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Genes & Genomics

, Volume 39, Issue 10, pp 1083–1094 | Cite as

Strand-specific RNA sequencing in pig testes identifies developmentally regulated genes and circular RNAs

  • Maoliang Ran
  • Bo Weng
  • Bin ChenEmail author
  • Maisheng Wu
  • Changqing He
  • Shanwen Zhang
Research Article

Abstract

Testicular development and spermatogenesis are strictly regulated with the complex interactions between several cell types in testis. However, the limited availability of genomic and molecular information limits our understanding of this complex physiological process. In this study, we characterized the transcriptome between immature (30-day-old) and mature (180-day-old) pig testes using RNA-seq technology. 24,469 known coding gene transcripts corresponding to 20,566 genes were mapped in these two developmental stages, 3,328 genes were differentially expressed, and numerous novel transcripts and alternative splicing events were also identified. Ten differentially expressed genes were validated by measuring the relative expression using real-time quantitative polymerase chain reaction (PCR). 125 Gene Ontology (GO) terms were significantly enriched, and most of them involved in GO terms related to male reproduction, testicular development, and spermatogenesis. In addition, this study also represented the prediction of 10,000 circRNAs, as well as the validation of six pig circRNAs using Find_cric algorithm. Our study substantially expanded our knowledge about the transcriptomic profile of immature and mature pig testes, and provided a useful resource to study the mechanisms of pig testis development and spermatogenesis at the molecular level.

Keywords

Transcriptomic profile CircRNAs Developmental Testis Pig RNA-seq 

Notes

Acknowledgements

This work was financially supported by China Agriculture Research System (CARS-36), Excellent Doctoral Dissertation Cultivating Fund of Hunan Agricultural University (YB2015001), and Hunan Provincial Innovation Foundation for Postgraduate (CX2015B251).

Author contributions

The present study was conceived by Bin Chen and Maoliang Ran. Pig testis samples were collected by Bo Weng, Maisheng Wu, Changqing He, and Shanwen Zhang. Data analysis and bioinformatics analysis was finished by Maoliang Ran and Bo Weng. Manuscript was written by Maoliang Ran and Bo Weng. All authors had read and approved the final manuscript. The authors would like to thank Jie Yin for critical reading of the manuscript.

Compliance with ethical standards

Conflict of interest

Maoliang Ran declares that he/she does not have conflict of interest. Bo Weng declares that he/she does not have conflict of interest. Bin Chen declares that he/she does not have conflict of interest. Maisheng Wu declares that he/she does not have conflict of interest. Changqing He declares that he/she does not have conflict of interest. Shanwen Zhang declares that he/she does not have conflict of interest.

Ethical approval

Methods were performed according to the guidelines of the Declaration of Helsinki. Procedures involving animals were approved by the animal welfare committee of College of Animal Science and Technology, Hunan Agriculture University.

Supplementary material

13258_2017_576_MOESM1_ESM.png (80 kb)
Fig. S1—12 significantly enriched GO terms formed a directed acyclic graph structure in regulating pig testes development and spermatogenesis (PNG 80 KB)
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Fig. S2—The venn diagram of circRNAs between D30 and D180 libraries (TIF 1136 KB)
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Fig. S3—The TPM density distribution results of circRNAs from D30 and D180 libraries (TIF 1252 KB)
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Supplementary material 6 (XLS 12 KB)
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Supplementary material 12 (XLS 13 KB)

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Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Maoliang Ran
    • 1
    • 3
  • Bo Weng
    • 1
    • 3
  • Bin Chen
    • 1
    • 3
    Email author
  • Maisheng Wu
    • 2
  • Changqing He
    • 1
    • 3
  • Shanwen Zhang
    • 2
  1. 1.College of Animal Science and TechnologyHunan Agriculture UniversityChangshaChina
  2. 2.Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic ProductXiangtanChina
  3. 3.Hunan Provincial Key Laboratory for Genetic Improvement of Domestic AnimalChangshaChina

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