheep heart transcriptome

Background: The sheep is an extensively studied animal model with unique potential for the study of developmental programming yet genomic resources are lacking. We aimed to identify the expressed genome from the fetal sheep heart in order to identify genes and gene variants relevant to developmental studies and to provide a genomic resource for development of sheep-specific genetic tools. We used high throughput sequencing technologies to achieve these goals. Results: Using the bovine genome as a reference for assembly and annotation of 75-bp paired-end reads, we identified 13,444 sheep fetal heart genes of which 13,064 are novel in the sheep. In addition, we identified 8,617 high confidence SNPs and 240 genes with exon splicing that differed between the cow and the sheep fetal heart transcriptome. The genes with the highest expression levels and genes with novel exons with the highest expression levels in the fetal heart transcriptome are known to play central roles in muscle development and function. Conclusions: In this study we show that high throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provides a resource for development of genetic tools and combined with the polymorphism data will enable annotation and assembly of the sheep genome. In addition, identification of novel splice variants in the fetal sheep heart transcriptome followed by KEGG pathway analysis is a first step towards revealing mechanisms of genetic variation and gene environment interaction during fetal heart development.

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