CoChat
Sign Up
PreprintCited by 5Chromosomal and Genetic VariationsEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Pre-Cambrian origin of envelope -carrying retrotransposons in metazoans

Open access
Chary, Shashank, Hayashi, Rippei·2023·eLife
DOI 10.1101/2023.10.26.564294PMC PMC13524379

Preprint — published as 10.7554/elife.108449 · Paper page

Open this paper in CoChat — free account

Abstract

Retrotransposons or endogenous retroviruses (ERVs) essentially carry open reading frames of gag and pol , which are utilized to selfishly replicate themselves in the host germline genome. One rare example of ERVs that additionally carry envelope genes is Ty3/gypsy errantiviruses in Drosophila. Though they are structurally analogous to retroviruses, it remained unclear whether envelope -containing Ty3/gypsy elements represent recent, lineage-specific acquisitions of viral fusogens or an ancient association between retrotransposons and envelope -like genes. We systematically searched for intact envelope -containing ERVs that are homologous to Ty3/gypsy in invertebrate metazoan genomes and found that they are widespread across taxa including ancient animals such as cnidarians, ctenophores and tunicates. Many elements occur as multiple highly similar copies in their respective genomes, consistent with recent genomic expansion in some host lineages. Envelope genes are classified into those that resemble glycoprotein F from paramyxoviruses and glycoprotein B from herpesviruses, and both types are equally abundant and widespread. Phylogenetic and structural analyses revealed that envelope genes have largely diverged with pol genes as well as with the host organisms throughout their evolutionary history and recombined infrequently, suggesting that the envelope acquisition to ERVs is ancient and likely dates to before the split of bilaterian and non-bilaterian animals in Pre-Cambrian era.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.10.26.564294

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

  • Highly accurate protein structure prediction with AlphaFold

    Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · cited 1×

    “We then analysed trimeric configurations of these ectodomains from representative errantiviruses from the phylogenetic tree using Alphafold 2 (Jumper et al. 2021).”

