title: A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).
abstract: Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage.
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Gallus
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
authors.forename: V
authors.initials: V
authors.lastname: Kumar
authors.affiliation: Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark.
authors.forename: M F
authors.initials: MF
authors.lastname: Bertelsen
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; Goethe University Frankfurt Institute for Ecology, Evolution & Diversity Biologicum Max-von-Laue-Str.13, D-60439 Frankfurt am Main, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Janke
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany. Electronic address: maria.nilsson-janke@senckenberg.de.
authors.forename: M A
authors.initials: MA
authors.lastname: Nilsson
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D016678:Genome; D054629:Genome, Mitochondrial; D020084:Long Interspersed Nucleotide Elements; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D012418:Ruminants / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D020086:Short Interspersed Nucleotide Elements; D013045:Species Specificity
chemical_list: D018626:Retroelements
keywords: BovB; CHR; Cetartiodactyla; Genome survey; Retrotransposition; Transposable elements