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Background  Because few studies exist to describe the unique molecular network regulation behind pig pre-implantation embryonic development (PED), genetic engineering in the pig embryo is limited. Also, this lack of research has hindered derivation and application of porcine embryonic stem cells and porcine induced pluripotent stem cells (iPSCs).    Results  We identified and analyzed the genome wide transcriptomes of pig  in vivo -derived and somatic cell nuclear transferred (SCNT) as well as mouse  in vivo -derived pre-implantation embryos at different stages using mRNA deep sequencing. Comparison of the pig embryonic transcriptomes with those of mouse and human pre-implantation embryos revealed unique gene expression patterns during pig PED. Pig zygotic genome activation was confirmed to occur at the 4-cell stage via genome-wide gene expression analysis. This activation was delayed to the 8-cell stage in SCNT embryos. Specific gene expression analysis of the putative inner cell mass (ICM) and the trophectoderm (TE) revealed that pig and mouse pre-implantation embryos share regulatory networks during the first lineage segregation and primitive endoderm differentiation, but not during ectoderm commitment. Also, fatty acid metabolism appears to be a unique characteristic of pig pre-implantation embryonic development. In addition, the global gene expression patterns in the pig SCNT embryos were different from those in  in vivo -derived pig embryos.    Conclusions  Our results provide a resource for pluripotent stem cell engineering and for understanding pig development.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-4) contains supplementary material, which is available to authorized users.

Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing