We carried out a global survey of all major types of transposable elements in Silene latifolia, a model species with sex chromosomes that are in the early stages of their evolution. A shotgun genomic library was screened with genomic DNA to isolate and characterize the most abundant elements. We found that the most common types of elements were the subtelomeric tandem repeat X-43.1 and Gypsy retrotransposons, followed by Copia retrotransposons and LINE non-LTR elements. SINE elements and DNA transposons were less abundant. We also amplified transposable elements with degenerate primers and used them to screen the library. The localization of elements by FISH revealed that most of the Copia elements were accumulated on the Y chromosome. Surprisingly, one type of Gypsy element, which was similar to Ogre elements known from legumes, was almost absent on the Y chromosome but otherwise uniformly distributed on all chromosomes. Other types of elements were ubiquitous on all chromosomes. Moreover, we isolated and characterized two new tandem repeats. One of them, STAR-C, was localized at the centromeres of all chromosomes except the Y chromosome, where it was present on the p-arm. Its variant, STAR-Y, carrying a small deletion, was specifically localized on the q-arm of the Y chromosome. The second tandem repeat, TR1, co-localized with the 45S rDNA cluster in the subtelomeres of five pairs of autosomes. FISH analysis of other Silene species revealed that some elements (e.g., Ogre-like elements) are confined to the section Elisanthe while others (e.g. Copia or Athila-like elements) are present also in more distant species. Similarly, the centromeric satellite STAR-C was conserved in the genus Silene whereas the subtelomeric satellite X-43.1 was specific for Elisanthe section. Altogether, our data provide an overview of the repetitive sequences in Silene latifolia and revealed that genomic distribution and evolutionary dynamics differ among various repetitive elements. The unique pattern of repeat distribution is found on the Y chromosome, where some elements are accumulated while other elements are conspicuously absent, which probably reflects different forces shaping the Y chromosome.

Laboratory of Plant Developmental Genetics Institute of Biophysics ASCR Kralovopolska 135 CZ 61265 Brno Czech Republic

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Genetics. 2006 Jun;173(2):1047-56 PubMed

Chromosoma. 1999 Aug;108(4):266-70 PubMed

Chromosome Res. 2004;12(3):245-50 PubMed

Bioinformatics. 2004 Jan 22;20(2):279-81 PubMed

Genome. 2002 Aug;45(4):745-51 PubMed

Chromosoma. 2006 Oct;115(5):376-82 PubMed

Chromosome Res. 2004;12(2):117-23 PubMed

Curr Biol. 2008 Apr 8;18(7):545-9 PubMed

J Plant Res. 2003 Aug;116(4):317-26 PubMed

Mol Genet Genomics. 2007 Dec;278(6):633-8 PubMed

Chromosome Res. 2001;9(5):387-93 PubMed

BMC Genomics. 2007 Nov 21;8:427 PubMed

Bioessays. 2005 Oct;27(10):1076-83 PubMed

Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9454-9 PubMed

Mol Gen Genet. 2000 Jun;263(5):741-51 PubMed

Plant Cell Physiol. 1999 Jan;40(1):60-8 PubMed

Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):280-5 PubMed

Chromosome Res. 2001;9(7):591-605 PubMed

Plant Mol Biol. 2003 Oct;53(3):399-410 PubMed

Curr Biol. 2004 Aug 24;14(16):1416-24 PubMed

Cytogenet Genome Res. 2005;110(1-4):462-7 PubMed

Genome. 2008 May;51(5):350-6 PubMed

Nucleic Acids Res. 1999 Jan 15;27(2):573-80 PubMed

Theor Appl Genet. 2004 May;108(7):1193-9 PubMed

PLoS Biol. 2005 Jun;3(6):e181 PubMed

Nucleic Acids Res. 2003 Jan 1;31(1):383-7 PubMed

BMC Bioinformatics. 2006 Oct 25;7:474 PubMed

Chromosome Res. 2007;15(8):1051-9 PubMed

Chromosome Res. 2001;9(4):309-23 PubMed

Chromosome Res. 2000;8(3):229-36 PubMed

Genome. 1999 Jun;42(3):442-6 PubMed

Plant Mol Biol. 2000 Dec;44(6):723-32 PubMed

Plant J. 1998 Dec;16(6):721-8 PubMed

Chromosome Res. 1997 Feb;5(1):57-65 PubMed

Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PubMed

Gene. 2007 Apr 1;390(1-2):92-7 PubMed

Plant Physiol. 2001 Dec;127(4):1418-24 PubMed

Plant Mol Biol. 1995 Nov;29(3):441-52 PubMed

Nucleic Acids Res. 1992 Jul 25;20(14):3639-44 PubMed

Mol Genet Genomics. 2006 Sep;276(3):254-63 PubMed

Nature. 2004 Jan 22;427(6972):348-52 PubMed

Mol Cell Biol. 1999 Sep;19(9):6260-8 PubMed

Nature. 1994 Sep 15;371(6494):215-20 PubMed

Plant Mol Biol. 2006 Jun;61(3):505-14 PubMed

Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11778-83 PubMed

Genome. 2006 May;49(5):520-30 PubMed

Science. 1996 Nov 1;274(5288):765-8 PubMed

Fungal Genet Biol. 2001 Jun;33(1):49-57 PubMed

Gene. 2007 Apr 1;390(1-2):108-16 PubMed

Evolution. 2001 Jan;55(1):1-24 PubMed

Mol Biol Evol. 2000 May;17(5):804-12 PubMed

Plant Physiol. 2001 Mar;125(3):1293-303 PubMed

Mol Gen Genet. 1999 Feb;261(1):71-9 PubMed

Plant Mol Biol. 2002 May;49(1):1-14 PubMed

Mol Biol Evol. 2001 Jul;18(7):1176-88 PubMed

Plant J. 1998 Mar;13(5):699-705 PubMed

Philos Trans R Soc Lond B Biol Sci. 2000 Nov 29;355(1403):1563-72 PubMed

PLoS Biol. 2005 Jan;3(1):e4 PubMed

Genetica. 2006 Sep-Nov;128(1-3):167-75 PubMed

Bioinformatics. 2007 Nov 1;23(21):2947-8 PubMed

Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PubMed

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