ArticleGenome biology2024
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Cross-Species Sex Identification and Comparative Analysis of theAnimals : an open access journal from MDPI · 2026Article
- ZNF274 constrains lineage plasticity and drives intrinsic resistance to CDK7 inhibitors in pancreatic cancer.Nature communications · 2026Article
- Computational Discovery of Angiotensin-(1-7)-like Peptides Targeting the MAS Receptor from the Genomic Dark Matter ofInternational journal of medical sciences · 2026Article
- HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements.Bioinformatics (Oxford, England) · 2025Article
- 2024 taxonomy update for the family Retroviridae.Archives of virology · 2025Article
- detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.Molecular ecology resources · 2025Article
- Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors.BMC genomics · 2025Article
- Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts.PLoS pathogens · 2024Article
- Article
- Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink.Frontiers in cellular and infection microbiology · 2024Article
- Evolution of theVirus evolution · 2024Article
- Endogenous viral elements: insights into data availability and accessibility.Virus evolution · 2024Article
- Resurrection of 2'-5'-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication.PLoS biology · 2023Article
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9 authors.
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Abstract
backgroundGenomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.
resultsUsing DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.
conclusionsWe comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
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