| Summary: | The Chinese soft-shelled turtle (<i>Pelodiscus sinensis</i>), an economically important aquatic species in China, displays considerable sexual dimorphism: the male <i>P. sinensis</i> is larger and, thus, more popular in the market. In this study, we obtained the full-length (FL) transcriptome data of <i>P. sinensis</i> by using Pacific Biosciences (PacBio)’s isoform sequencing and analyzed the transcriptome structure. In total, 1,536,849 high-quality FL transcripts were obtained through single-molecule real-time (SMRT) sequencing, which were then corrected using Illumina sequencing data. Next, 89,666 nonredundant FL transcripts were generated after mapping to the reference genome of <i>P. sinensis</i>; 291 fusion genes and 17,366 novel isoforms were successfully annotated using data from the nonredundant protein sequence database (NR), eukaryotic orthology groups (KOG), the Gene Ontology (GO) project, and the KEGG Orthology (KO) database. Additionally, 19,324 alternative polyadenylation sites, 101,625 alternative splicing events, 12,392 long noncoding RNAs, and 5916 transcription factors were identified. <i>Smad4</i>, <i>Wif1</i>, and 17-<i>β-hsd</i> were identified as female-biased genes, while <i>Nkd2</i> and <i>Prp18</i> held a higher expression level in males than females. In summary, we found differences between male and female <i>P. sinensis</i> individuals in AS, lncRNA, genes, and transcripts, which relate to the Wnt pathway, oocyte meiosis, and the TGF-β pathway. Female-biased genes such as <i>Smad4</i>, <i>Wif1,</i> and <i>17-β-hsd</i> and male-biased genes such as <i>Nkd2</i> and <i>Prp18</i> played important roles in the sex determination of <i>P. sinensis</i>. FL transcripts are a precious resource for characterizing the transcriptome of <i>P. sinensis</i>, laying the foundation for further research on the sex-determination mechanisms of <i>P. sinensis</i>.
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