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

Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome.

Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

Usage notes

HA412_trinity_noAltSplice_400bpmin.fa Link to reference transcriptome described in Renaut et al. 2013 (NatCom), used for all alignments, and previously deposited in Dryad as part of dx.doi.org/10.5061/dryad.9q1n4. new_provean_results_all 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. new_sift_results_all 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. unique_orf Unique (longest) open reading frames identified in the reference transcriptome snp_table_all3 Genotypes and positions of all SNPs identified in the dataset. new_snp_table_effect 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. table_S1_24_02_15 Table S1 with information about samples (location, sequencing stats, etc.)