Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

Table 1 Comparison of conserved optimal codon numbers at paired and unpaired sites.

Method	Algorithm	ALL	GC-ending	AT-ending	GC leu & lys
Genes shorter than 800 bp
RNAfold S. cerevisiae	MFE	0.646 ***	0.624 **	0.503 ***	1.353 ***
	Mc	0.542 ***	0.567 ***	0.422 ***	0.910 ***
RNAfold S. paravensis	MFE	0.667 ***	0.608 ***	0.542 NS	1.137 ***
	Mc	0.560 ***	0.571 ***	0.407 **	1.119 ***
RNAfold S. mikitae	MFE	0.653 ***	0.590 ***	0.544 *	1.172 ***
	Mc	0.572 ***	0.623 ***	0.411 ***	1.131 ***
RNAfold S. bayanus	MFE	0.640 ***	0.597 **	0.502 ***	1.181 ***
	Mc	0.537 **	0.557 ***	0.401 ***	1.003 ***
ALIfold	MFE	0.638 ***	0.577 ***	0.465 NS	1.499 ***
	Mc	0.468 **	0.444 ***	0.326 ***	0.997 ***
All genes
RNAfold S. cerevisiae	MFE	0.920 ***	0.863 ***	0.751 ***	1.584 ***
	Mc	0.841 ***	0.866 ***	0.676 ***	1.436 ***
RNAfold S. paravensis	MFE	0.878 ***	0.826 ***	0.733 ***	1.497 ***
	Mc	0.819 ***	0.822 ***	0.659 ***	1.460 ***
RNAfold S. mikitae	MFE	0.912 ***	0.814 ***	0.790 NS	1.160 ***
	Mc	0.839 ***	0.869 ***	0.740 NS	1.404 ***
RNAfold S. bayanus	MFE	0.904 ***	0.855 ***	0.742 ***	1.590 ***
	Mc	0.833 ***	0.840 ***	0.675 ***	1.455 ***
ALIfold	MFE	0.899 ***	0.759 **	0.739 NS	1.937 ***
	Mc	0.770 ***	0.724 ***	0.645 ***	1.529 ***

I combine contingency tables for all amino acids and genes (ALL) and subsets of amino acids with GC- and AT- ending optimal codons (leu and lys are treated separately, as these two GC-ending amino acids behave very opposing, see below Table 2). Mantel Haenzsel estimators and significances are presented, W_MH <1 = lower optimal codon use at paired than at unpaired sites.
* < 0.05, ** < 0.01, *** < 0.005, NS = not significant. Structure prediction is based on ALIfold and RNAfold using MFE and McCaskill's (Mc) algorithm.

ISSN: 2730-7182