Abstract
Background Endogenous retroviruses (ERVs) are genetic remnants of exogenous retroviral infections that have endured selective processes and made their way into ancestral host genomes. While many of them have deteriorated beyond the ability to code for detectable proteins, some still retain activity or the potential for coding activity [1-3]. A few active ERVs have been coopted into fully functional genes that play important roles in development or disease [1, 2, 4]. New high throughput data revealed that these ERVs are far more common than previously thought and different software packages have been created to search genomes for these structures. In this study, we build on such a tool to look at several vertebrate genomes, search for ERV remnants and identify loci with long, intact open reading frames for the major retroviral genes and dating these loci of interest using the long terminal repeat (LTR) divergence method [5].
Highlights
Endogenous retroviruses (ERVs) are genetic remnants of exogenous retroviral infections that have endured selective processes and made their way into ancestral host genomes
Materials and methods The genomes of twelve vertebrates were acquired from UCSC Genome Browser and analyzed with an in-house method based on the Itrharvest[6] software package, complemented with additional filtering and data retrieval
Candidate ERV loci were probed for full-length open reading frames, which were classified within one of the three major retroviral genes: gag, pol or env by a BlastX [7] against a retroviral protein database
Summary
Endogenous retroviruses (ERVs) are genetic remnants of exogenous retroviral infections that have endured selective processes and made their way into ancestral host genomes. Materials and methods The genomes of twelve vertebrates were acquired from UCSC Genome Browser and analyzed with an in-house method based on the Itrharvest[6] software package, complemented with additional filtering and data retrieval.
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