TF network components in S. cerevisiae and sequence orthologs in C. neoformans have generally diverged in expression timing.

Putative orthologous gene pairs were identified, if any (S4 Table) [30]. The peak time (minutes) and time to half-peak expression (minutes) was identified for the first cell cycle in each yeast. Peak times were similar for some pairs (e.g. SWI4, CNAG_07464), but many pairs have diverged in ordering (e.g. FHL1, CNAG_05934, and CNAG_05535). The protein global alignment score is also shown for each putative ortholog pair (S4 Table). Some reported ortholog pairs did not have a significant global alignment score (i.e. E-value > 10), which was likely due to similar local sequence matches (e.g. homologous protein domains) and divergent regions elsewhere in the proteins (see S1 File).