The Yangtze finless porpoise (Neophocaena asiaeorientalis, YFP) is the only extant cetacean in the Yangtze River, and is listed as critically endangered species in the IUCN Red List. There are significant differences in growth and development between male and female YFPs. In order to reveal the potential mechanism of non-coding RNA (ncRNA) involved in this phenomenon, this study took female and male YFP blood as experimental samples, built a database for RNA transcriptome sequencing, and detected ncRNA gene expression profiles such as circRNA, miRNA and lncRNA, and screened differentially expressed genes (DEGs), and performed GO and KEGG functional annotation analysis on DEGs. A total of 205 differentially expressed circRNAs were detected, 87 up-regulated and 118 down-regulated in female YFPs, and the enriched items mainly included energy metabolism and nutritional development of nerves. There were 122 differentially expressed lncRNAs, 54 up-regulated and 68 down-regulated in female YFPs, and the enriched items mainly included heme synthesis and metabolism, immune regulation and immune function. There were 48 differentially expressed miRNAs, 32 up-regulated and 16 down-regulated in female YFPs, and the enriched items mainly included cancer occurrence, energy metabolism and signal transduction. Real-time PCR verified the expression levels of MAPK1, IRS1, ALAD and CIQC were consistent with the sequencing results. This study revealed that ncRNA differentially expressed genes may be involved in the mechanism of sex differences in growth through metabolism, immunity and signal transduction, which provides a new perspective for explaining the growth differences between male and female YFPs, and provides a scientific reference for the protection of YFPs.
