Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens

Abstract

A 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. Our conclusion is supported by four independent lines of evidence: 1) Very weak or nonsignificant correlation between gene expression and codon usage bias, 2) no increased codon usage bias in more broadly expressed genes, 3) no evidence that codon usage bias would constrain synonymous and nonsynonymous divergence, and 4) predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens.

Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales

“…However, changes in the generation time alone are seemingly insufficient to explain all cases of mutation rate heterogeneity observed so far, and other factors such as effective population size, growth rate, changes in molecular mechanisms or environmental conditions also should be contemplated. For example, theoretically well‐grounded arguments predict a dramatic reduction of effective population size in haploids with the onset of self‐fertilization (Söveny et al., ), and in the present study not all liverworts that are considered to be short‐lived, such as epiphyllous taxa (e.g. Cololejeunea ; Schuster, ; Zartman and Nascimento, ), have long branches.…”

Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing

“…Principal component analysis (PCA) of SNPs as well as InDels recapitulates the SNP clustering results (Supplementary Figure S9). The samples from Szövényi et al (2017) went into the SNP calling pipeline as a blind test. The sample origin was originally marked as unknown.…”

“…However, P. patens gDNA samples are rare. Nevertheless, the recent publication of RNA-seq datasets (Demko et al, 2014;Frank and Scanlon, 2015;Stevenson et al, 2016;Szövényi et al, 2017;Perroud et al, 2018;Fernandez-Pozo et al, 2019) provides a source of information that can be used to detect SNPs. Due to the high number of RNA-seq samples analyzed, efficient pipeline processing is essential.…”

Combination of the Endogenous lhcsr1 Promoter and Codon Usage Optimization Boosts Protein Expression in the Moss Physcomitrella patens

“…Codon usage of P. patens has been calculated and published based on expressed sequence tag (EST) data that were created before the genome sequence was published ( Rensing et al, 2005 ; Stenoien, 2005 ) and recently based on the gene models predicted from genome sequencing ( Szovenyi et al, 2017 ). In our analysis of codon usage bias based on v1.6 gene models in P. patens , we detect a bias in highly expressed genes to prefer certain codons.…”

“…In a subgroup of genes from one species, a bias for certain codons can be found, e.g., in highly expressed genes of Caenorhabditis elegans , Drosophila melanogaster , and A. thaliana codon usage differs from more weakly expressed genes of the same species ( Duret and Mouchiroud, 1999 ). In P. patens , this codon usage bias seems to be driven by a combination of weak natural selection and the predominant mutational biases ( Szovenyi et al, 2017 ).…”