Flagged first, then by citations

Research works printed but not linked: 62

  1. 10.1128/JVI.00280-12 · DOI
  2. 10.1016/j.sbi.2009.02.012 · DOI
  3. 10.1186/s13100-017-0090-3 · DOI
  4. 2020, Crystal structure of Mokola virus glycoprotein in its post-fusion conformation, PLoS Pathog, 16, e1008383, 10.1371/journal.ppat.1008383 · DOI
  5. Boeke JD , Eickbush TH , Sandmeyer SB , Voytas DF . 2000. Metaviridae. in Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses (eds. MHV van Regenmortel , CM Fauquet , DHL Bishop , EB Carstens , MK Estes , SM Lemon , J Maniloff , MA Mayo , DJ McGeoch , CR Pringle , et al.), pp. 359–367. Academic Press, New York.
  6. 10.1186/1742-4690-2-57 · DOI
  7. 10.1016/j.cell.2007.01.043 · DOI · Paper page
  8. 10.1371/journal.ppat.1005227 · DOI
  9. 10.1038/nrg.2016.139 · DOI
  10. 10.1038/nrmicro2548 · DOI
  11. 10.1038/nrg2640 · DOI
  12. 10.1038/s41594-019-0308-9 · DOI
  13. 10.1016/j.str.2004.02.032 · DOI · Paper page
  14. 10.1186/1471-2148-9-205 · DOI
  15. 10.3389/fgene.2020.542437 · DOI
  16. 10.1016/j.virusres.2007.12.010 · DOI
  17. 2014, Retroviral Integrase Structure and DNA Recombination Mechanism, Microbiol Spectr, 2, 1
  18. 10.1186/s13100-019-0157-4 · DOI
  19. 10.1093/molbev/msh057 · DOI
  20. 10.1186/gb-2004-5-6-225 · DOI
  21. 10.1016/j.coviro.2017.06.006 · DOI
  22. 10.1073/pnas.1915400117 · DOI
  23. 10.1126/science.1126548 · DOI
  24. Jambunathan N , Clark CM , Musarrat F , Chouljenko VN , Rudd J , Kousoulas KG . 2021. Two Sides to Every Story: Herpes Simplex Type-1 Viral Glycoproteins gB, gD, gH/gL, gK, and Cellular Receptors Function as Key Players in Membrane Fusion. Viruses 13. · DOI
  25. 10.1128/JVI.00011-11 · DOI
  26. 10.1016/j.gene.2004.12.017 · DOI
  27. 10.1128/JVI.74.22.10658-10669.2000 · DOI
  28. 10.1128/JVI.76.12.6073-6082.2002 · DOI
  29. 10.1101/gr.185101 · DOI · Paper page
  30. 10.1101/gr.145000 · DOI
  31. 10.1007/978-3-642-38919-1_4 · DOI
  32. 10.1038/S41592-022-01488-1 · DOI · Paper page
  33. 10.1128/JVI.02715-09 · DOI
  34. 10.1073/pnas.2220392121 · DOI
  35. 10.1016/S0965-1748(02)00088-7 · DOI
  36. 10.1002/j.1460-2075.1994.tb06760.x · DOI
  37. 10.1101/gr.073486.107 · DOI
  38. Rodriguez F , Kenefick AW , Arkhipova IR . 2017. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. Viruses 9. · DOI
  39. 10.1186/1471-2148-1-1 · DOI
  40. Sacco MA , Lau J , Godinez-Vidal D , Kaloshian I . 2022. Non-canonical nematode endogenous retroviruses resulting from RNA virus glycoprotein gene capture by a metavirus. J Gen Virol 103. · DOI
  41. 2022, Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders, PLoS Genet, 18, e1010458, 10.1371/journal.pgen.1010458 · DOI
  42. 10.1101/gad.8.17.2046 · DOI
  43. 10.1242/dev.124.14.2789 · DOI
  44. 10.1093/molbev/mss181 · DOI
  45. 10.4161/mge.19234 · DOI
  46. 10.1186/s12859-019-3019-7 · DOI · Paper page
  47. 10.1038/nature04841 · DOI · Paper page
  48. 10.1186/1471-2148-1-3 · DOI
  49. 10.1186/s13100-020-00224-w · DOI
  50. 2025, A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats, Mob DNA, 16, 4, 10.1186/s13100-024-00337-6 · DOI
  51. 10.1093/molbev/msh207 · DOI
  52. Vollmer B , Pražák V , Vasishtan D , Jefferys EE , Hernandez-Duran A , Vallbracht M , Klupp BG , Mettenleiter TC , Backovic M , Rey FA et al. 2020. The prefusion structure of herpes simplex virus glycoprotein B. Sci Adv 6. · DOI
  53. 10.1093/molbev/msaa180 · DOI
  54. 10.1093/molbev/msaa272 · DOI
  55. 2022, A Missing Link between Retrotransposons and Retroviruses, mBio, 13, e0018722, 10.1128/mbio.00187-22 · DOI
  56. Wang W , Zhao H , Han GZ . 2020. Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors. J Virol 94. · DOI
  57. Wanner NM , Faulk C . 2021. Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes (Basel ) 12. · DOI
  58. 10.1038/nrg2165 · DOI
  59. 10.1007/PL00000937 · DOI
  60. 10.1093/oxfordjournals.molbev.a040521 · DOI
  61. 10.1002/j.1460-2075.1990.tb07536.x · DOI · Paper page
  62. 10.1186/s12977-020-00541-1 · DOI

Metadata

Authors
Chary, S., & Hayashi, R.
Affiliations
Australian National University (AU)
Corresponding author
Hayashi, Rippei
ORCID
Venue
eLife
Publisher
openRxiv
Published
2023-10-28
Volume
14
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2023.10.26.564294
PMC
PMC13524379
OpenAlex
W4416864306
Cited by
5
References
1
Citations by year
2026: 3 · 2025: 2
Type
posted content
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • eLife (acceptedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
Australian Research Council (DP210102385)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
retrotransposons, endogenous retroviruses, env gene, animal evolution, Cnidaria, ctenophores, tunicates, glycoprotein B, pol gene, recombination, host-virus coevolution
MeSH terms
Animals, Invertebrates, Phylogeny, Retroelements, Evolution, Molecular, Endogenous Retroviruses

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review