DOI: 10.5061/dryad.pnvx0k6ps
title: Data from: Tempo of degeneration across independently evolved nonrecombining regions

description: 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.
description: <strong>Codon usage</strong>
 Optimal codons where identified as the most often used synonymous
 codon among the 10% most highly expressed genes in two
 <em>Microbotryum</em> species grown in two conditions. The
 most highly expressed genes correspond to the genes with the lowest PC1
 coordinates in a within-group correspondence analysis (WCA, see http://pbil.univ-lyon1.fr/datasets/charif04/). Input data were the best TPM (from kallisto pseudo alignmet of trimmed paired-end reads on <em>M. intermedium</em>) per gene. We checked that expression was highly correlated between single-copy orthologous genes of <em>Microbotryum intermedium</em> and <em>M. lychnidis-dioicae</em>. <strong>Molecular dating</strong> Single-copy genes were assigned to genome compartments based on orthology with genes in <em>M. lagerheimi</em> and rearrangement scenarios. Concatenated codon-based alignments (obtained per orthologous group with macse v2.04) were imported into beauti to generate beast2's XML input files. We estimated the species and genome compartment divergence times under a calibrated Yule model and a HKY substitution model (kappa = 2, estimated frequencies) with 10,000,000 or 20,000,000 mcmc generations in beast v2.5.0. We used three unlinked site models (one per codon position). The clock model and tree parameters were kept linked. We used the split of <em>M. lychnidis-dioicae</em> and <em>M. silenes-dioicae</em> as a calibration point, with a normal prior with a mean of 0.42 Ma and sigma of 0.04.
description: <strong>External software used</strong>
 Beast v2.5.0
 https://github.com/CompEvol/beast2/releases R
 3.6.3 <em>R packages and
 libraries</em>
 ade4<br>ape<br>car<br>cowplot<br>dplyr<br>ggplot2<br>ggpubr<br>grid<br>interactions<br>plyr<br>pscl<br>reshape2<br>seqinr<br>sjmisc<br>sjPlot<br>tidyr
description: # Tempo of Degeneration Across Independently Evolved Nonrecombining
 Regions
 [https://doi.org/10.5061/dryad.pnvx0k6ps](https://doi.org/10.5061/dryad.pnvx0k6ps) This repo pertains to the analysis of optimal codon usage in non-recombining regions of fungal mating type chromosomes ## Description of the data and file structure All associated data is described in [https://doi.org/10.1093/molbev/msac060](https://doi.org/10.1093/molbev/msac060) The file `dS_dN_FOP_FINAL.txt` contains per gene tabular data with synonymous substitutions per synonymous site, non-synonymous substitutions per non-synonymous site (yn00) and fraction of optimal codons obtained with scripts available at https://zenodo.org/records/6334670 (using transcripts per million of mapped reads per gene). ## Sharing/Access information Data was derived from the following sources: * [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA747176](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA747176) * [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA246470](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA246470) ## Code/Software See Usage Note for external software and package versions. See accompanying scripts for Tempo of degeneration across independently evolved non-recombining regions available at [https://zenodo.org/records/6334670](https://zenodo.org/records/6334670)