The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an IIlumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes （40 814） had significant similarity with proteins in the National Center of Biotechnology Information （NCBI） non-redundant protein database and Swiss-Prot database （E-value 〈10-5）. Of these annotated unigenes, 9156 and 11 947 unigenes were assigned to 52 gene ontology categories （GO） and 25 clusters of orthologous groups （COG）, respectively. In total, 26496 （35.83%） unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database （KEGG）. In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsatu- rated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA se- quencing （RNA-Seq） of terrapin animals and would enrich the knowledge of turtles for future research.
