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The large number of organisms and of genes sequenced at the present time permits now to study molecular evolution in such lower clades as genera, species, and subspecies. Here, we focus our attention on the genus Mycobacterium, in which we examined codon and aminoacid usage in 13 species, and in 12 subspecies for a total of 8,836,513 codons from 26,755 sequences. Within the genus Mycobacterium, frequencies of codon and aminoacid usage correlate between species and between subspecies. In the groups studied, aminoacid molecular weight and codon degeneracy influence correlations between frequencies, while GC content is the main factor influencing the effective number of codons. The coding GC, which is highly correlated with total genomic GC content, seems to be the main factor influencing present synonymous codon usage in the genus. In particular, the GC content at the 3rd base position seems to shape heavily the effective number of codons, giving indication that here mutational bias dominates over translational selection. Evolutionary trees based on codon and aminoacid usage are consistent with traditional phylogenies of species within the genus.

We tested the hypothesis of optimal adaptation of viral infectors to eukaryotic hosts, using (1) correlation in codon and amino acid usage between organisms, and (2) canonical correlation between groups of hosts and infectors. The codon correlations between parasites and hosts vary, being low between swine and African swine fever virus (ASF; r = 0.18), and highest between potato and potato virus X (r = 0.60). The correlations might indicate different stages of evolution toward optimal adaptation of the parasite codon distribution to the host tRNA pools. The amino acid correlations vary from r = 0.71 between pig and ASF, to 0.88 between catfish and its herpesvirus. It was observed that both in virus and hosts, there is a negative correlation between frequency of an amino acid and molecular weight. Therefore, it was advanced that viral infectors might be preadapted to their hosts because of similarities of the tRNA pools of hosts, and that evolution toward optimization would be dependent on the size of the divergence between the codon distributions of infector and host. Preadaptation does not imply origin of the virus by lateral transfer from the present host, since the correlation of the molecular weight of amino acids with their abundance in proteins is a general phenomenon., (Copyright 2008 S. Karger AG, Basel.)

Objective: The aim of this study was to compare the use of amino acids and codons in influenza viruses A and B and in their common hosts, to highlight any relevant difference., Methods: The frequency of the 20 amino acids and of the 61 codons was studied in influenza viruses A, B, and in man, pig, and chicken. The correlation in amino acid and codon use among these hosts was calculated., Results: The correlation between the frequency of the 20 amino acids and the molecular weight was also calculated and it was very similar in all studied hosts, ranging from 0.506 to 0.595. The correlation of codon frequency among these organisms was highest between man and chicken (r=0.974), and lowest between pig and virus B (r=0.147)., Conclusions: The important correlation in codon use among the three hosts and the two viruses suggests there was a remote lateral gene transfer among the three hosts and the two viruses. The higher use of alanine, leucine, and proline in man versus virus A is significant.