Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryzaand their phylogenetic utility across various taxonomic levels

Table 3 Shared single copy nuclear genes are a rich source of phylogenetic information.

ATH	Annotation	# SEQ	# NT	# VAR	PI	>50 MP	>50 ML
At2 g13360	AGT1	49	1203	703	51%	63%	65%
At3 g47810	MAIGO 1	91	573	359	49%	66%	73%
At2 g32520	dienelactone hydrolase family protein	73	721	536	64%	75%	81%
At3 g52300	ATPQ	129	519	395	62%	65%	66%
At5 g06360	Ribosomal protein S8e	51	780	449	47%	58%	58%
At5 g04600	RNA recognition motif (RRM)-containing protein	63	579	475	74%	68%	71%
At2 g21870	probable atp synthase 24 kda subunit, mitochondrial precursor	95	606	492	68%	78%	78%
At4 g33250	eukaryotic translation initiation factor 3 subunit 11 (eif3k)	60	662	453	59%	68%	66%
At4 g30010	fiber protein Fb15	129	251	217	77%	62%	63%
At1 g77710	Probable ubiquitin-fold modifier 1 precursor	143	254	202	55%	46%	45%
At4 g08230	glycine-rich protein	51	413	286	54%	60%	68%
At4 g31720	STG1, TAFII15	64	448	323	51%	63%	67%
At4 g37830	putative cytochrome c oxidase subunit VIa precursor	151	216	192	71%	43%	45%
At5 g47570	similar to hypothetical protein 25.t00006 [Brassica oleracea]	90	387	288	64%	58%	65%
At5 g23290	putative c-myc binding protein	69	404	289	64%	62%	69%
At1 g27530	expressed protein	60	525	332	51%	68%	71%
At3 g20390	Endoribonuclease L-PSP, putative	132	372	313	69%	70%	70%
At5 g63135	hypothetical protein	64	448	323	51%	65%	63%
	Concatenated alignment of 13 shared single copy genes	69	7701	5072	55%	81%	87%

This table provides the following information about the 18 shared single copy genes that were used for phylogenetic analysis based on EST and finished cDNA sequences: the Arabidopsis thaliana locus ID (ATH); the TAIR annotation in Arabidopsis (Annotation); the number of sequences in the final alignment (# SEQ); the number of nucleotides in the final alignment (# NT); the number of variable characters in the final alignment (# VAR); the percentage of characters that are parsimony-informative (% PI); the percent of nodes in the MP bootstrap consensus trees that are supported in greater than 50% of the bootstrap replicates; the percent of nodes in the ML bootstrap consensus trees that are supported in greater than 50% of the bootstrap replicates.

ISSN: 2730-7182