title: Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification.
abstract: BACKGROUND
  Polyploidization can activate specific transposable elements, leading to their accumulation. At the same time, the preferential loss of repetitive elements in polyploids may be central to diploidization. The paucity of studies of transposable element (TE) dynamics in closely related diploid and polyploid species, however, prevents generalizations about these patterns. Here, we use low-coverage Illumina sequencing data for a clade of three tetraploid Orobanche species and a diploid relative to quantify the abundance and relative frequencies of different types of TEs. We confirmed tetraploidy in the sequenced individuals using standard cytogenetic methods and inferred the time of origin of the tetraploid clade with a rate-calibrated molecular clock.
  
  
  RESULTS
  The sequenced individuals of Orobanche austrohispanica, Orobanche densiflora, and Orobanche gracilis have 2n = 76 chromosomes, are tetraploid, and shared a most recent common ancestor some 6.7 Ma ago. Comparison of TE classifications from the Illumina data with classification from 454 data for one of the species revealed strong effects of sequencing technology on the detection of certain types of repetitive DNA. The three tetraploids show repeat enrichment especially of Gypsy TE families compared to eight previously analyzed Orobanchaceae. However, the diploid Orobanche rapum-genistae genome also has a very high proportion (30%) of Gypsy elements.
  
  
  CONCLUSIONS
  We had earlier suggested that tetraploidization might have contributed to an amplification of Gypsy elements, particularly of the Tekay clade, and that O. gracilis underwent genome downsizing following polyploidization. The new data reveal that Gypsy amplification in Orobanchaceae does not consistently relate to tetraploidy and that more species sampling is required to generalize about Tekay accumulation patterns.
authors.affiliation: Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany ; Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, 50829 Germany.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Piednoël
authors.affiliation: Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany.
authors.forename: Aretuza
authors.initials: A
authors.lastname: Sousa
authors.affiliation: Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany.
authors.forename: Susanne S
authors.initials: SS
authors.lastname: Renner
keywords: Chromosomes; Copia; Gypsy; Orobanche; Ploidy; Transposable elements
references.citation: PLoS One. 2012;7(12):e52249
references.pmid: 23284954
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Am J Bot. 2004 Mar;91(3):439-48
references.pmid: 21653400
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):15-8
references.pmid: 10592170
references.citation: Mol Biol Evol. 2004 May;21(5):781-98
references.pmid: 14739248
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D70-4
references.pmid: 21036865
references.citation: BMC Bioinformatics. 2010 Jul 15;11:378
references.pmid: 20633259
references.citation: Gene. 2007 Jan 31;387(1-2):75-86
references.pmid: 17008031
references.citation: Syst Biol. 2015 Jan;64(1):112-26
references.pmid: 25261464
references.citation: Mol Phylogenet Evol. 2004 Feb;30(2):465-78
references.pmid: 14715236
references.citation: Plant J. 2013 Aug;75(4):699-709
references.pmid: 23663083
references.citation: Biol Direct. 2009 Nov 02;4:41
references.pmid: 19883502
references.citation: Annu Rev Plant Biol. 2014;65:505-30
references.pmid: 24579996
references.citation: Plant Cell. 2001 Aug;13(8):1749-59
references.pmid: 11487690
references.citation: Bioinformatics. 2013 Mar 15;29(6):792-3
references.pmid: 23376349
references.citation: Cytogenet Genome Res. 2013;140(2-4):79-96
references.pmid: 23751271
references.citation: Bioinformatics. 2011 Jul 1;27(13):i304-9
references.pmid: 21685085
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17811-6
references.pmid: 19815511
references.citation: Mol Biol Evol. 2012 Aug;29(8):1969-73
references.pmid: 22367748
references.citation: Mol Biol Evol. 2011 Oct;28(10):2843-54
references.pmid: 21512105
references.citation: Nat Commun. 2013;4:1595
references.pmid: 23481403
references.citation: Genome Res. 2008 Mar;18(3):359-69
references.pmid: 18256242
references.citation: BMC Evol Biol. 2006 Apr 25;6:36
references.pmid: 16638138
references.citation: PLoS One. 2012;7(11):e50352
references.pmid: 23185607
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D834-40
references.pmid: 17202173
references.citation: PLoS One. 2013 Nov 12;8(11):e79204
references.pmid: 24265760
references.citation: Heredity (Edinb). 2013 Feb;110(2):194-204
references.pmid: 23321774
references.citation: Genome Res. 2007 Jul;17(7):1072-81
references.pmid: 17556529
references.citation: New Phytol. 2010 Apr;186(1):37-45
references.pmid: 20002321
references.citation: Mol Biol Evol. 2012 Nov;29(11):3601-11
references.pmid: 22723303
references.citation: BMC Plant Biol. 2010 Sep 16;10:204
references.pmid: 20846365