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Novel miRNA identification and comparative profiling of miRNA regulations revealed important pathways in Jinding duck ovaries by small RNA sequencing

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Abstract

Functional studies have revealed miRNAs play pivotal roles in ovulation and ovary development in mammalians, whereas little is known about the miRNA function in ducks. In this study, miRNA deep sequencing in the ovary tissues was carried out to obtain the miRNA profile from ovaries before oviposition (BO) and after oviposition (AO) in Jinding duck. Overall, an average of 23,128,075 and 26,020,523 reads were identified in the BO and AO samples, respectively, and 6739 miRNAs were identified from them through further mapping and analysis. Besides, 1570 miRNAs were identified as differentially expressed miRNAs compared with BO, including 493 miRNAs up-regulated and 1077 down-regulated in AO. Moreover, 2291 target genes were predicted from 443 significantly differentially expressed miRNAs. In addition, GO and KEGG pathway analysis indicated that target genes were enriched in some basic cell metabolism pathways as well as the productive pathways such as MAPK signaling pathway, gonadotropin-releasing hormone signaling pathway, TGF-beta signaling pathway which had been significantly changed. Our results helped to replenish the duck miRNA database and illustrate the potential mechanism of miRNA function in duck ovary development and reproduction process.

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Availability of data and materials

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

This work was supported by the National key research and development program (No. 2016YFD0500510).

Author information

Conceptualization: MQ and ZZ. Data curation: CY and XX. Formal analysis: XJ and HD. Funding acquisition: MQ and ZZ. Investigation: CY, QL and HL. Methodology: XX, WG and CY. Software: HP and BX. Writing—original draft: CY and XX. Writing—review & editing: JC, XS, LY and CH. All authors read and approved the final manuscript.

Correspondence to Mohan Qiu or Zengrong Zhang.

Ethics declarations

Ethics approval

The animal experiment in this study was approved via the animal care and ethical committee of Sichuan Animal Science Academy. All ducks were carried out on the guidelines of China legislations on the ethical use and care of laboratory animals.

Consent for publication

The authors declare that there is no conflict of interest regarding the publication of this paper.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Fig. 1. Per base sequence quality of 6 sRNA sequencing. (JPEG 2746 kb)

Supplemental Fig. 2. The number of reads mapped to mallard, chicken and zebra finch and identified as potential novel miRNAs. AO-1 to AO-3 samples represents 3 biological replicates of Jinding duck after oviposition. BO-1 to BO-3 samples represents 3 biological replicates before oviposition. (JPEG 177 kb)

Supplemental Fig. 3. miRNA targeted gene prediction based on RNAhybrid and Miranda database. A total of 2291 genes were predicted by the intersection results between two prediction tools. (JPEG 338 kb)

Supplementary material 4 (DOCX 14 kb)

Supplementary material 5 (XLSX 503 kb)

Supplementary material 6 (XLSX 161 kb)

Supplementary material 7 (XLSX 168 kb)

Supplementary material 8 (XLSX 213 kb)

Supplementary material 9 (XLSX 32 kb)

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Yang, C., Xiong, X., Jiang, X. et al. Novel miRNA identification and comparative profiling of miRNA regulations revealed important pathways in Jinding duck ovaries by small RNA sequencing. 3 Biotech 10, 38 (2020). https://doi.org/10.1007/s13205-019-2015-y

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Keywords

  • Duck ovaries
  • Oviposition
  • miRNA
  • Small RNA sequencing