Table 2. Global statistics for each dataset.

Species	# of contigs			Total length	# of SNPS		Base composition					Polymorphism
	Total	Genotyped	With outgroup		Total	Polarized	GC	GC3	Average ENC	Codon Preferencea	Cor(GC3,Expression)b	πS (in %)	πN (in %)	πN/πS
Sorghum bicolor	29448	18518	3884	25849393	77703	12201	0.52	0.56	40.33	15 / 7	0.30	0.407	0.065	0.161
Pennisetum glaucum	24618	12443	9616	8870196	95068	78360	0.48	0.53	39.75	13 / 10	0.27	0.710	0.121	0.170
Triticum monococcum	33381	3766	1319	1758789	4409	3522	0.46	0.48	40.06	26 / 2	0.38	0.272	0.033	0.122
Musa acuminata	36115	14366	10546	6796494	113585	89793	0.49	0.52	39.42	28 / 1	0.31	1.223	0.237	0.194
Elaeis guineensis	26791	14970	9144	10623105	28097	27514	0.47	0.47	39.33	28 / 4	0.28	0.175	0.046	0.261
Dioscorea abyssinica	30551	18497	11544	16125630	84961	49552	0.46	0.46	41.10	26 / 12	0.17	0.417	0.085	0.205
Coffea canephora	28975	13290	9064	11180913	115483	78519	0.45	0.42	40.68	27 / 6	0.22	0.593	0.145	0.245
Solanum pimpinellifolium	34727	12357	1074	9438177	25392	3253	0.43	0.38	42.79	22 / 8	0.18	0.213	0.051	0.238
Olea europaea	45389	12816	8512	6718947	90397	68299	0.44	0.42	39.09	28 / 6	0.23	1.070	0.231	0.216
Theobroma cacao	28798	9918	7901	5510955	37455	32674	0.45	0.42	44.06	27 / 8	0.31	0.484	0.124	0.257
Vitis vinifera	29971	12398	9325	12513219	101351	68315	0.46	0.45	44.30	27 / 8	0.21	0.744	0.147	0.197

GC and GC3 have been computed on the total number of contigs

^a # of preferred codons ending in G or C / ending in A or T

^b correlation between GC at third codon positions and gene expression (log10(RPKM))

ENC: effective number of codons (computed with method X)

π_S: nucleotide diversity at synonymous sites

π_N: nucleotide diversity at non-synonymous sites