Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions
Jürgen Schmitz, Angela Noll, Carsten A. Raabe, Gennady Churakov, Reinhard Voss, Martin Kiefmann, Timofey Rozhdestvensky, Jürgen Brosius, Robert Baertsch, Hiram Clawson, Christian Roos, Aleksey Zimin, Patrick Minx, Michael J. Montague, Richard K. Wilson & Wesley C. Warren
Nature Communications 7, Article number: 12997 (2016)
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Evolutionary biology Genome evolution Interspersed repetitive sequences
Received: 29 October 2015 Accepted: 17 August 2016 Published online: 06 October 2016
A tarsier (Carlito syrichta) with his prey.
Credit: David Haring/Duke Lemur Center
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.
Author information
Affiliations
Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany
Jürgen Schmitz, Angela Noll, Carsten A. Raabe, Gennady Churakov, Martin Kiefmann, Timofey Rozhdestvensky & Jürgen Brosius
Münster Graduate School of Evolution, University of Münster, 48149 Münster, Germany
Jürgen Schmitz & Angela Noll
Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
Angela Noll & Christian Roos
Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), 16816 Neuruppin, Germany
Carsten A. Raabe & Jürgen Brosius
Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
Gennady Churakov
Integrated Functional Genomics, Interdisciplinary Center for Clinical Research, University of Münster, 48149 Münster, Germany
Reinhard Voss
Medical Faculty (TRAM), University of Münster, 48149 Münster, Germany
Timofey Rozhdestvensky
Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
Robert Baertsch & Hiram Clawson
Institute for Physical Science and Technology, University of Maryland, 3300 Metzerott Rd, Adelphi, Maryland 20783, USA
Aleksey Zimin
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
Patrick Minx, Michael J. Montague, Richard K. Wilson & Wesley C. Warren
Contributions
J.S. and W.C.W. are the principal investigators who conceived the project, analysed the data, and wrote the manuscript. R.K.W., A.Z. and P.M. sequenced and assembled the genome. C.R. provided tarsier tissue sources for RNAseq data. M.J.M. and A.N. identified and performed analyses on candidate genes under positive selection and aided in writing the manuscript. R.B. and H.C. derived genome alignments. A.N., C.A.R., G.C., C.R., R.V., M.K., T.R. and J.B carried out various transposable element, numt, and small RNA analyses and aided in writing the manuscript.
Competing interests
The authors declare no competing financial interests.
Corresponding author
Correspondence to Wesley C. Warren.
