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Renaut, Sebastien; Rieseberg, Loren H.

<b>Abstract</b><br/>For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. 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.; <b>Usage notes</b><br /><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">HA412_trinity_noAltSplice_400bpmin.fa</h4><div class="o-metadata__file-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.</div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">new_provean_results_all</h4><div class="o-metadata__file-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.</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">new_sift_results_all</h4><div class="o-metadata__file-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.</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">unique_orf</h4><div class="o-metadata__file-description">Unique (longest) open reading frames identified in the reference transcriptome</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">snp_table_all3</h4><div class="o-metadata__file-description">Genotypes and positions of all SNPs identified in the dataset.</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">new_snp_table_effect</h4><div class="o-metadata__file-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.</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">table_S1_24_02_15</h4><div class="o-metadata__file-description">Table S1 with information about samples (location, sequencing stats, etc.)</div><div class="o-metadata__file-name"></div></div>

Dataset

2020-06-24

CC0 1.0

https://doi.org/10.5683/SP2/FU77BF

http://creativecommons.org/publicdomain/zero/1.0