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Background  Sexual precocity is a common biological phenomenon in animal species. A large number of precocity individuals were identified in Chinese mitten crab  Eriocheir sinensis , which caused huge economic loss annually. However, the underlying genetic basis of precocity in  E. sinensis  remains unclear to date.    Results  In this study, morphological and histological observation and comparative transcriptome analysis were conducted among different stages of precocious one-year-old and normal two-year-old sexually mature  E. sinensis . The expression profiles of the ovary, hepatopancreas, and eyestalk tissues were presented and compared. Genes associated with lipid metabolic process, lipid transport, vitelline membrane formation, vitelline synthesis, and neuropeptide hormone-related genes were upregulated in the ovary, hepatopancreas, and eyestalk of precocious  E. sinensis . Our results indicated that the eyestalk was involved in the neuroendocrine system providing neuropeptide hormones that may induce vitellogenesis in the hepatopancreas and further stimulate ovary development. The hepatopancreas is a site for energy storage and vitellogenin synthesis, and it may assist oogenesis through lipid transport in precocious  E. sinensis .    Conclusion  We provided not only an effective and convenient phenotype measurement method for the identification of potential precocious  E. sinensis  detection but also valuable genetic resources and novel insights into the molecular mechanism of precocity in  E. sinensis . The genetic basis of precocity in  E. sinensis  is an integrated gene regulatory network of eyestalk, hepatopancreas, and ovary tissues.    Electronic supplementary material  The online version of this article (10.1186/s12863-019-0716-1) contains supplementary material, which is available to authorized users.

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Tissue expression profiles unveil the gene interaction of hepatopancreas, eyestalk, and ovary in the precocious female Chinese mitten crab, Eriocheir sinensis