Mutation rate analysis via parent–progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids

Abstract

Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10−9 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0–7.4 × 10−9 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10−9 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10−8 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.

Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin

“…In addition to effects caused by parental alleles, an increased rate of de novo structural mutations in hybrids appears possible, similar to the finding of increased point mutations in heterozygotes (“heterozygosity instability”; Amos, ; Xie et al., ). Whether this actually occurs and leaves detectable genetic signatures has received comparatively little attention in studies on hybrid speciation.…”

Pleistocene glacial cycles drive isolation, gene flow and speciation in the high‐elevation Andes

“…Thus, to obtain absolute estimates for speciation times, we need estimates of current population sizes and generation times of each species. If we use a mutation rate of 7.0 × 10 −9 per generation per site, which is similar to the available estimates in plants ( Arabidopsis thaliana (Ossowski et al ., ) and Prunus (Xie et al ., )), to convert the genome‐wide estimates of nucleotide diversity of each species (Table ) into effective population sizes, we get estimates of current N e = 14 285 (for L. alopecuroides ), N e = 21 428 (for Pisba/Cocuy ) and N e = 25 000 (for Ocetá and L. triananus ). From these current population sizes, we can estimate the ancestral size of each species pair using the relative population size parameters ( N 1 and N 2 in Table ), which gives average values of N A = 15 458 ( for L. alopecuroides and L. triananus ) and N A = 7673 (for Ocetá and Pisba/Cocuy ).…”

Interspecific Hybrids Show a Reduced Adaptive Potential Under DNA Damaging Conditions

“…This is unlikely since the hybrid genotype is less sensitive than S. paradoxus at the concentration used. We rather hypothesize that in the specific case of stress caused by DNA damage, hybrids may be at a disadvantage because they are genetically unstable (Fontdevila 2005;Marfil et al 2006;Baack & Rieseberg 2007;Morales & Dujon 2012;Guerreiro 2014;Xie et al 2016;Dion-Côté & Barbash 2017;Mwathi et al 2019) and DNA damaging agents may further enhance this instability, preventing the occurrence or fixation of adaptive mutations. Consistent with the instability of hybrids, recent study of mutation accumulation in yeast reported that hybrids from more divergent parents lines were lost at a greater rate than the less divergent ones (Charron et al 2019) .…”

“…For instance, genomic changes of large effects, such as changes in ploidy, lead to hybrid inviability (Burton & Husband 2000) . Similarly, high rates of genomic changes could lead to an increased acquisition rate of deleterious mutations (Bashir et al 2014;Xie et al 2016) . Recently, S prouffske et al (2018) showed how Escherichia coli strains with a 100-fold increase in the mutation rate experienced a reduction in adaptation in many environments.…”