Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome
Version of Record online: 23 JAN 2014
© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust
Volume 202, Issue 2, pages 662–678, April 2014
How to Cite
Kubat, Z., Zluvova, J., Vogel, I., Kovacova, V., Cermak, T., Cegan, R., Hobza, R., Vyskot, B. and Kejnovsky, E. (2014), Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. New Phytologist, 202: 662–678. doi: 10.1111/nph.12669
- Issue online: 20 MAR 2014
- Version of Record online: 23 JAN 2014
- Manuscript Accepted: 25 NOV 2013
- Manuscript Received: 13 SEP 2013
- Czech Science Foundation. Grant Numbers: P501/10/P483, P501/10/0102, P305/10/0930, P501/12/2220
- European Regional Development Fund. Grant Number: CZ.1.05/1.1.00/02.0068
- OPVK. Grant Number: CZ.1.07/2.3.00/20.0045
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Fig. S1 RACE mapped transcription starts and polyA signals of Ogre CL5 and Ogre CL5del and putative splice site of Ogre CL5 and Ogre CL5del in the Silene latifolia genome.
Fig. S2 Chronogram showing divergence times estimated in BEAST based on sequences of four genes in species of the genus Silene.
Fig. S3 Chronograms showing divergence times estimated in BEAST for species of the genus Silene.
Fig. S4 Linear regression of X–Y split time in millions of years and percentage of synonymous substitutions in Silene latifolia.
Fig. S5 The spatial distribution and abundance of 24-nucleotide (24-nt) small RNAs (sRNAs) along four genomic copies of Ogre elements in Silene latifolia.
Fig. S6 Microview of CHH methylation of the right LTR in the TE Ogre CL5 in Silene latifolia.
Fig. S7 Detailed view of the spatial distribution of 24-nucleotide (24-nt) small RNAs (sRNAs) along LTRs of Retand and Ogre elements (first three rows) in Silene latifolia.
Table S1 Primers used in this study
Table S2 Copy numbers of TEs in the Silene latifolia genome (1C) estimated by two methods – BAC library hybridization and in silico read mapping
Table S3 List of sequences used in the phylogenetic analyses of Ogre elements in Silene including their accession numbers
Table S4 P-values for the Mann–Whitney test in Silene latifolia
Table S5 Percentages of synonymous substitutions per codon and time of X–Y chromosome split into four sex-linked Silene latifolia genes
Table S6 Percentages of disturbed open reading frames (ORFs) in each group of retrotransposons in Silene latifolia
Table S7 Branch analysis of terminal and internal branches in the Silene latifolia genome
Table S8 Abundance of 19–24-nucleotide small RNAs (sRNAs) complementary to LTRs in sense (+) and antisense (−) orientation in Silene latifolia
Methods S1 Materials and Methods explained in detail.
Notes S1 Original tree files.
Notes S2 Branching order of Silene Ogre retrotransposon groups.