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Gao Y, Suding Z, Wang L, et al. Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. Parasit Vectors. 2021;14(1):502doi: 10.1186/s13071-021-05015-7.
Gao, Y., Suding, Z., Wang, L., Liu, D., Su, S., Xu, J., Hu, J., & Tao, J. (2021). Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. Parasites & vectors, 14(1), 502. https://doi.org/10.1186/s13071-021-05015-7
Gao, Yang, et al. "Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing." Parasites & vectors vol. 14,1 (2021): 502. doi: https://doi.org/10.1186/s13071-021-05015-7
Gao Y, Suding Z, Wang L, Liu D, Su S, Xu J, Hu J, Tao J. Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. Parasit Vectors. 2021 Sep 27;14(1):502. doi: 10.1186/s13071-021-05015-7. PMID: 34579769; PMCID: PMC8474931.
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Parasit Vectors. 2021 Sep 27;14(1):502. doi: 10.1186/s13071-021-05015-7.

Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing.

Parasites & vectors

Yang Gao, Zeyang Suding, Lele Wang, Dandan Liu, Shijie Su, Jinjun Xu, Junjie Hu, Jianping Tao

Affiliations

  1. College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
  2. Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
  3. Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
  4. Biology Department, Yunnan University, Kunming, 650500, China.
  5. College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. [email protected].
  6. Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. [email protected].
  7. Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China. [email protected].

PMID: 34579769 PMCID: PMC8474931 DOI: 10.1186/s13071-021-05015-7

Abstract

BACKGROUND: Eimeria necatrix is one of the most pathogenic parasites, causing high mortality in chickens. Although its genome sequence has been published, the sequences and complete structures of its mRNA transcripts remain unclear, limiting exploration of novel biomarkers, drug targets and genetic functions in E. necatrix.

METHODS: Second-generation merozoites (MZ-2) of E. necatrix were collected using Percoll density gradients, and high-quality RNA was extracted from them. Single-molecule real-time (SMRT) sequencing and Illumina sequencing were combined to generate the transcripts of MZ-2. Combined with the SMRT sequencing data of sporozoites (SZ) collected in our previous study, the transcriptome and transcript structures of E. necatrix were studied.

RESULTS: SMRT sequencing yielded 21,923 consensus isoforms in MZ-2. A total of 17,151 novel isoforms of known genes and 3918 isoforms of novel genes were successfully identified. We also identified 2752 (SZ) and 3255 (MZ-2) alternative splicing (AS) events, 1705 (SZ) and 1874 (MZ-2) genes with alternative polyadenylation (APA) sites, 4019 (SZ) and 2588 (MZ-2) fusion transcripts, 159 (SZ) and 84 (MZ-2) putative transcription factors (TFs) and 3581 (SZ) and 2039 (MZ-2) long non-coding RNAs (lncRNAs). To validate fusion transcripts, reverse transcription-PCR was performed on 16 candidates, with an accuracy reaching up to 87.5%. Sanger sequencing of the PCR products further confirmed the authenticity of chimeric transcripts. Comparative analysis of transcript structures revealed a total of 3710 consensus isoforms, 815 AS events, 1139 genes with APA sites, 20 putative TFs and 352 lncRNAs in both SZ and MZ-2.

CONCLUSIONS: We obtained many long-read isoforms in E. necatrix SZ and MZ-2, from which a series of lncRNAs, AS events, APA events and fusion transcripts were identified. Information on TFs will improve understanding of transcriptional regulation, and fusion event data will greatly improve draft versions of gene models in E. necatrix. This information offers insights into the mechanisms governing the development of E. necatrix and will aid in the development of novel strategies for coccidiosis control.

© 2021. The Author(s).

Keywords: Alternative polyadenylation; Alternative splicing; Eimeria necatrix; Fusion transcripts; Long non-coding RNAs; Novel genes; Transcription factors

