Transcriptome profile analysis of porcine adipose tissue by high-throughput sequencing

Novel high-throughput deep sequencing technology has dramatically changed the study of the functional complexity of transcriptomes. Here, we report the first use of this technology for analysing the wide range of transcriptional changes in porcine adipose tissue from different breeds and different growth phases in a model of obesity. Digital gene expression (DGE) data sets were instrumental to verifying the predicted gene models. We obtained a sequencing depth of over 3 million tags per sample (lean, obese-a and obese-b). Tag mapping indicated expression of more than 76% of all genes represented in three transcript databases. We found the expression level of 1596 genes was significantly different between lean and obese-a library (P < 0.01). Among them, we found 84 genes expressed only in the obese-a library and 95 genes expressed only in the lean library. Moreover, the expression of 4403 genes was found to be remarkably different between the obese-a and obese-b library (P < 0.01); 642 of these were only expressed in obese-a, and 618 were only expressed in obese-b. When mapping to genes, it was found that the sense transcripts account for 67.42%, 68.65% and 66.61% of all clean tags in the lean, obese-a and obese-b libraries respectively. By comparison, the ratio of sense to antisense mapping of the total number of tags was approximately 6:1 for all libraries. This suggests that transcriptional regulation on the sense strand has a major role in adipose deposition, although a high number of antisense mapping events were also detected. We anticipated more than 20,000 different novel tags to be localized to the porcine genome. Among them, 799 different clean tags with a copy number of more than 1000 were detected. In conclusion, our deep sequencing analysis revealed a high degree of transcriptional complexity in the regulatory mechanisms of adipogenesis and resulted in the discovery and validation of new gene products in porcine adipose tissue.