title: VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila.
abstract: Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.
authors.affiliation: Pós Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil Departamento de Entomologia, Centro de Pesquisas Aggeu Magalhães-FIOCRUZ-CPqAM, Recife, PE, Brazil gabriel.wallau@gmail.com gabriel.wallau@cpqam.fiocruz.br.
authors.forename: Gabriel Luz
authors.initials: GL
authors.lastname: Wallau
authors.affiliation: Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Capy
authors.affiliation: Pós Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
authors.forename: Elgion
authors.initials: E
authors.lastname: Loreto
authors.affiliation: Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Le Rouzic
authors.affiliation: Laboratoire Évolution, Génomes, Comportement, Écologie; CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Hua-Van
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D023281:Genomics; D010802:Phylogeny; D013045:Species Specificity; D019895:Transposases / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; C111652:mariner transposases; D019895:Transposases
keywords: Drosophila; codon usage; horizontal transfer; mariner element; synonymous substitutions; transposable elements; vertical transmission