ABSTRACT The giant freshwater prawn (Macrobrachium rosenbergii), which is widely distributed in Southeast Asia and the western Pacific, is an important commercial prawn species. However, the molecular mechanism of ovarian development is unclear, and available data on the ovarian transcriptome of M. rosenbergii are limited. In this study, we constructed transcriptomes of female (ZW) and super female (WW) of M. rosenbergii ovaries to discover genes and pathways related to ovarian development. A total of 71,555 unigenes were obtained, with an average length of 1,530 bp and N50 of 3001 bp, and 15,792 (29.3%) of them were annotated. A total of 13,610 differentially expressed genes (DEGs) were detected. KEGG pathway analysis showed that multiple pathways related to ovarian development were significantly regulated, such as retinol metabolism, notch signalling pathway, cell cycle, wnt signalling pathway, FoxO signalling pathway, and mTOR signalling pathway. In addition, 12 putative ovarian development-related genes, including FZD9, DDR2, PSMC3IP, CREBBP, DMC1, WBP2NL, DHRS4, SPO11, BCDO2, SDR16C5, CPEB, RDH5, were identified. Our findings will provide a valuable archive for future functional analysis of genes related to ovarian development and future discoveries of the underlying molecular mechanisms of ovarian development.

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