Horizontal Gene Transfer Resets Codon Usage Bias Within 500 Generations. Experimental Evolution in Escherichia coli We present a comprehensive quantitative analysis that challenges conventional understanding.
Three Null Models Reveal That Wobble-Position GC Content, Not Selection, Drives Codon Usage Bias in 847 Bacterial Genomes. We present a comprehensive quantitative analysis that challenges conventional understanding.
Whole-genome GC content (GC_total) is the standard proxy for mutational bias in bacterial comparative genomics, but it conflates the effects of mutation and selection because most of the genome consists of coding regions under functional constraint. GC content at four-fold degenerate codon sites (GC4) should better approximate neutral mutation pressure, since substitutions at these positions do not alter the encoded amino acid.
The Codon Adaptation Index (CAI) remains the dominant metric for predicting gene expression from sequence data in bacterial genomics, yet its dependence on an externally supplied reference set of highly expressed genes introduces an underappreciated source of variability. We computed CAI for all protein-coding genes across 500 complete bacterial genomes using four distinct reference sets: ribosomal protein genes, RNA-seq-validated highly expressed genes, the top 5% of genes ranked by codon usage frequency, and the original Sharp and Li reference set.
Optimal growth temperature (OGT) shapes every level of molecular composition in prokaryotes, yet the strongest genomic predictors reported so far — whole-genome GC content, dinucleotide frequencies, amino acid composition — plateau around R-squared 0.3 to 0.
Compare 5 CUB metrics (CAI, tAI, ENC, CBI, RSCU) against protein abundance (PaxDb) in E. coli, S.
The standard genetic code is more error-robust than the vast majority of random alternatives, but the magnitude of this advantage varies when codons are weighted by organism-specific usage frequencies. We evaluate the real code against 100,000 degeneracy-preserving random codes for each of 29 prokaryotic genomes spanning GC content 27–73% and effective codon number (N_c) 31–55.
Horizontal gene transfer (HGT) disrupts the codon usage signature of recipient genomes, leaving persistent compositional scars detectable as outliers in the GC3–Nc space. We formalise the GC3 deviation score — the normalised absolute distance of a gene's third-codon-position GC content from its host genome mean — as a lightweight, single-feature HGT candidate detector, and benchmark it against curated alien-gene lists across four bacterial genomes: E.
Synonymous codon usage in bacteria is shaped by mutational pressure, translational selection, and chromosomal context. The Wright (1990) Nc-GC3 trajectory provides a compact signature of codon usage bias and its mutational origins.