title: Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome.
abstract: The placozoan Trichoplax adhaerens has a compact genome with many primitive eumetazoan characteristics. In order to gain a better understanding of its genome architecture, we conducted a detailed analysis of repeat content in this genome. The transposable element (TE) content is lower than that of other metazoans, and the few TEs present in the genome appear to be inactive. A new phylogenetic clade of the gypsy-like LTR retrotransposons was identified, which includes the majority of gypsy-like elements in Trichoplax. A particular microsatellite motif (ACAGT) exhibits unexpectedly high abundance, and also has strong association with its nearby genes.
authors.affiliation: Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA. swang@mail.utexas.edu
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.forename: Eli
authors.initials: E
authors.lastname: Meyer
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D000818:Animals; D018503:Genome, Protozoan / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D018626:Retroelements
references.citation: Nature. 2008 Apr 10;452(7188):745-9
references.pmid: 18322464
references.citation: Science. 2007 Jun 15;316(5831):1586-91
references.pmid: 17569856
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Mol Biol Evol. 2001 Aug;18(8):1474-83
references.pmid: 11470838
references.citation: Mol Ecol. 2002 Dec;11(12):2453-65
references.pmid: 12453231
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Bioinformatics. 2007 Jul 1;23(13):1683-5
references.pmid: 17463017
references.citation: Genome Res. 2000 Jul;10(7):939-49
references.pmid: 10899143
references.citation: Science. 1998 Dec 11;282(5396):2012-8
references.pmid: 9851916
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8
references.pmid: 17485477
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Genome Res. 2003 Jul;13(7):1686-95
references.pmid: 12805276
references.citation: Nature. 2008 Aug 21;454(7207):955-60
references.pmid: 18719581
references.citation: Trends Biotechnol. 2007 Nov;25(11):490-8
references.pmid: 17945369
references.citation: Genome Res. 2000 Jul;10(7):967-81
references.pmid: 10899146
references.citation: Annu Rev Genomics Hum Genet. 2007;8:241-59
references.pmid: 17506661
references.citation: DNA Seq. 2008 Jun;19(3):195-205
references.pmid: 17852361
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: PLoS Biol. 2009 Jan 27;7(1):e20
references.pmid: 19175291
references.citation: Mol Biol Evol. 2001 Jul;18(7):1161-7
references.pmid: 11420357
references.citation: Mol Biol Evol. 2001 May;18(5):691-9
references.pmid: 11319253
references.citation: Science. 2004 Mar 12;303(5664):1626-32
references.pmid: 15016989
references.citation: Nature. 2004 Oct 21;431(7011):946-57
references.pmid: 15496914
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15518-22
references.pmid: 16230622
references.citation: Gene. 2009 May 1;436(1-2):1-7
references.pmid: 19393167
references.citation: Science. 2000 Mar 24;287(5461):2185-95
references.pmid: 10731132
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Nat Rev Genet. 2004 Jun;5(6):435-45
references.pmid: 15153996
references.citation: J Virol. 1999 Jun;73(6):5186-90
references.pmid: 10233986
references.citation: Bioessays. 2005 Dec;27(12):1294-302
references.pmid: 16299758