Table 1. Single copy nuclear genes used in the 19-gene-matrix.

Annotations are given for the indicated Arabidopsis gene.

Gene homologin A. thaliana	Annotation	LengthCDS inA. thaliana	length intronwithin CDS inA. thaliana	alignmentlength in19-gene-matrix	number ofPICs
At2G13360	Alanine-Glyoxylate-Aminotransferase (agt1)	1218	284	1214	593
At3G47810	MAIGO1 (mag1)	573	1200	554	239
At2G32520	Carboxymethylenebutenolidase	720	909	714	396
At3G52300	ATP synthase subunit d (atpQ)	507	934	497	251
At5G06360	Ribosomal protein S8e family protein	783	905	781	352
At5G04600	RNA-binding family protein	669	1131	506	322
At2G21870	Male Gametophyte Defective1 (mgp1)	723	1455	603	352
At4G33250	Eucaryotic Initiation Factor 3 subunit K (eiF3k)	681	887	661	356
At4G30010	Unknown protein	273	0	251	169
At4G08230	Glycine-rich protein	342	1199	402	194
At4G31720	TBP-associated factor II 15 (tafII15)	405	1088	446	204
At4G37830	Cytochrome c oxidase-related protein	309	793	162	94
At5G47570	NADH dehydrogenase 1 beta subcomplex subunit 8 (nduB8)	378	1435	384	218
At5G23290	Prefoldin 5 (pfd5)	456	838	429	253

The 14 genes used here were originally selected from a set of 959 genes shared by 4 angiosperms in single copy by Duarte et al. [11]. The alignment length excludes sites of uncertain homology. Abbreviations: PICs: Parsimony informative characters. For more statistics on the 19-gene-matrix see Table S2.