Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species

West C, James SA, Davey RP, Dicks J, Roberts IN

Date Published: March 10, 2014

DOI: http://dx.doi.org/10.5061/dryad.0674n

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Appendix 1 - S. paradoxus Variation Table
Downloaded 50 times
Description pSNP and SNP frequencies for SGRP sequence reads of 26 S. paradoxus strains and the S288c S. cerevisiae strain compared with the rDNA consensus sequence of the CBS432 S. paradoxus type strain.
Download West_rDNA_Appendix_1.xlsx (176.3 Kb)
Details View File Details
Title Appendix 2 - S. cerevisiae Variation Table
Downloaded 45 times
Description pSNP and SNP frequencies for SGRP sequence reads of 34 S. cerevisiae strains and the Q32.3 S. paradoxus strain compared with the rDNA consensus sequence of the S288c S. cerevisiae type strain.
Download West_rDNA_Appendix_2.xlsx (250.1 Kb)
Details View File Details
Title Appendix 3 - Phylogenetic Networks of S. paradoxus and S. cerevisiae Strains
Downloaded 49 times
Description Both a) and b) show an enlargement of the main population structure in the network, with the small boxed inset showing the whole network including the outgroup. a) The S. paradoxus network shows a clear separation of each geographic population. b) The S. cerevisiae network shows a more complex network structure, consistent with our knowledge of this population.
Download West_rDNA_Appendix_3.pdf (1.520 Mb)
Details View File Details
Title Appendix 4 - Bar Charts of the pSNP Percentage Occupancy in S. cerevisiae by Population Type
Downloaded 39 times
Description a) Bar chart of the S. cerevisiae structured strains, with number of pSNPs against the pSNP occupancy. The boxed section highlights pSNPs with occupancies greater than 10% and less than 90%. The Malaysian, North American and West African strains have very few pSNPs within this boxed area, and these are denoted as structured clean strains. Those strains with a number of pSNPs within this boxed area show a degree of mosaicism, and we classify these strains as being structured mosaic strains. b) Bar chart of S. cerevisiae mosaic strains, where there are a large number of pSNPs within the 10% to 90% occupancy range.
Download West_rDNA_Appendix_4.pdf (112.2 Kb)
Details View File Details
Title S. paradoxus CE distance matrix
Downloaded 11 times
Description Cavalli-Sforza and Edwards rDNA-based distance matrix for 26 S. paradoxus strains plus S. cerevisiae strain S288c
Download S_paradoxus_CE_Dist.nex (7.423 Kb)
Details View File Details
Title S. cerevisiae CE distance matrix
Downloaded 9 times
Description Cavalli-Sforza and Edwards rDNA-based distance matrix for 34 S. cerevisiae strains plus S. paradoxus strain Q32.3
Download S_cerevisiae_CE_Dist.nex (12.14 Kb)
Details View File Details
Title S. paradoxus NJ tree
Downloaded 8 times
Description Neighbor-Joining phylogenetic tree derived from the S. paradoxus CE distance matrix
Download S_paradoxus_tree.nex (6.698 Kb)
Details View File Details
Title S. cerevisiae NJ tree
Downloaded 8 times
Description Neighbor-Joining phylogenetic tree derived from the S. cerevisiae CE distance matrix
Download S_cerevisiae_tree.nex (7.287 Kb)
Details View File Details
Title Perl script for coverage/copy number estimation
Downloaded 26 times
Description Perl script to calculate the rDNA unit coverage from a sequence read dataset and to estimate the number of rDNA units (copy number) in an rDNA tandem array.
Download coverage_v2.pl (5.176 Kb)
Details View File Details
Title Updated Appendix 3 - Phylogenetic Networks of S. paradoxus and S. cerevisiae Strains
Downloaded 13 times
Description Both a) and b) show an enlargement of the main population structure in the network, with the small grey inset showing the whole network including the outgroup. a) The S. paradoxus network shows a clear separation of each geographic population. b) The S. cerevisiae network shows a more complex network structure, consistent with our knowledge of this population.
Download West_rDNA_Appendix_3.svg (705.5 Kb)
Details View File Details
Title S. paradoxus CE distance matrix
Downloaded 6 times
Description Cavalli-Sforza and Edwards rDNA-based distance matrix for 26 S. paradoxus strains plus S. cerevisiae strain S288c
Download S_paradoxus_CE_dist.nex (7.657 Kb)
Details View File Details
Title Updated S cerevisiae CE distance matrix
Downloaded 5 times
Description Cavalli-Sforza and Edwards rDNA-based distance matrix for 34 S. cerevisiae strains plus S. paradoxus strain Q32.3
Download S_cerevisiae_CE_dist.nex (12.38 Kb)
Details View File Details
Title Updated S. paradoxus NJ tree
Downloaded 5 times
Description Neighbor-Joining phylogenetic tree derived from the S. paradoxus CE distance matrix
Download S_paradoxus_tree.nex (1.468 Kb)
Details View File Details
Title Updated S. cerevisiae NJ tree
Downloaded 10 times
Description Neighbor-Joining phylogenetic tree derived from the S. cerevisiae CE distance matrix
Download S_cerevisiae_tree.nex (1.898 Kb)
Details View File Details

When using this data, please cite the original publication:

West C, James SA, Davey RP, Dicks J, Roberts IN (2014) Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species. Systematic Biology 63(4): 543-554. http://dx.doi.org/10.1093/sysbio/syu019

Additionally, please cite the Dryad data package:

West C, James SA, Davey RP, Dicks J, Roberts IN (2014) Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0674n
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: