title: Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions.
abstract: Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syrichta), and provide extended analyses of the genome and detailed history of transposable element insertion events. We describe the silencing of Alu monomers on the lineage leading to anthropoids, and recognize an unexpected abundance of long terminal repeat-derived and LINE1-mobilized transposed elements (Tarsius interspersed elements; TINEs). For the first time in mammals, we identify a complete mitochondrial genome insertion within the nuclear genome, then reveal tarsier-specific, positive gene selection and posit population size changes over time. The genomic resources and analyses presented here will aid efforts to more fully understand the ancient characteristics of primate genomes.
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Münster Graduate School of Evolution, University of Münster, 48149 Münster, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Münster Graduate School of Evolution, University of Münster, 48149 Münster, Germany.|Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany.
authors.forename: Angela
authors.initials: A
authors.lastname: Noll
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), 16816 Neuruppin, Germany.
authors.forename: Carsten A
authors.initials: CA
authors.lastname: Raabe
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany.
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: Integrated Functional Genomics, Interdisciplinary Center for Clinical Research, University of Münster, 48149 Münster, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Voss
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kiefmann
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Medical Faculty (TRAM), University of Münster, 48149 Münster, Germany.
authors.forename: Timofey
authors.initials: T
authors.lastname: Rozhdestvensky
authors.affiliation: Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.|Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), 16816 Neuruppin, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Baertsch
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany.
authors.forename: Christian
authors.identifier: 0000-0003-0190-4266
authors.initials: C
authors.lastname: Roos
authors.affiliation: Institute for Physical Science and Technology, University of Maryland, 3300 Metzerott Rd, Adelphi, Maryland 20783, USA.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zimin
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Michael J
authors.identifier: 0000-0003-0253-4404
authors.initials: MJ
authors.lastname: Montague
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism; D004251:DNA Transposable Elements; D005260:Female; D020868:Gene Silencing; D016678:Genome; D054629:Genome, Mitochondrial; D020084:Long Interspersed Nucleotide Elements; D008390:Markov Chains; D035683:MicroRNAs / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism; D009132:Muscles / Q000378:metabolism; D010802:Phylogeny; D020537:RNA, Small Nucleolar / Q000378:metabolism; D016699:Tarsiidae / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D020537:RNA, Small Nucleolar