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10 05, 2023;10 (1): 678.

Long- and short-read RNA sequencing from five reproductive organs of boar.

Zhipeng Liu, Xia Zhang, Libin Huang, Hailong Huo, Pei Wang, Weizhen Li, Hongmei Dai, Fuhua Yang, Guowen Fu, Guiying Zhao, Yu H Sun, Jinlong Huo
Author Information
  1. Zhipeng Liu: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China. ORCID
  2. Xia Zhang: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China. ORCID
  3. Libin Huang: Department of Biology, College of Science, Northeastern University, Boston, Massachusetts, 02115, USA. ORCID
  4. Hailong Huo: Yunnan Open University, Kunming, 650500, Yunnan, China.
  5. Pei Wang: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
  6. Weizhen Li: College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
  7. Hongmei Dai: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
  8. Fuhua Yang: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
  9. Guowen Fu: College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
  10. Guiying Zhao: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China. zhaoguiying2006@163.com. ORCID
  11. Yu H Sun: Department of Biology, University of Rochester, Rochester, New York, 14627, USA. yu.sun.rochester@gmail.com. ORCID
  12. Jinlong Huo: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China. jinlonghuo973@163.com. ORCID
PMID: 37798273 DOI: 10.1038/s41597-023-02595-0

Abstract

The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome.

References

  1. Bioinformatics. 2012 Aug 15;28(16):2184-5 [PMID: 22743226]
  2. Bioinformatics. 2014 Apr 1;30(7):923-30 [PMID: 24227677]
  3. Genome Med. 2011 Nov 22;3(11):74 [PMID: 22113004]
  4. Int J Mol Sci. 2020 Jun 25;21(12): [PMID: 32630462]
  5. Gigascience. 2021 Feb 16;10(2): [PMID: 33590861]
  6. Nucleic Acids Res. 2015 Jul 13;43(12):e78 [PMID: 25870408]
  7. Genome Biol. 2018 Mar 23;19(1):40 [PMID: 29571299]
  8. Bioinformatics. 2005 May 1;21(9):1859-75 [PMID: 15728110]
  9. Bioinformatics. 2013 Jan 1;29(1):15-21 [PMID: 23104886]
  10. BMC Genomics. 2019 May 7;20(1):344 [PMID: 31064321]
  11. Nucleic Acids Res. 2013 Apr 1;41(6):e74 [PMID: 23335781]
  12. Genome Biol. 2009;10(3):R25 [PMID: 19261174]
  13. Genome Res. 2018 Feb 9;: [PMID: 29440222]
  14. Nucleic Acids Res. 2010 Aug;38(14):4570-8 [PMID: 20371516]
  15. Nat Methods. 2021 Apr;18(4):366-368 [PMID: 33828273]
  16. Nat Commun. 2021 Mar 1;12(1):1361 [PMID: 33649327]
  17. Nucleic Acids Res. 2013 Jan;41(2):727-37 [PMID: 23221645]
  18. PLoS One. 2016 Oct 5;11(10):e0163962 [PMID: 27706213]
  19. Bioinformatics. 2011 Aug 1;27(15):2156-8 [PMID: 21653522]
  20. Nat Rev Urol. 2016 Jul;13(7):379-86 [PMID: 27245504]
  21. Theriogenology. 2022 Sep 1;189:92-106 [PMID: 35738035]
  22. Sci Data. 2023 Oct 5;10(1):678 [PMID: 37798273]
  23. Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419 [PMID: 33125078]
  24. F1000Res. 2017 Feb 3;6:100 [PMID: 28868132]
  25. Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51 [PMID: 21097890]
  26. Biol Reprod. 2023 Mar 13;108(3):465-478 [PMID: 36477198]
  27. Nucleic Acids Res. 2017 Jul 3;45(W1):W12-W16 [PMID: 28521017]
  28. Anim Genet. 2022 Feb;53(1):146-151 [PMID: 34658041]
  29. Nat Methods. 2017 Apr;14(4):417-419 [PMID: 28263959]
  30. Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89 [PMID: 26542840]

Grants

  1. 32060733/National Natural Science Foundation of China (National Science Foundation of China)
  2. 31460580/National Natural Science Foundation of China (National Science Foundation of China)
  3. 31160439/National Natural Science Foundation of China (National Science Foundation of China)
  4. 31660650/National Natural Science Foundation of China (National Science Foundation of China)
  5. 201808535037/China Scholarship Council (CSC)

MeSH Term

Animals
Male
Alternative Splicing
Genitalia
MicroRNAs
Sequence Analysis, RNA
Swine
Swine, Miniature
Testis
Transcriptome
Polymorphism, Single Nucleotide

Chemicals

MicroRNAs
Dataset Journal Article

Word Cloud

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