title: When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.
abstract: The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads.
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Johann Wolfgang Goethe University Frankfurt Am Main, Max-von-Laue Straβe 9, 60438 Frankfurt am Main, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Gallus
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Johann Wolfgang Goethe University Frankfurt Am Main, Max-von-Laue Straβe 9, 60438 Frankfurt am Main, Germany.
authors.forename: Fritjof
authors.initials: F
authors.lastname: Lammers
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany maria.nilsson-janke@senckenberg.de.
authors.forename: Maria Anna
authors.initials: MA
authors.lastname: Nilsson
mesh_terms: D000818:Animals; D001315:Australia; D003198:Computer Simulation; D019143:Evolution, Molecular; D023281:Genomics; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008322:Mammals / Q000235:genetics; D008394:Marsupialia / Q000235:genetics*; D010802:Phylogeny
keywords: LINE-1; Tasmanian devil; marsupials; retrotransposition; transposable element