References

  1. Parasit Vectors. 2014 Jan 15;7:27 - PubMed
  2. Nat Rev Genet. 2019 Oct;20(10):599-614 - PubMed
  3. PLoS Pathog. 2015 May 27;11(5):e1004905 - PubMed
  4. J Parasitol. 2010 Feb;96(1):95-102 - PubMed
  5. Parasitology. 2012 Oct;139(12):1553-61 - PubMed
  6. Nucleic Acids Res. 2005 Jul 21;33(13):3994-4006 - PubMed
  7. Vet Parasitol. 2018 Mar 15;252:35-46 - PubMed
  8. Cell. 2009 Aug 21;138(4):673-84 - PubMed
  9. Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89 - PubMed
  10. Front Cell Infect Microbiol. 2019 May 14;9:132 - PubMed
  11. Genome Res. 2012 Jun;22(6):1184-95 - PubMed
  12. New Phytol. 2018 Jan;217(1):163-178 - PubMed
  13. Parasit Vectors. 2019 Jun 4;12(1):285 - PubMed
  14. Methods Mol Biol. 2018;1783:209-241 - PubMed
  15. PLoS Pathog. 2010 Oct 28;6(10):e1001165 - PubMed
  16. PLoS One. 2018 Aug 30;13(8):e0203317 - PubMed
  17. BMC Bioinformatics. 2014 Sep 19;15:311 - PubMed
  18. Parasit Vectors. 2017 Aug 16;10(1):388 - PubMed
  19. Science. 2010 Jan 1;327(5961):94-7 - PubMed
  20. PLoS One. 2015 Jul 15;10(7):e0132628 - PubMed
  21. Nucleic Acids Res. 2017 May 19;45(9):5061-5073 - PubMed
  22. Bioinformatics. 2014 Dec 15;30(24):3506-14 - PubMed
  23. Parasit Vectors. 2020 Apr 3;13(1):167 - PubMed
  24. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37 - PubMed
  25. Gene. 2001 Jul 11;272(1-2):209-18 - PubMed
  26. Plant Cell. 2014 Sep;26(9):3472-87 - PubMed
  27. Clin Microbiol Rev. 2002 Jan;15(1):58-65 - PubMed
  28. Parasite. 2017;24:50 - PubMed
  29. Genome Res. 2010 May;20(5):646-54 - PubMed
  30. Trends Parasitol. 2014 Jan;30(1):12-9 - PubMed
  31. Vet Parasitol. 2021 Aug;296:109480 - PubMed
  32. Nat Biotechnol. 2015 Jul;33(7):736-42 - PubMed
  33. Genome Res. 2014 Oct;24(10):1676-85 - PubMed
  34. Avian Pathol. 1997;26(2):221-44 - PubMed
  35. Mol Biochem Parasitol. 2020 Nov;240:111318 - PubMed
  36. Parasitol Res. 2019 Mar;118(3):783-792 - PubMed
  37. J Parasitol. 1987 Oct;73(5):993-7 - PubMed
  38. J Invertebr Pathol. 2020 Oct;176:107475 - PubMed
  39. Wiley Interdiscip Rev RNA. 2016 Nov;7(6):811-823 - PubMed
  40. Avian Dis. 2005 Mar;49(1):1-8 - PubMed
  41. Int J Parasitol. 2001 Jan;31(1):1-8 - PubMed
  42. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W345-9 - PubMed
  43. BMC Genomics. 2018 Jan 23;19(1):73 - PubMed
  44. BMC Genomics. 2015 Feb 18;16:94 - PubMed
  45. Genes (Basel). 2019 May 31;10(6): - PubMed
  46. DNA Res. 2019 Aug 1;26(4):301-311 - PubMed
  47. Genome Biol. 2019 Aug 1;20(1):151 - PubMed
  48. Genome Biol. 2011 Jun 20;12(6):R56 - PubMed
  49. Parasitol Res. 2010 Jun;107(1):187-8 - PubMed
  50. Bioinformatics. 2005 May 1;21(9):1859-75 - PubMed
  51. Genome Res. 2012 Sep;22(9):1760-74 - PubMed
  52. Cell. 2014 Nov 20;159(5):1110-1125 - PubMed
  53. Nat Med. 2015 Nov;21(11):1253-61 - PubMed
  54. J Mol Biol. 2005 Feb 11;346(1):29-42 - PubMed
  55. Sci Rep. 2018 Oct 9;8(1):15017 - PubMed
  56. Plant Biotechnol J. 2019 Jan;17(1):206-219 - PubMed
  57. G3 (Bethesda). 2019 Jun 5;9(6):1831-1838 - PubMed
  58. Gene. 2010 May 1;455(1-2):32-42 - PubMed
  59. Nat Commun. 2016 Jun 24;7:11708 - PubMed
  60. Nucleic Acids Res. 2013 Sep;41(17):e166 - PubMed
  61. Poult Sci. 2020 May;99(5):2444-2451 - PubMed
  62. Oncogene. 1996 Jul 18;13(2):223-35 - PubMed
  63. Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85 - PubMed
  64. Parasitol Res. 2019 Jun;118(6):1701-1710 - PubMed
  65. Plant Mol Biol. 2019 Feb;99(3):219-235 - PubMed
  66. Nat Commun. 2016 Jun 24;7:11706 - PubMed
  67. BMC Plant Biol. 2018 Nov 26;18(1):300 - PubMed
  68. Sci Rep. 2017 Sep 5;7(1):10508 - PubMed
  69. Nucleic Acids Res. 2015 Jan;43(Database issue):D76-81 - PubMed
  70. Expert Rev Vaccines. 2006 Feb;5(1):143-63 - PubMed
  71. Plant J. 2017 Aug;91(4):684-699 - PubMed
  72. Nat Struct Mol Biol. 2013 Mar;20(3):300-7 - PubMed
  73. RNA. 2015 Sep;21(9):1521-31 - PubMed

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