Sequencing of randomly sheared total genomic DNA of the cytotype B6B6 of P. autumnale was performed by the Center for Medical Research, Graz, Austria using a Roche/454 GS FLX instrument with Titanium reagents (Roche Diagnostics). Sequencing half a 70 × 75 picotitre plate yielded 555 480 reads of average length 350 bp. Quality-filtered reads (397 694 corresponding to 2·2% coverage of the genome) were subjected to graph-based clustering analysis, as described by Novák et al. (2010) (link), to identify groups of reads representing repetitive elements (H. Weiss-Schneeweiss et al., unpubl. res.). One hundred and ninety-five out of a total of 19 751 clusters, corresponding to the most abundant families of genomic repeats, were analysed for their similarity to known sequences using RepeatMasker Open-3.0 (http://www.repeatmasker.org ) and BLAST (Altschul et al., 1990 (link)) searches against GenBank databases and a database of plant mobile element protein sequences (Novák et al., 2013 (link)). Graphical layouts of individual clusters were examined using the SeqGrapheR program (Novák et al., 2010 (link)).
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Sequencing and Characterization of Genomic Repeats in P. autumnale
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Other organizations : University of Vienna, Czech Academy of Sciences, University of Cambridge
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Variable analysis
independent variables
- Sequencing of randomly sheared total genomic DNA of the cytotype B^6B^6 of P. autumnale
- Number of reads
- Average length of reads
- Number of quality-filtered reads
- Genome coverage
- Number of clusters representing repetitive elements
- Roche/454 GS FLX instrument with Titanium reagents (Roche Diagnostics)
- Sequencing half a 70 × 75 picotitre plate
- Quality-filtering of reads
- Graph-based clustering analysis to identify repetitive elements
- Similarity analysis of repetitive element clusters using RepeatMasker and BLAST
- Examination of graphical layouts of individual clusters using SeqGrapheR program
- Positive control: Not mentioned
- Negative control: Not mentioned
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