Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

Renaut S, Rieseberg LH

Date Published: May 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.8s459

 

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Title HA412_trinity_noAltSplice_400bpmin.fa
Description Link to reference transcriptome described in Renaut et al. 2013 (NatCom), used for all alignments, and previously deposited in Dryad as part of http://dx.doi.org/10.5061/dryad.9q1n4.
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Title new_provean_results_all
Description Results of PROVEAN analyses identifying deleterious non-synonymous mutations. First column identifies the non-synonymous AA changes and their position (e.g. P113A). The correspondence between this AA change and the SNPs identified in the dataset can be found in this file (new_snp_table_effect). Second column is the Provean score. Third column are the name of the genes.
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Title new_sift_results_all
Description Results of SIFT analyses identifying deleterious non-synonymous mutations. First column identifies the non-synonymous AA changes and their positions (e.g. S11T). Column 2-6 are the SIFT statistics. Last column are the name of the genes.
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Title unique_orf
Description Unique (longest) open reading frames identified in the reference transcriptome
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Title snp_table_all3
Downloaded 4 times
Description Genotypes and positions of all SNPs identified in the dataset.
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Title new_snp_table_effect
Downloaded 2 times
Description List of all SNPs. Column 4-43 indicate whether this SNP was noncoding (nc), non-synonymous (ns), synonymous (s), alternate stop codon (STOP), or homozygous reference allele (0). Column 44 indicates whether this mutation was analyzed by PROVEAN. Column 45 indicates PROVEAN score, if applicable. Column 46-50 indicate frequency of alternate allele in different classes of individuals.
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Title table_S1_24_02_15
Downloaded 1 time
Description Table S1 with information about samples (location, sequencing stats, etc.)
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When using this data, please cite the original publication:

Renaut S, Rieseberg LH (2015) The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Molecular Biology and Evolution 32(9): 2273-2283. http://dx.doi.org/10.1093/molbev/msv106

Additionally, please cite the Dryad data package:

Renaut S, Rieseberg LH (2015) Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8s459
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