ABSTRACT: The goal of this study was to compare the transcriptome profiles (RNA-seq) of fetal and six month old goat in skeletal muscle. Total RNAs from the Chinese Xuhuai goat longissimus thoracis at fetal and six month old stages were used to construct cDNA libraries for Solexa SBS technology sequencing. After remove reads with adapters, reads in which unknown bases were more than 5% and low quality reads, we obtained 27,512,850 clean reads from the fetal caprine (FC) library and 27,582,908 clean reads from the six month old caprine (SMC) library. The total basepairs were 2,476,156,500 for FC and 2,482,461,720 for SMC. The ratio of clean reads mapped to reference genome was 45.43% for FC and 33.73% for SMC. The ratio of reads mapped to reference gene was 47.77% for FC and 34.03% for SMC. To reveal the molecular events during different development stages, genes that differentially expressed between the two libraries were identified. Clean reads that matched reference genes in each library were used to evaluate the expression level of transcripts. In total, 11663 genes were differentially expressed between the two development stages. There were 5134 genes with at least a two-fold difference in expression between FC and SMC libraries (FDR, 0.001), of which 1070 genes were up-regulated, 4064 were down-regulated in the six month old caprine compared to the fetal caprine muscle tissue, and 4911 were expressed in both library. Genes with less than one fold changes between FC and SMC libraries were excluded from further analysis. The results indicated that there were significant difference between the two development phase in gene-expression. In addition, some muscle related genes such as MyoD, Myf5, Myogenin, Mrf4, myosin heavy chain 3 (MYH3), Myoglobin and DLK1 were differentially expressed.
