title: Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil.
abstract: The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
authors: Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
authors: Susanne
authors: S
authors: Gallus
authors: Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
authors: Björn M
authors: BM
authors: Hallström
authors: LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
authors: Vikas
authors: V
authors: Kumar
authors: LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Qld, Australia.
authors: William G
authors: WG
authors: Dodt
authors: LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany.
authors: Axel
authors: A
authors: Janke
authors: Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
authors: Gerald G
authors: GG
authors: Schumann
authors: LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany maria.nilsson-janke@senckenberg.de.
authors: Maria A
authors: MA
authors: Nilsson
mesh_terms: D000818:Animals; D060435:Carnivory; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D008394:Marsupialia / Q000235:genetics*; D010802:Phylogeny; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics; D013648:Tasmania
chemical_list: D004251:DNA Transposable Elements
keywords: DNA transposon; Sarcophilus; retrotransposon
references: Genome Biol. 2010;11(2):R16
references: 20144222
references: Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):234-9
references: 23248290
references: PLoS Genet. 2014 Jun;10(6):e1004395
references: 24968166
references: Nature. 2007 May 10;447(7141):167-77
references: 17495919
references: Bioinformatics. 2008 Dec 15;24(24):2818-24
references: 18952627
references: Nature. 1997 Aug 14;388(6643):666-70
references: 9262399
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D70-4
references: 21036865
references: Bioinformatics. 2013 Feb 1;29(3):389-90
references: 23233656
references: Nature. 2010 Jan 21;463(7279):311-7
references: 20010809
references: BMC Genomics. 2012;13:172
references: 22559330
references: PLoS Biol. 2006 Apr;4(4):e91
references: 16515367
references: Oncogene. 2008 Dec;27 Suppl 2:S19-30
references: 19956175
references: BMC Bioinformatics. 2006;7:474
references: 17064419
references: Genome Res. 2007 Nov;17(11):1675-89
references: 17975172
references: Trends Genet. 1992 Sep;8(9):307-11
references: 1365396
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: BMC Evol Biol. 2004 Jun 28;4:18
references: 15222900
references: Genome Res. 2007 Jul;17(7):992-1004
references: 17495012
references: BMC Bioinformatics. 2011;12:271
references: 21718538
references: Genome Biol. 2002 Sep 19;3(10):research0052
references: 12372140
references: Int Rev Cell Mol Biol. 2010;285:115-88
references: 21035099
references: Genome Res. 2007 Nov;17(11):1547-9
references: 17975171
references: Nat Methods. 2011 Jan;8(1):61-5
references: 21102452
references: Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62
references: 23884656
references: Cytogenet Genome Res. 2005;110(1-4):407-15
references: 16093693
references: Genome Biol. 2011;12(8):R81
references: 21854559
references: Genome Res. 2006 Jan;16(1):78-87
references: 16344559
references: Nat Rev Genet. 2011 Sep;12(9):615-27
references: 21850042
references: J Virol. 2011 Dec;85(23):12315-23
references: 21957310
references: Genetics. 2008 Jan;178(1):393-404
references: 18202382
references: Gene. 2007 Jul 1;396(1):46-58
references: 17442506
references: Mol Biol Evol. 2013 May;30(5):1041-5
references: 23429857
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: BMC Bioinformatics. 2014;15:71
references: 24629057
references: Mob Genet Elements. 2014 Mar 06;4:e28439
references: 25346866
references: Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53
references: 21709235
references: Biotechniques. 2000 Dec;29(6):1310-6
references: 11126134
references: Genome Inform. 2001;12:141-54
references: 11791233
references: J Mol Biol. 1995 Feb 24;246(3):401-417
references: 7877164
references: BMC Genomics. 2013;14:134
references: 23445260
references: Bioinformatics. 2010 Jun 15;26(12):i350-7
references: 20529927
references: Nature. 2002 Dec 5;420(6915):520-62
references: 12466850
references: Nat Methods. 2011 Jan;8(1):59-60
references: 21191376
references: Annu Rev Genomics Hum Genet. 2011;12:187-215
references: 21801021
references: Annu Rev Genet. 2007;41:331-68
references: 18076328
references: Genome Res. 2005 Dec;15(12):1798-808
references: 16339378
references: Cell. 2012 Feb 17;148(4):780-91
references: 22341448
references: Curr Opin Genet Dev. 2012 Jun;22(3):191-203
references: 22406018
references: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references: 22039361
references: Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1012-6
references: 23277587
references: Science. 2013 Jan 25;339(6118):456-60
references: 23258410
references: Genetics. 2000 Apr;154(4):1809-17
references: 10747071
references: BMC Evol Biol. 2010;10:376
references: 21126360
references: Nucleic Acids Res. 1995 Jan 11;23(1):170-5
references: 7870583
references: Gene. 2008 Jan 15;407(1-2):176-85
references: 17988807
references: Nat Rev Genet. 2012 Jan;13(1):36-46
references: 22124482
references: Mol Ecol. 2013 Mar;22(6):1503-17
references: 23293987
references: Cell. 2008 Oct 3;135(1):23-35
references: 18854152
references: J Mol Evol. 1984;20(1):86-93
references: 6429346
references: Gene. 2012 May 25;500(1):47-53
references: 22465530
references: Gene. 2008 Jan 15;407(1-2):75-85
references: 17976929
references: Cytogenet Genome Res. 2005;110(1-4):416-25
references: 16093694
references: Annu Rev Genomics Hum Genet. 2012;13:207-22
references: 22657390
references: Gene. 2010 Jan 1;449(1-2):85-94
references: 19747963
references: PLoS Biol. 2010;8(7):e1000436
references: 20668664
references: Pharmacogenomics. 2012 Jun;13(8):901-15
references: 22676195
references: Cell. 2013 Sep 26;155(1):27-38
references: 24074859
references: Nature. 2001 Feb 15;409(6822):860-921
references: 11237011