Open Access Highly Accessed Research article

Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

Roman Matyášek1, Simon Renny-Byfield23, Jaroslav Fulneček1, Jiří Macas4, Marie-Angele Grandbastien5, Richard Nichols2, Andrew Leitch2 and Aleš Kovařík1*

  • * Corresponding author: Aleš Kovařík kovarik@ibp.cz

  • † Equal contributors

Author Affiliations

1 Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, Brno, CZ-612 65, Czech Republic

2 Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK

3 Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA

4 Biology Centre, Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-370 05, Czech Republic

5 Institut Jean-Pierre Bourgin, Laboratoire de Biologie Cellulaire, INRA-Centre de Versailles, Versailles Cedex, F-780 26, France

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BMC Genomics 2012, 13:722  doi:10.1186/1471-2164-13-722

Published: 23 December 2012

Additional files

Additional file 1:

List of 18S gene clusters from 454 amplicon sequencing. Description: Each MsExcell list contains information about cluster ID, mutation pattern, number of reads, number of reads expressed as a percentage and total number of reads for a given species. For N. sylvestris and N. tomentosiformis, positions of variable sites read the non-coding DNA strands; for N. otophora and N. kawakamii, these read the coding strands.

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Additional file 2:

List of ITS1 clusters from 454 amplicon sequencing. The MsExcell charts are organized as in Additional file 1.

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Additional file 3:

Substitution mutation patterns in ITS1 region (single read clusters were excluded).

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Additional file 4:

Abundance of individual clusters (number of reads/total number of reads per cluster, expressed as a percentage) in 454 sequencing data from N. tomentosiformis, N. sylvestris, N. otophora and N. kawakamii ITS1 and 18S rDNA sequences. The clusters are distinguished by polymorphisms, i.e. SNPs or indels.

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Additional file 5:

Output of SNP algorithm in CLC genomics of Illumina ITS1 reads from N. sylvestris and N. tomentosiformis.

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Additional file 6:

Output of DIP algorithm in CLC genomics of Illumina ITS1 reads from N. sylvestris and N. tomentosiformis.

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Additional file 7:

Comparison of polymorphisms analyzed by different sequencing methods. The data are for N. sylvestris ITS1. Position (coding DNA strand) and type of mutation is in brackets : [−] – no mutation (usually the most abundant cluster), [57:C>T] – substitution C into T; [49:50>G] – insertion of G between nucleotides 49 and 50.

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Additional file 8:

Representation of IGS sequences in 454 reads. The plots show number of similarity hits along (A) N. sylvestris and (B) N. tomentosiformis, obtained in BLASTN searches against 454 reads from N. sylvestris and N. tomentosiformis, respectively [22]. The analysis was run using the PROFREP server (http://w3lamc.umbr.cas.cz/profrep/public/) with e-value cutoff of 1e-15. The curves were smoothed by value averaging in a 10-bp sliding window. Conversion of the hit numbers to genomic copy numbers (per 1C) based on genome coverage of the 454 sequencing is provided on the right side of the plots.

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