A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms.

ABSTRACT: Strand biases reflect deviations from a null expectation of DNA evolution that assumes strand-symmetric substitution rates. Here, we present strong evidence that nearest-neighbour preferences are a strand-biased feature of bacterial genomes, indicating neighbour-dependent substitution asymmetries. To detect such asymmetries we introduce an alignment free index (relative abundance skews). The profiles of relative abundance skews along coding sequences can trace the phylogenetic relations of bacteria, suggesting that the patterns of neighbour-dependent substitution strand-biases are not common among different lineages, but are rather species-specific. Analysis of neighbour-dependent and codon-site skews sheds light on the origins of substitution asymmetries. Via a simple model we argue that

SUBMITTER: Apostolou-Karampelis K 

PROVIDER: S-EPMC4991834 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature