Data from: Tempo of degeneration across independently evolved nonrecombining regions

Recombination is beneficial over the long term, allowing more effective
selection. Despite long-term advantages of recombination, local
recombination suppression can evolve and lead to genomic degeneration, in
particular on sex chromosomes. Here, we investigated the tempo of
degeneration in nonrecombining regions, that is, the function curve for
the accumulation of deleterious mutations over time, leveraging on 22
independent events of recombination suppression identified on mating-type
chromosomes of anther-smut fungi, including newly identified ones. Using
previously available and newly generated high-quality genome assemblies of
alternative mating types of 13 Microbotryum species, we estimated
degeneration levels in terms of accumulation of nonoptimal codons and
nonsynonymous substitutions in nonrecombining regions. We found a reduced
frequency of optimal codons in the nonrecombining regions compared with
autosomes, which was not due to less frequent GC-biased gene conversion or
lower ancestral expression levels compared with recombining regions. The
frequency of optimal codons rapidly decreased following recombination
suppression and reached an asymptote after ca. 3 Ma. The strength of
purifying selection remained virtually constant at dN/dS = 0.55, that is,
at an intermediate level between purifying selection and neutral
evolution. Accordingly, nonsynonymous differences between mating-type
chromosomes increased linearly with stratum age, at a rate of 0.015 per
My. We thus develop a method for disentangling the effects of reduced
selection efficacy from GC-biased gene conversion in the evolution of
codon usage and we quantify the tempo of degeneration in nonrecombining
regions, which is important for our knowledge of genomic evolution and the
maintenance of regions without recombination.