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BackgroundEstrous cycle is one of female characteristics after sexual maturity, including estrus (ES) and diestrus (DS) stages. Estrous cycle is important in female physiology and its disorder may lead to diseases. In the latest years, effects of non-coding RNAs and mRNA on estrous cycle start to arouse much concern, however, a whole transcriptome analysis among non-coding RNAs and mRNA has not been reported.ResultsHere we report a whole transcriptome analysis of goat ovary in estrus and diestrus periods. Estrus synchronization was conducted to induce the estrus phase and on day 32, the goats naturally shifted into diestrus stage. The ovary RNA of estrus and diestrus stages was respectively collected to perform RNA-sequencing. Then the circular RNA; microRNA; long non-coding RNA; mRNA databases of goat ovary were acquired, and the differentially expressions between estrus and diestrus stages were screened to construct circRNA-miRNA-mRNA/lncRNA and lncRNA-miRNA/mRNA networks, thus providing potential pathways that involved in the regulation of estrous cycle. Differentially expressed mRNAs, such as MMP9, TIMP1, 3BHSD and PTGIS, and differentially expressed microRNAs, such as miR-21-3p，miR-202-3p and miR-223-3p, which play key roles in estrous cycle regulation were extracted from the network.ConclusionsOur data provided the miRNA, circRNA, lncRNA and mRNA databases of goat ovary and each differentially expressed profile between ES and DS. Networks among differentially expressed miRNAs, circRNAs, lncRNAs and mRNAs were constructed to provide valuable resources for the study of estrous cycle and related diseases.

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