Therefore, we first compared tetranucleotide usage in eHwalsbyiGI1s, genomes of H. walsbyi and genomes of other CR30 microbes with low GC-content (Fig. 1a).
Vicario et al. (2007) previously proposed this possibility in a comparison of codon usage in the genomes of 12 Drosophila species.
Thus the experimental isolation and sequencing of the Tiberius strain, from a different environment to strain HD100, does support the in silico predictions [ 5, 6] garnered from analyses of phylogeny and codon usage in the genome of the single type strain HD100 by evolutionary geneticists.
We performed a correspondence analysis on codon usage in each genome of all available Mamiellophyceae host virus pairs (fig. 1).
The statistical results indicate the presence of phylogenetic dependence of codon usage in DENV genomes.
DNA binding factors and other development-related genes show a bimodal distribution of CpG usage, in methylated genomes only, and are noticeably overrepresented in or near clusters of three or more CGIs.
Then, we chose a start codon of gene 2 either according to the empirical start codon usage in prokaryotic genomes (80% ATG, 17% GTG, and 3% TTG) or assuming equal usage (one-third each).
While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.
In totality, our data provide marked evidence that elevated gene expression is associated with usage of an optimal set of codons in Neurospora taxa, a finding consistent with selection on codon usage in their genomes.
Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes.
