Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens.

Long term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded this assertion received mixed experimental support. Here we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak to nonexistent. Our conclusion is supported by four independent lines of evidence: a) Very weak or nonsignificant correlation between gene expression and codon usage bias; b) No increased codon usage bias in more broadly expressed genes; c) No evidence that codon usage bias would constrain synonymous and nonsynonymous divergence; d) Predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. Therefore, we propose that synonymous codon usage is mainly driven by nucleotide compositional biases of unknown origin and that the co-adaptation recovered between synonymous codon usage and copy number of cognate tRNA genes is not an indication of translational/transcriptional selection. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens.