The most common entities in vertebrate genomes are transposable elements (TEs), DNA sequences that have been repeatedly copied and inserted into new locations throughout the genome. Some TEs have been replicated hundreds of thousands of times, and their ecology and evolutionary history within a genome is thus critical to understanding how genome structure evolves. It was once thought that only a few “master gene” copies could replicate, while the rest were inactive (dead on arrival), but recent computational and laboratory studies have indicated that this is not the case. However, previous methods for reconstructing TE evolutionary history were not designed to solve the problem of determining the ancestral source sequence for large numbers of elements. Here, we present a new method that is. Our method surveys all likely TE ancestors and determines the probability that each modern element arose from each of its plausible ancestors. We applied our method to the gibbon-derived LAVA TE family and to the human AluSc subfamily and inferred many more source elements than indicated by previous methods. This new method will help us better understand TE evolution, including both the impact of sequence on replication and the substitution process after replication.
Vyšlo v časopise: Inference of Transposable Element Ancestry. PLoS Genet 10(8): e32767. doi:10.1371/journal.pgen.1004482 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004482
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