A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

Blanco-Melo, Daniel; Campbell, Matthew A.; Zhu, Henan; Dennis, Tristan P. W.; Modha, Sejal; Lytras, Spyros; Hughes, Joseph; Gatseva, Anna; Gifford, Robert J.

doi:10.1186/s13059-024-03258-y

Cited by 7 publications

(1 citation statement)

References 136 publications

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“…We examined the genomic area encompassing BTN1A1 and BTN2A1 as well as the regions extending 150 kb past SPTLC3 to study synteny in Carnivora for ERV- env and associated ERV duplicates ( Simpson et al., 2022 ). The segments were obtained from the latest GenBank assembly for each species ( Supplementary Table S1 ), and a sequence alignment was performed using MultiPipMaker ( Chen et al., 2017 ; Horie and Tomonaga, 2019 ; Blanco-Melo et al., 2024 ).…”

Section: Methodsmentioning

confidence: 99%

Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink

Zhang,

Wang,

Zhu

et al. 2024

Front. Cell. Infect. Microbiol.

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IntroductionEndogenous retroviruses (ERVs), which originated from exogenous retroviral infections of germline cells millions of years ago and were inherited by subsequent generations as per Mendelian inheritance patterns, predominantly comprise non-protein-coding sequences due to the accumulation of mutations, insertions, deletions, and truncations. Nevertheless, recent studies have revealed that ERVs play a crucial role in diverse biological processes by encoding various proteins.MethodsIn this study, we successfully identified an ERV envelope (env) gene in a mink species. A phylogenetic tree of mink ERV-V env and reference sequences was constructed using Bayesian methods and maximum-likelihood inference.ResultsPhylogenetic analyses indicated a significant degree of sequence conservation and positive selection within the env-surface open reading frame. Additionally, qRT-PCR revealed diverse patterns of mink ERV-V env expression in various tissues. The expression of mink ERV-V env gene in testicular tissue strongly correlated with the seasonal reproductive cycles of minks.DiscussionOur study suggests that the ERV-V env gene in mink may have been repurposed for host functions.

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Section: Methodsmentioning

confidence: 99%

Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink

Zhang,

Wang,

Zhu

et al. 2024

Front. Cell. Infect. Microbiol.

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Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes

Litvin,

Wang,

Stanton

et al. 2024

Virus Evolution

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Cytomegalovirus is a genus of herpesviruses, members of which share a long history of co-evolution with their primate hosts including Great Apes, Old and New World monkeys. These viruses are ubiquitous within their host populations and establish lifelong infection in most individuals. Although asymptomatic in healthy individuals, infection poses a significant risk to individuals with a weakened or underdeveloped immune system. The genome of human cytomegalovirus is the largest among human-infecting viruses, and comprises at least fifteen separate gene families, which may have arisen by gene duplication. Within human cytomegalovirus, the RL11 gene family is the largest. RL11 genes are non-essential in vitro but have immune evasion roles that are likely critical to persistence in vivo. These genes demonstrate an extreme level of inter-species and intra-strain sequence diversity, that makes it challenging to deduce the evolutionary relationships within this gene family. Understanding the evolutionary relationships of these genes, especially accurate ortholog identification, is essential for reconstructing ancestral genomes, deciphering gene repertoire and order, and enabling reliable functional analyses across the Cytomegalovirus species, thereby offering insights into evolutionary processes, genetic diversity, and the functional significance of genes. In this work, we combined in silico genome screening with sequence-based and structure-guided phylogenetic analysis to reconstruct the evolutionary history of the RL11 gene family. We confirmed that RL11 genes are unique to cytomegaloviruses of Old World monkeys and Great Apes, showing that this gene family was formed by multiple early duplication events and later lineage-specific losses. We identified four main clades of RL11 genes and showed that their expansions were mainly lineage-specific and happened independently in cytomegaloviruses of Great Apes, African Old World monkeys and Asian Old World monkeys. We also identified groups of orthologous genes across the Cytomegalovirus tree showing that some human cytomegalovirus-specific RL11 genes emerged before the divergence of human and chimpanzee cytomegaloviruses but were subsequently lost in the latter. The extensive and dynamic species-specific evolution of this gene family suggests their functions target elements of host immunity that have similarly co-evolved during speciation.

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Endogenous viral elements: insights into data availability and accessibility

Ritsch,

Brait,

Harvey

et al. 2024

Virus Evolution

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Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR (‘findable, accessible, interoperable, and reusable’) principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.

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A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

Cited by 7 publications

References 136 publications

Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink

Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink

Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes

Endogenous viral elements: insights into data availability and accessibility

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