The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.

Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci

To study the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patterns in the Deinococcus radiodurans, D. geothermalis, and Thermus thermophilus genomes for nucleotide replacement dependent on the surrounding nucleotide context. Nucleotides on the third codon site were found to be strongly correlated with nucleotide sites at most six nucleotides away in all three species, where abundance patterns were dependent on whether two nucleotides share the same purine(R)/pyrimidine(Y) status. In the class Deinococci adjacent third site nucleotides were strongly correlated, where NNR|NNR and NNY|NNY codon pairs were overabundant while NNR|NNY and NNY|NNR codon pairs were underabundant. By far the largest deviations in all three species occur for NN(YR)|(YR)NN codon pairs. In the Thermus species, the NNY|YNN and NNR|RNN codon pairs were overabundant versus the underabundant NNY|RNN and NNR|YNN codon pairs, whereas in the Deinococcus species the opposite over-/underabundance relationship held for adjacent (GC) bases. We also observed a weaker overabundance of NNR|NRN and NNY|NYN codon pairs versus the underabundant NNR|NYN and NNY|NRN codon pairs. The perfect purine/pyrimidine symmetry of each of these cases, plus the lack of significant deviations for nucleotide pairs on other length scales up to 20 codons apart demonstrates that a pervasive pattern of nucleotide replacement dependent on local nucleotide context, and not codon bias, has occurred in these species. This nucleotide replacement has led to modified synonymous codon usage within the class Deinococci that affects which codons are positioned at particular codon sites dependent on the local nucleotide context.

Convergent host-parasite codon usage between honeybee and bee associated viral genomes

By correlating the codon usage in four insects (the honeybee, red flour beetle, mosquito and fruit fly) with six honeybee host specific viruses, we found that the codon usage patterns of the bee viruses were strongly related to that of the honeybee and only weakly related to the red flour beetle. The insects shared varying degrees of codon usage similarity which roughly follow the known phylogenetic relatedness. All of the codon usage similarity can be described by relatedness-by-descent except for the high codon usage similarity between the honeybee and honeybee associated viruses. This evidence for the convergent evolution of the honeybee viruses toward the codon usage of the honeybee suggests that small host specific viral genomes have the freedom to quickly optimize codon usage to successfully parasitize their preferred host. The codon usage co-evolution of the six host specific honeybee viruses towards the codon usage of the honeybee described in this paper is the first evidence for codon usage correlation between an insect host and a single stranded RNA virus.