DOI QR코드

DOI QR Code

Genealogical Diversity of Endogenous Retrovirus in the Jawless Fish Genome

  • Song Jing (College of Life Sciences, Shaanxi Normal University) ;
  • Wei Jie (College of Environment and Life Sciences, Weinan Normal University) ;
  • Ma Yongping (College of Biological Sciences and Engineering, North Minzu University) ;
  • Sun Yan (College of Life Sciences, Shaanxi Normal University) ;
  • Li Zhi (College of Life Sciences, Shaanxi Normal University)
  • 투고 : 2023.06.12
  • 심사 : 2023.07.19
  • 발행 : 2023.11.28

초록

Retroviral integration into ancient vertebrate genomes left traces that can shed light on the early history of viruses. In this study, we explored the early evolution of retroviruses by isolating nine Spuma endogenous retroviruses (ERVs) and one Epsilon ERV from the genomes of Agnatha and Chondrichthyes. Phylogenetic analysis of protein sequences revealed a striking pattern of co-evolution between jawless fish ERV and their host, while shark ERV underwent ancient cross-class viral transmission with jawless fish, ray-finned fish, and amphibians. Nucleotide sequence analysis showed that jawless fish ERV emerged in the Palaeozoic period, relatively later than ray-finned fish ERV. Moreover, codon analysis suggested that the jawless fish ERV employed an infection strategy that mimics the host codon. The genealogical diversity of ERVs in the jawless fish genome highlights the importance of studying different viral species. Overall, our findings provide valuable insights into the evolution of retroviruses and their interactions with their hosts.

키워드

과제정보

This work was supported by grants from the National Natural Science Foundation of China (No. 31670163) and the Fundamental Research Funds for the Central Universities (GK202302003).

참고문헌

  1. Srinivasachar Badarinarayan S, Sauter D. 2021. Switching sides: how endogenous retroviruses protect us from viral infections. J. Virol. 95: e02299-20.
  2. Robin A Weiss. 2006. The discovery of endogenous retroviruses. Retrovirology 3: 67.
  3. Magiorkinis GA, Katzourakis, Lagiou P. 2017. Roles of endogenous retroviruses in early life events. Trends Microbiol. 25: 876-877. https://doi.org/10.1016/j.tim.2017.09.002
  4. Aris Katzourakis, Robert J Gifford, Michael Tristem, M Thomas P Gilbert, Oliver G Pybus. 2009. Macroevolution of complex retroviruses. Science 325: 1512.
  5. Aiewsakun P, Katzourakis A. 2015. Time dependency of foamy virus evolutionary rate estimates. BMC Evol. Biol. 15: 119.
  6. Aiewsakun P, Simmonds P, Katzourakis. 2019. The first co-opted endogenous foamy viruses and the evolutionary history of reptilian foamy viruses. Viruses 11: 641.
  7. Aris Katzourakis, Robert J Gifford, Michael Tristem, M Thomas P Gilbert, Oliver G Pybus. 2009. Paleovirology reveals the macroevolution of complex retroviruses. Retrovirology 6. 01.
  8. Xiaoman Wei, Yicong Chen, Guangqian Duan, Edward C Holmes, Jie Cui. 2019. A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol. 5: vez001.
  9. Han GZ, Worobey M. 2012. An endogenous foamy-like viral element in the coelacanth genome. PLoS Pathog. 8: e1002790.
  10. J Kimble Frazer, Lance A Batchelor, Diana F Bradley, Kim H Brown, Kimberly P Dobrinski, Charles Lee, et al. 2012. Genomic amplification of an endogenous retrovirus in zebrafish T-cell malignancies. Adv. Hematol. 2012: 627920.
  11. Aiewsakun P, Katzourakis A. 2017. Marine origin of retroviruses in the early Palaeozoic Era. Nat. Commun. 8: 13954.
  12. Han GZ. 2015. Extensive retroviral diversity in shark. Retrovirology 12: 34.
  13. Robert J Gifford, Jonas Blomberg, John M Coffin, Hung Fan, Thierry Heidmann, Jens Mayer, et al. 2018. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 15: 59.
  14. Ruboyianes R, Worobey M. 2016. Foamy-like endogenous retroviruses are extensive and abundant in teleosts.Virus Evol. 2: vew032.
  15. Dong Zhang, Fangluan Gao, Ivan Jakovlic, Hong Zou, Jin Zhang, Wen X Li, et al. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour. 20: 348-355. https://doi.org/10.1111/1755-0998.13096
  16. Milton Tan, Anthony K Redmond, Helen Dooley, Ryo Nozu, Keiichi Sato, Shigehiro Kuraku, et al. 2021. The whale shark genome reveals patterns of vertebrate gene family evolution. Elife 10: e65394.
  17. Jeramiah J Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler, Ning Jiang, Michael S Campbell, et al. 2013. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat. Genet. 45: 415-21, 421e1-2.
  18. Xiaoyu Xu, Huayao Zhao, Zhen Gong, Guan-Zhu Han. 2018. Endogenous retroviruses of non-avian/mammalian vertebrates illuminate diversity and deep history of retroviruses. PLoS Pathog. 14: e1007072.
  19. Jun Bai, Zuo-Zhen Yang, Hao Li, Yun Hong, Dong-Dong Fan, Ai-Fu Lin, et al. 2021. Genome-wide characterization of zebrafish endogenous retroviruses reveals unexpected diversity in genetic organizations and functional potentials. Microbiol. Spectr. 9: e02254-21.
  20. Hayward A, Cornwallis CK, Jern P. 2015. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proc. Natl. Acad. Sci. USA 112: 464-469. https://doi.org/10.1073/pnas.1414980112
  21. William M Switzer, Marco Salemi, Vedapuri Shanmugam, Feng Gao, Mian-Er Cong, Carla Kuiken , et al. 2005. Ancient co-speciation of simian foamy viruses and primates. Nature 434: 376-380. https://doi.org/10.1038/nature03341
  22. Lin Tian, Xuejuan Shen, Robert W Murphy, Yongyi Shen. 2018. The adaptation of codon usage of +ssRNA viruses to their hosts. Infect. Genet. Evol. 63: 175-179. https://doi.org/10.1016/j.meegid.2018.05.034
  23. Kunlakanya Jitobaom, Supinya Phakaratsakul, Thanyaporn Sirihongthong, Sasithorn Chotewutmontri, Prapat Suriyaphol, Ornpreya Suptawiwat, et al. 2020. Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. Heliyon 6: e03915.
  24. Pandit A, Sinha S. 2011. Differential trends in the codon usage patterns in HIV-1 genes. PLoS One 6: e28889.
  25. Mijia Lu, Zijie Zhang, Miaoge Xue, Boxuan Simen Zhao, Olivia Harder, Anzhong Li, et al. 2020. N6-methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I. Nat. Microbiol. 5: 584-598. https://doi.org/10.1038/s41564-019-0653-9