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Table 5.

Genes Selected as Phylogenetic Correlates Specific to Each Tree Branch

	DI score	Syn prot	Gene	Profile	Protein function
	Branch CyaPar
1	0.0400	sll0534	clpP	10001000000000000000	ATP-dep. translocation rel. protease
2	0.0400	slr0739	crtE	10001000000000000000	geranylgeranyl pyrophosphate synthase
3	0.0400	slr2075	groES	10001000000000000000	10kD chaperonin 1
4	0.0400	slr1808	hemA	10001000000000000000	transfer RNA-Gln reductase
5	0.0400	sll1599	mntA	10001000000000000000	Mn transporter
6	0.0400	sll1600	mntB	10001000000000000000	Mn transporter
7	0.0400	sll0622	nadA	10001000000000000000	quinolinate synthetase
8	0.0400	slr2034	ycf	10001000000000000000	hypothetical protein
9	0.0400	slr2073	ycf	10001000000000000000	hypothetical protein
10	0.0400	slr0181	ycf	10001000000000000000	hypothetical protein
11	0.0400	slr1552	ycf	10001000000000000000	hypothetical protein
12	0.0400	sll1702	ycf	10001000000000000000	hypothetical protein
	Branch Nongreen algae (and CyaPar)
1	0.1192	sll1325	atpD	10011001000010001000	ATP synthase d subunit
2	0.1192	sll1323	atpG	10011001000010001000	ATP synthase subunit b′
3	0.1192	sll0170	dnaK	10011001000010001000	DnaK protein chaperonin
4	0.1192	slr2076	groEL	10011001000010001000	60kD chaperonin 1
5	0.1192	sll0998	lysR	10011001000010001000	LysR transcriptional regulator
6	0.1192	sal0020	petF	10011001000010001000	ferredoxin
7	0.1192	ssr2831	psaE	10011001000010001000	photosystem I subunit IV
8	0.1192	sll0819	psaF	10011001000010001000	photosystem I subunit III
9	0.1192	sll1398	psbW	10011001000010001000	photosystem II 13 kD protein
10	0.1192	sll0258	ptbV	10011001000010001000	cytochrome c550
11	0.1192	sml0007	psbY	10011001000010001000	photosystem II PsbY protein
12	0.1192	slr0012	rbcS	10011001000010001000	ribulose bisphosphate carboxylase small sub.
13	0.1192	sll1744	rpl1	10011001000010001000	50S ribosomal protein L1
14	0.1192	sll1799	rpl3	10011001000010001000	50S ribosomal protein L3
15	0.1192	sll1810	rpl6	10011001000010001000	50S ribosomal protein L6
16	0.1192	sll1743	rpl11	10011001000010001000	50S ribosomal protein L11
17	0.1192	sll1811	rpl18	10011001000010001000	50S ribosomal protein L18
18	0.1192	sll1812	rps5	10011001000010001000	30S ribosomal protein S5
19	0.1192	sll1767	rps6	10011001000010001000	30S ribosomal protein S6
20	0.1192	sll1102	rps10	10011001000010001000	30S ribosomal protein S10
21	0.1192	sll1816	rps13	10011001000010001000	30S ribosomal protein S13
22	0.1192	sal3437	rps17	10011001000010001000	30S ribosomal protein S17
23	0.1192	sll1814	secY	10011001000010001000	preprotein translocase subunit Y
24	0.1192	slr0075	ycf16	10011001000010001000	ABC transporter subunit
25	0.1192	slr0399	ycf39	10011001000010001000	hypothetical protein
	Branch Red algae (and CyaPar)
1	0.0712	slr2067	apcA	10011000000000001000	allophycocyanin a chain
2	0.0712	slr1986	apcB	10011000000000001000	allophycocyanin b chain
3	0.0712	slr0335	apcE	10011000000000001000	phycobilisome LCM core-membrane linker prot.
4	0.0712	slr0611	sds	10011000000000001000	solanesyl diphosphate synthase
5	0.0712	slr0055	trpG	10011000000000001000	anthranilate synthase component II
6	0.0712	slr2032	ycf23	10011000000000001000	hypothetical protein
	Branch Nongreen algae (but no CyaPar)
1	0.1460	—	cfxQ	00010001000010001000	rubisco expression protein
2	0.1339	—	ycf	00010001000000001000	hypothetical protein
3	0.1192	slr0228	ftsH	10010001000010011000	cell division protein
4	0.1192	sll0020	clpC	10010001000010001010	ATP-dep. translocation rel. protease, regulator
5	0.1306	sal2084	acp	10010001000010001000	acyl carrier protein
6	0.1306	slr0833	dnaB	10010001000010001000	replicative DNA helicase
7	0.1306	slr0737	psaD	10010001000010001000	photosystem I subunit II
8	0.1306	slr1655	psaL	10010001000010001000	photosystem I subunit XI
9	0.1306	sll1800	rpl4	10010001000010001000	50S ribosomal protein L4
10	0.1306	sll1821	rpl13	10010001000010001000	50S ribosomal protein L13
11	0.1306	sll1807	rpl24	10010001000010001000	50S ribosomal protein L24
12	0.1306	sar2799	rpl27	10010001000010001000	50S ribosomal protein L27
13	0.1306	sal3436	rpl29	10010001000010001000	50S ribosomal protein L29
