Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB

Date Published: February 26, 2015

DOI: http://dx.doi.org/10.5061/dryad.65th6

 

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Title PairwiseLD
Description This file contains estimates of pairwirse linkage disequilibrium (r^2) for all 623 SNPs significantly associated with gender in mapping population T52.
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Title chr19_tree_ML
Description Newick tree file for Figure 3 panel b (concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107)
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Title chr19
Description Fasta aligment of concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.
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Title chr19_tree
Description Fasta aligment of concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for generating phylogenetic tree on Figure 3b.
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Title sanger_7690067_oneclone_ML
Description Newick tree file for Figure 3 panel a (Amplicon1:Chr09:7690067)
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Title sanger_7690067_anno
Description Fasta aligment of Amplicon1:Chr09:7690067, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.
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Title sanger_7690067_oneclone
Description Fasta aligment of Amplicon1:Chr09:7690067, used for generating phylogenetic tree on Figure 3a.
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Title sanger_7690067_ML
Description Newick tree file for Figure S2 panel a (Amplicon1:Chr9:7690067, all P. tremuloides clones included)
Download sanger_7690067_ML.nwk (2.335 Kb)
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Title sanger_7690067
Description Fasta aligment of Amplicon1:Chr9:7690067 with all P. tremuloides clones included used for generating phylogenetic tree on Figure S2 panel a
Download sanger_7690067.fas (29.13 Kb)
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Title 40024_sanger_nousat_fortree_ML
Description Newick tree file for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)
Download 40024_sanger_nousat_fortree_ML.nwk (2.481 Kb)
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Title 40024_sanger_nousat_fortree
Description Fasta alignment for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)
Download 40024_sanger_nousat_fortree.fas (74.93 Kb)
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Title 41515_sanger_all_tree_ML
Description Newick tree file for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)
Download 41515_sanger_all_tree_ML.nwk (2.712 Kb)
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Title 41515_sanger_all_tree
Description Fasta alignment for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)
Download 41515_sanger_all_tree.fas (79.20 Kb)
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Title 44107_sanger_tree_ML
Description Newick tree file for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)
Download 44107_sanger_tree_ML.nwk (2.712 Kb)
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Title 44107_sanger_tree
Description Fasta alignment for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)
Download 44107_sanger_tree.fas (71.66 Kb)
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Title Association_SNPfiles_Plink
Description Plink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for GWAS in T52 (T52v2maf01gr09), B34 (B34v2maf01gr09) and BT68 (BT68v2maf01gr09new)
Download README.txt (657 bytes)
Download Association_SNPfiles_Plink.zip (252.1 Mb)
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Title Admixture_inputfiles
Description Plink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for Admixture analysis in T52 (T52v2maf01gr1_LDprunned_thin01), B34 (B34v2maf01gr1_LDprunned) and BT68 (BT68v2POPSTnew)
Download Admixture_inputfiles.zip (742.7 Kb)
Download README.txt (697 bytes)
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When using this data, please cite the original publication:

Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB (2015) Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Molecular Ecology 24(13): 3243-3256. http://dx.doi.org/10.1111/mec.13126

Additionally, please cite the Dryad data package:

Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB (2015) Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.65th6
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