Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.
Bottom Line: Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions.Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome.Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome.
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.Show MeSH
Related in: MedlinePlus
Mentions: We separately analyzed different positions in coding DNA and calculated the G + C and dinucleotide frequencies for each of three codon positions. Under “first codon position,” we assume the first and the second nucleotide in the codon, the “second position” are the second and the third nucleotides, whereas the “third position” are the third nucleotide and the first one in the next codon. For each environment and each dinucleotide frequency we determined the Mann–Whitney statistic separately (using R), and normalized it to the readily interpretable AUROC score by dividing with the product of the sample sizes for the two classes. The analyses in figure 6 implicitly account for phylogenetic relatedness, as the first sites are compared with second sites (and 2nd vs. 3rd, and 3rd vs. 1st) in the exact same set of genomes. In other words, if a high AUROC score is purely due to phylogenetic signal confounded with the environmental labels, it should be equally so at all codon sites, and no significant difference in AUROC scores will be found.
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.