Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank complete genome sequences, and compared codon usage of class I (CI-29 sequences containing 132,675 codons) and class II (CII-259 sequences containing 1,184,925 codons) APMV-1 genomes. We also compared available complete fusion protein gene sequences (CI-175 sequences containing 96,775 codons; CII-1166 sequences containing 644,798 codons). Adaptation to Gallus gallus was compared among the different classes of viruses, among different genomic regions based on transcriptional levels, or among the fusion gene. Interestingly, distinctive codon usage determined by differences in relative synonymous codon usage and by codon adaptation indexes was observed for the two APMV-1 classes and for different transcriptional regions within classes. Furthermore, differential use of the third codon position and preferential use of codon pairs were seen for the two different classes and for selected genotypes of class II despite the fact that there were no large differences in nucleotide composition. The data suggest that codon usage has changed significantly since the two APMV-1 classes diverged, however, these changes are not significantly pronounced among viruses of the same genotype, suggesting that codon adaptation in APMV-1 occurs through a slow evolutionary process.