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Cited by 5Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

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Discovery of novel non-retroviral endogenous viral elements reveals their long-term integration history in spiders

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Hu, Hengrui, Vlak, Just M., Hu, Zhihong, Wang, Manli·2025·Nature Communications
DOI 10.1038/s41467-025-61035-2PMC PMC12219104

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Abstract

Abstract Endogenous viral elements (EVEs) are widespread in the genomes of various organisms and have played a crucial role in evolution. Historically, research on EVEs primarily focused on those derived from retroviruses; however, the significance of non-retroviral EVEs (nrEVEs) has gradually gained recognition. In this study, we employed a novel approach that combines protein structure prediction with sequence analysis to identify a large group of previously unrecognized nrEVEs across spider genomes. Additionally, we identified nrEVE-related messenger RNAs, microRNAs, and PIWI-interacting RNAs in spiders, suggesting that these nrEVEs may be functionally active. We also experimentally confirmed the presence of spider nrEVEs and their transcripts in individual spiders. Evolutionary analysis suggests that these spider nrEVEs originated from an ancestral nuclear arthropod large DNA virus (NALDV) belonging to the order Lefavirales, class Naldaviricetes, approximately 270 million years ago. The integration of these nrEVEs occurred prior to the last common ancestor of the Araneae, indicating a long-term co-evolutionary relationship between these nrEVEs and spiders. Our findings reveal a novel group of nrEVEs and provide valuable insights into their evolutionary relationship with arthropods.

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Metadata

Authors
Hu, H., Vlak, J. M., Hu, Z., & Wang, M.
Affiliations
  • Chinese Academy of Sciences (CN)
  • Wageningen University & Research (NL)
Corresponding author
Wang, Manli
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-07-01
Volume
16
Issue
1
Pages
6006-6006
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-61035-2
PMC
PMC12219104
OpenAlex
W4411847105
Cited by
5
References
5
Citations by year
2026: 4 · 2025: 1
FWCI
2.70
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by-nc-nd)
Funders
National Natural Science Foundation of China (32370182, 37277104, 32170156)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
endogenous viral elements, spiders, siRNA, piRNA, arthropod evolution, genome evolution
MeSH terms
Animals, DNA Viruses, Phylogeny, Spiders, Virus Integration, Evolution, Molecular, RNA, Small Interfering

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