Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.

ABSTRACT: Single-stranded RNA molecules can form intramolecular bonds between nucleotides to create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural selection. Here, we examined the population genetics of these mutations within Arabidopsis thaliana genes. We began by identifying derived SNPs with the potential to alter secondary structures within coding regions, using a combination of computational prediction and empirical data analysis. We identified 8,469 such polymorphisms, representing a small portion (∼0.024%) of sites within transcribed genes. We examined nucleotide diversity and allele frequencies of these "pair-changing mutations" (pcM) in 1,001 A. thaliana genomes. The pcM SNPs at synonymous sites

SUBMITTER: Martin GT 

PROVIDER: S-EPMC12199705 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature