S4 Appendix - The complex evolution and genomic dynamics of mating-type loci in <i>Cryptococcus</i> and <i>Kwoniella</i>

GC content and codon composition/usage analysis. (A) Genome-wide GC content and deviation from genome mean in clade B and D strains included in Fig 2. (B) GC content reduction in the P/R locus relative to genome-wide background (clades C and D). (C) Neutral comparison of noncoding GC in P/R locus vs. chromosome-matched background windows (Test 1). (D) Third-position codon usage (AT3 vs. GC3) in P/R locus vs. background (Test 2). (E) Codon usage and bias metrics in P/R vs. matched background genes (Tests 2 and 3). (F) Statistical tests for codon usage bias in P/R vs. background (Tests 3 and 4). (G) Tests for reduced codon adaptation (CAI) after controlling for GC3 and gene length (Test 4). (XLSX)