The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an 1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 3 10 210 mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.KEYWORDS mutation accumulation; effective population size; biased gene conversion; fission yeast M UTATION is the ultimate source of all genetic differences within and among species. Mutation may alter the sequence of the genome via single-base substitutions; change the length of the genome by means of insertions, deletions, and duplications; or alter genome architecture via changes in chromosomal ploidy. The rate at which each of these events occurs in nature is largely obscured in a comparison of individuals or species owing to the action of natural selection and drift. An unbiased estimate of the rate and spectrum of spontaneous mutations can be obtained by passing replicate individuals through thousands of generations of mutation accumulation (MA). Under this protocol, which imposes a very small effective population size during passage, selection will have little influence on the fate of new mutations.The fission yeast Schizosaccharomyces pombe is a member of the largest and most diverse fungal phylum, Ascomycota, and is a key model system in cell biology. In the wild, S. pombe occurs in small, incompletely isolated populations with only weak population structure resulting from recent global dispersal (Brown et al. 2011;Jeffares et al. 2015). Beyond this, little is known of its natural ecology. It is, however, often recovered from natural fermentations and was isolated originally from East African millet beer.Notwithstanding the uncertainty regarding its ecology, the life cycle of S. pombe in the wild is likely to be predominantly haploid. In a collection of 81 natural isolates, all but one were haploid, with the sole diploid most likely resulting from biparental inbreeding (Brown et al. 2011). ...
Significance Centromeres are the fundamental unit required for segregation of chromosomes during mitosis and meiosis, and they are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). In contrast to the relatively well-known process of de novo assembly of CenH3 at centromeres, little is known of how CenH3 is actively removed, leading to centromere disassembly, an essential biological process during the life of a cell. This study describes the process of centromere disassembly, demonstrating that it occurs via an active, proteolytic mechanism, which is also linked to major changes in chromosome dynamics: chromatin decondensation and bulk rRNA gene activation.
Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.
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