PT  - JOURNAL ARTICLE
AU  - Bohdan B. Khomtchouk
AU  - Claes Wahlestedt
AU  - Wolfgang Nonner
TI  - A global perspective of codon usage
AID  - 10.1101/076679
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 076679
4099  - http://biorxiv.org/content/early/2017/01/14/076679.short
4100  - http://biorxiv.org/content/early/2017/01/14/076679.full
AB  - Codon usage in 2730 genomes is analyzed for evolutionary patterns in the usage of synonymous codons and amino acids across prokaryotic and eukaryotic taxa. We group genomes together that have similar amounts of intra-genomic bias in their codon usage, and then compare how usage of particular different codons is diversified across each genome group, and how that usage varies from group to group. Inter-genomic diversity of codon usage increases with intra-genomic usage bias, following a universal pattern. The frequencies of the different codons vary in robust mutual correlation, and the implied synonymous codon and amino acid usages drift together. This kind of correlation indicates that the variation of codon usage across organisms is chiefly a consequence of lateral DNA transfer among diverse organisms. The group of genomes with the greatest intra-genomic bias comprises two distinct subgroups, with each one restricting its codon usage to essentially one unique half of the genetic code table. These organisms include eubacteria and archaea thought to be closest to the hypothesized last universal common ancestor (LUCA). Their codon usages imply genetic diversity near the hypothesized base of the tree of life. There is a continuous evolutionary progression across taxa from the two extremely diversified usages toward balanced usage of different codons (as approached, e.g. in mammals). In that progression, codon frequency variations are correlated as expected from a blending of the two extreme codon usages seen in prokaryotes.