14	0.1306	sal3445	rpl31	10010001000010001000	50S ribosomal protein L31
15	0.1306	sll0616	secA	10010001000010001000	preprotein translocase subunit A
16	0.1306	sll0194	ycf43	10010001000010001000	hypothetical protein
17	0.1306	slr2087	ycf44	10010001000010001000	hypothetical protein
	Branch Red algae (but no CyaPar)
1	0.0822	sll0728	accA	10010000000000001000	acetyl-CoA carboxylase alpha subunit
2	0.0822	slr0435	accB	10010000000000001000	biotin carboxyl carrier of acetyl-CoA carboxy
3	0.0822	slr1898	argB	10010000000000001000	N-acetylglutamate kinase
4	0.0822	sll1214	AT103	10010000000000001000	phytochrome-regulated gene
5	0.0822	sll1498	carA	10010000000000001000	carbamoyl-phosphate synthetase subunit A
6	0.0822	slr2051	cpcG	10010000000000001000	phycobilisome rod-core linker polypeptide
7	0.0822	sll0698	dfr	10010000000000001000	drug sensory protein A
8	0.0822	sal0707	glnB	10010000000000001000	nitrogen regulatory protein P-II
9	0.0822	sll1499	gltB	10010000000000001000	ferredoxin-dependent glutamate synthase
10	0.0822	slr0974	infC	10010000000000001000	initiation factor IF-3
11	0.0822	sll1536	moeB	10010000000000001000	molybdopterin biosynthesis protein
12	0.0822	sll1423	ntcA	10010000000000001000	global nitrogen regulator
13	0.0822	slr1934	pdhA	10010000000000001000	pyruvate dehydrogenase E1 component α sub
14	0.0822	sll1796	petJ	10010000000000001000	cytochrome c553
15	0.0822	slr0966	trpA	10010000000000001000	tryptophan synthase α chain
16	0.0822	slr0623	trxA	10010000000000001000	thioredoxin
17	0.0822	slr1780	ycf	10010000000000001000	hypothetical protein
18	0.0822	sll1737	ycf	10010000000000001000	hypothetical protein
19	0.0822	sll0558	ycf	10010000000000001000	hypothetical protein
20	0.0822	sll1879	ycf	10010000000000001000	hypothetical protein
	Branch EugGra
1	0.0731	—	ycf	00000010000000000010	hypothetical protein
2	0.0731	slr0913	ycf	10000010000000000000	hypothetical protein
3	0.0731	slr0914	ycf	10000010000000000000	hypothetical protein
	Branch Green algae
1	0.1373	sll1833	fts1	10000000011000000000	penicillin-binding protein
2	0.1373	slr1972	ycf	10000000011000000000	hypothetical protein
3	0.1333	slr1455	cysA	10100000111000000000	sulfate transport system permease protein
4	0.1333	slr1453	cysT	10100000111000000000	sulfate transport system permease protein
5	0.1064	sll0289	minD	10100001011000000000	septum site-determining protein
6	0.1054	slr0772	chlB	10101000111000011000	protochlorophyllide reductase subunit B
7	0.1054	slr0749	chlL	10101000111000011000	light-indep. protochlorophyllide reductase Fe
8	0.0899	slr0750	chlN	10101000011000011000	protochlorophillide reductase subunit N
9	0.0979	sll1463	ftsH	10100000101000000000	cell division protein
	Branch Land plants
1	0.1017	—	petL	01000000101101110101	cytochrome b6-f subunit VI
2	0.1006	—	ycf2	01000100000101000001	hypothetical protein
3	0.0965	—	matK	01000110100101110101	maturase K
4	0.0813	—	ycf1	01100100111101010100	hypothetical protein
5	0.0970	slr1281	ndhJ	11000000110101100101	NADH dehydrogenase subunit J
6	0.0921	sll0519	ndhA	11000000111101100101	NADH dehydrogenase subunit 1
7	0.0921	sll0223	ndhB	11000000111101100101	NADH dehydrogenase subunit 2
8	0.0921	slr1279	ndhC	11000000111101100101	NADH dehydrogenase subunit 3
9	0.0921	slr0331	ndhD	11000000111101100101	NADH dehydrogenase subunit 4
10	0.0921	sll0522	ndhE	11000000111101100101	NADH dehydrogenase subunit 4L
11	0.0921	slr0844	ndhF	11000000111101100101	NADH dehydrogenase subunit 5
12	0.0921	sll0521	ndhG	11000000111101100101	NADH dehydrogenase subunit 6
13	0.0921	slr0261	ndhH	11000000111101100101	NADH dehydrogenase subunit 7
14	0.0921	sll0520	ndhI	11000000111101100101	NADH dehydrogenase subunit I
15	0.0921	slr1280	ndhK	11000000111101100101	NADH dehydrogenase subunit K
16	0.0878	sml0003	psbM	11101000101101100101	photosystem II M protein
	EpiVir
1	0.0169	—	ycf2	01000100000101000001	hypothetical protein
2	0.0119	—	ycf1	01100100111101010100	hypothetical protein
3	0.0119	—	matK	01000110100101110101	maturase K
4	0.0119	ssl3441	infA	10100100111000110101	initiation factor IF-1

[i] Genes acting as phylogenetic correlates, as derived from the factor analysis and DP scoring.