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Research article
Xuejun Li
Corresponding Author
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Abstract Background: Gonad is the major factor affecting the animal reproduction. The regulation mechanism of protein coding genes expression involved reproduction is still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction had been investigated in some species. However, the regulation patterns of miRNA and lncRNA in sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of the soft-shelled turtle, Pelodiscus sinensis. Results: We identified 10 796 mature miRNAs, 44 678 mRNAs, and 58 923 lncRNAs in the testis and ovary. A total of 16 817 target genes were identified for miRNAs. Of these, 11 319 mRNAs, 10 495 lncRNAs, and 633 miRNAs were expressed differently. The predicted target genes of these differential expression (DE) miRNAs and lncRNAs included genes related to reproduction regulation. Furthermore, we found that 5 408 DElncRNAs and 186 DE miRNAs showed sex-specific expression. Of these, 3 miRNAs and 917 lncRNAs were testis specific and 186 DEmiRNAs and 4 491 DElncRNAs were ovary specific. We constructed compete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 273 DEmRNAs, 5 730 DEmiRNAs, and 2 945 DElncRNAs. The target genes for the different expressed of miRNAs and lncRNAs included Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1, etc. Conclusions: In animals, miRNA and lncRNA regulate the reproduction process, including the regulation of oocyte maturation and spermatogenesis. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproduction traits for aquaculture.
Keywords
gonad, miRNA, lncRNA, ceRNA
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CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 15 Jun, 2020
Submission checks complete
On 19 Jun, 2019
No comments provided
Editorial decision: Minor revision
On 11 Jun, 2020
Editor assigned
On 20 Apr, 2020
Submission checks complete
On 19 Apr, 2020
Editor invited
On 19 Apr, 2020
No comments provided
Editorial decision: Minor revision
On 17 Apr, 2020
Editor assigned
On 14 Apr, 2020
Submission checks complete
On 13 Apr, 2020
Editor invited
On 13 Apr, 2020
No comments provided
Submission checks complete
On 07 Apr, 2020
Editorial decision: Minor revision
On 07 Apr, 2020
No comments provided
Editorial decision: Minor revision
On 01 Apr, 2020
Review #1 received
Received 26 Mar, 2020
Reviewer #1 agreed
On 15 Mar, 2020
Reviewers invited
Invitations sent on 08 Jan, 2020
Editor assigned
On 18 Nov, 2019
Editor invited
On 17 Nov, 2019
Submission checks complete
On 16 Nov, 2019
No comments provided
Editorial decision: Major revision
On 27 Oct, 2019
Review #2 received
Received 15 Oct, 2019
Review #1 received
Received 03 Oct, 2019
Reviewer #2 agreed
On 01 Oct, 2019
Reviewer #1 agreed
On 01 Oct, 2019
Editor assigned
On 30 Sep, 2019
Reviewers invited
Invitations sent on 30 Sep, 2019
Submission checks complete
On 29 Sep, 2019
Editor invited
On 29 Sep, 2019
Version 1
Posted 02 Jul, 2019
No comments provided
Review #2 received
Received 30 Aug, 2019
Editorial decision: Major revision
On 30 Aug, 2019
Review #1 received
Received 18 Aug, 2019
Reviewer #2 agreed
On 16 Aug, 2019
Reviewers invited
Invitations sent on 13 Aug, 2019
Reviewer #1 agreed
On 13 Aug, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 13 Jun, 2019
Editor assigned
On 13 Jun, 2019
First submitted
On 11 Jun, 2019
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Xuejun Li
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 15 Jun, 2020
Submission checks complete
On 19 Jun, 2019
No comments provided
Editorial decision: Minor revision
On 11 Jun, 2020
Editor assigned
On 20 Apr, 2020
Submission checks complete
On 19 Apr, 2020
Editor invited
On 19 Apr, 2020
No comments provided
Editorial decision: Minor revision
On 17 Apr, 2020
Editor assigned
On 14 Apr, 2020
Submission checks complete
On 13 Apr, 2020
Editor invited
On 13 Apr, 2020
No comments provided
Submission checks complete
On 07 Apr, 2020
Editorial decision: Minor revision
On 07 Apr, 2020
No comments provided
Editorial decision: Minor revision
On 01 Apr, 2020
Review #1 received
Received 26 Mar, 2020
Reviewer #1 agreed
On 15 Mar, 2020
Reviewers invited
Invitations sent on 08 Jan, 2020
Editor assigned
On 18 Nov, 2019
Editor invited
On 17 Nov, 2019
Submission checks complete
On 16 Nov, 2019
No comments provided
Editorial decision: Major revision
On 27 Oct, 2019
Review #2 received
Received 15 Oct, 2019
Review #1 received
Received 03 Oct, 2019
Reviewer #2 agreed
On 01 Oct, 2019
Reviewer #1 agreed
On 01 Oct, 2019
Editor assigned
On 30 Sep, 2019
Reviewers invited
Invitations sent on 30 Sep, 2019
Submission checks complete
On 29 Sep, 2019
Editor invited
On 29 Sep, 2019
Version 1
Posted 02 Jul, 2019
No comments provided
Review #2 received
Received 30 Aug, 2019
Editorial decision: Major revision
On 30 Aug, 2019
Review #1 received
Received 18 Aug, 2019
Reviewer #2 agreed
On 16 Aug, 2019
Reviewers invited
Invitations sent on 13 Aug, 2019
Reviewer #1 agreed
On 13 Aug, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 13 Jun, 2019
Editor assigned
On 13 Jun, 2019
First submitted
On 11 Jun, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Abstract Background: Gonad is the major factor affecting the animal reproduction. The regulation mechanism of protein coding genes expression involved reproduction is still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction had been investigated in some species. However, the regulation patterns of miRNA and lncRNA in sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of the soft-shelled turtle, Pelodiscus sinensis. Results: We identified 10 796 mature miRNAs, 44 678 mRNAs, and 58 923 lncRNAs in the testis and ovary. A total of 16 817 target genes were identified for miRNAs. Of these, 11 319 mRNAs, 10 495 lncRNAs, and 633 miRNAs were expressed differently. The predicted target genes of these differential expression (DE) miRNAs and lncRNAs included genes related to reproduction regulation. Furthermore, we found that 5 408 DElncRNAs and 186 DE miRNAs showed sex-specific expression. Of these, 3 miRNAs and 917 lncRNAs were testis specific and 186 DEmiRNAs and 4 491 DElncRNAs were ovary specific. We constructed compete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 273 DEmRNAs, 5 730 DEmiRNAs, and 2 945 DElncRNAs. The target genes for the different expressed of miRNAs and lncRNAs included Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1, etc. Conclusions: In animals, miRNA and lncRNA regulate the reproduction process, including the regulation of oocyte maturation and spermatogenesis. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproduction traits for aquaculture.
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
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