As far as possible intermediate advantages in evolution of the operational code, putative r-aaRSs, and tRNAs are concerned, we feel that the reviewer might, figuratively speaking, be asking too much and not just from the proposed scenario, but from the field of the genetic code origin research in general.
Personally, I regard the biosynthesis of amino acids as a later stage in the evolution of the code.
This strict pattern in the evolution of the code and of the amino acid repertoire was previously noticed and formulated as the coevolutionary theory of the genetic code [ 62, 63], which states that precursor-product amino acids are assigned to codons that differ in only one base pair.
In contrast, synonymous substitutions have been prevalent in the evolution of the coding region of frq1 and frq2, indicating the presence of strong functional constraints following gene duplication.
Accordingly, we expanded our phylogenetic analyses of the RLN1 and RLN2 paralogs of primates to include noncoding sequences corresponding to the single intron plus the upstream and downstream flanking regions, and also explored the role of natural selection in the evolution of the coding sequence of these genes.
The matrix (2) has been used in numerous studies on the evolution of the code [ 22- 244 45] 45].
We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts.
To compare the performance of YN and MYN, we need to generate simulated and empirical datasets with careful considerations on possible features in evolution of diverged protein-coding sequences, such as biases in transitional rates and codon frequencies.
This strongly supports the existence of a fundamental take-over in the evolution of the genetic code, in which ancient type II tRNA molecules had their functional identities replaced relatively late in evolution by a modern code.
