Table 2.

Folding Potential of Coding Regions From Diverse Organisms

Empire	Species	No. genes	$\text{[math]}$	EFP	Wilcoxon t-test	%G + C
Archaea	Thermoplasma volcanium	1525	-143.2	+1.0	NS	43.14
	Methanobacterium thermoautotropicum	1873	-204.0	+4.0*	E-12	52.27
	Sulfolobus solfataricus	2977	-121.8	-0.2	NS	39.01
	Sulfolobus tokodaii	2826	-110.6	-0.2	NS	36.49
	Pyrococcus abyssi	1769	-165.4	+1.4	NS	47.22
	Aeropyrum pernix	1840	-244.6	+0.2	NS	58.86
	Archaeoglobus fulgidus	2407	-187.6	-0.6	NS	51.17
	Halobacterium sp. NRC-1	2058	-328.4	+5.2*	<E-16	69.43
Eubacteria	Escherichia coli	4290	-218.6	+4.8*	<E-16	52.90
	Salmonella typhi	4600	-227.6	+6.0*	<E-16	54.30
	Bacillus subtilis	4100	-165.6	+2.8*	E-13	45.92
	Mycoplasma pneumoniae	689	-147.6	+6.6*	<E-16	42.58
	Vibrio cholerae	2752	-193.2	+4.4*	<E-16	50.13
	Aquifex aeolicus	1522	-152.2	+1.4	NS	45.52
	Borellia burgdorferi	850	-98.4	+1.6	NS	31.47
	Thermotoga maritima	1846	-173.4	+2.2*	E-05	48.33
	Haemophilus influenzae	1709	-142.0	+2.2*	E-05	40.79
	Synechocystis PCC6803	3169	-185.4	-1.8*	E-07	50.35
	Treponema pallidum	1031	-219.0	+2.8*	E-03	54.85
	Clostridium acetobutylicum	3672	-106.0	+1.8*	<E-16	34.05
	Rickettsia prowazekii	834	-102.6	+1.2	NS	32.75
	Helicobacter pylori	1491	-139.2	-0.6	NS	41.96
Eukaryota	Plasmodium falciparum	422	-70.8	+0.8	NS	26.60
	Saccharomyces cerevisiae	6314	-129.0	+1.2*	<E-16	42.20
	Arabidopsis thaliana	2676	-162.2	-0.1	NS	47.80
	Caenorhabditis elegans	762	-149.0	-2.8*	E-07	46.40
	Homo sapiens	1855	-207.8	-0.8	NS	54.10
	Drosophila melanogaster	1956	-210.2	+0.01	NS	55.90

All sequences were randomized using the Dicodon Shuffle program. EFP as defined in Methods. (NS) Not significant.
↵* Statistically significant bias in favor (positive EFP) or against (negative EFP) RNA structure.

Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes