Table 1

Proteins of putative chlamydial origin in plastid-containing eukaryotes.
	Gene¹⁾	Bootstrap support	Comments

	(Chlamydiae, Plantae)
1	Asparaginyl-tRNA synthetase gi\|46445980	74
2	Aspartate aminotransferase gi\|46446319	98	(CB F) 100% ML
3	ATP/ADP translocase	n. a.	Only in intracellular parasites and plastid-containing eukaryotes
4	tRNA delta(2)-isopentenylpyro-phosphate transferase gi\|46446877	99
5	Diphosphate-fructose-6-phosphate 1-phosphotransferase gi\|46446514	58
	(Chlamydiae, Viridiplantae, Rhodoplantae)
6	Isopentenyl monophosphate kinase (ISPE) gi\|46447223	74
7	Queuine tRNA-ribosyltransferase gi\|46446428	100	Dictyostelium sister to [P]
8	Putative 7-dehydrocholesterol reductase gi\|46446854	94	Only eukaryotes except Protochlamydia and Coxiella, Coxiella sister to Protochlamydia (87% ML)
9	Putative 23S rRNA (Uracil-5-)-methyltransferase gi\|46447632	100
10	Putative 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (ISPD) gi\|46445961	99	(CB F) 73% ML
11	Hypothetical protein pc1328 gi\|46446962	82
12	Putative glycerol-3-phosphate acyltransferase gi\|46446952	n. a.	Only present in Chlamydiae and plastid containing eukaryotes
13	Probable polyribonucleotide nucleotidyltransferase gi\|46446277	100	(CB F) 100% ML
14	Probable S-adenosyl-methyltransferase gi\|46445945	62
15	Putative tRNA pseudouridylate synthase I gi\|46445962	79
16	3-oxoacyl-(acyl carrier protein) synthase (FABB) gi\|46446872	100	Bacillariophyceae in eubacterial clade
17	Putative endopeptidase (ATP-dependent serine protease) La gi\|46446096	83
18	Probable tyrosine-tRNA ligase gi\|46446803	97	Bacillariophyceae in bacterial clade
19	Probable isoamylase gi\|46446740	99
20	Probable S-adenosyl-methyltransferase gi\|46445945	81	Bacillariophyceae in eukaryotic clade
21	Putative oligoendopeptidase F gi\|46446812	73
	(Chlamydiae, Viridiplantae)
22	Phosphate transporter gi\|46445733	88
23	Phosphoglycerate mutase gi\|46399436	94
24	Probable gcpE protein (ISPG) gi\|46446374	91	(CB G R) 100% ML
25	Enoyl-(acyl carrier protein) reductase (FABI) gi\|46446786	100	(CB R)
26	DNA mismatch repair protein (MUTS) gi\|46446855	54	(CB R) 95% ML
27	Putative lipoate-protein ligase gi\|46447472	98	Dictyostelium sister to [B V]
28	Gut Q protein gi\|46447416	100
29	Malate dehydrogenase gi\|46447406	92	NADP⁺-dependent plastidial homologue of the Viridiplantae
30	Putative ribosome recycling factor gi\|46447510	68	(CB R G) 88% ML
31	Putative tyrosine/tryptophan transport protein gi\|46445802	99
32	Hypothetical protein pc0324 gi\|46445958	n. a.	Only present in Viridiplantae and Protochlamydia
33	Hypothetical protein pc0378 gi\|46446012\|	99
34	Probable 3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) gi\|46400100	86
	(Chlamydiae, Rhodoplantae)
35	Probable 23S RNA-specific pseudouridine synthase D gi\|46445989	96
36	Hypothetical protein pc0339 gi\|46445973	100	Geobacter sister to [V]
37	Cysteinyl-tRNA synthetase gi\|46446869	100	Leptosira sister to [C P]
	(Chlamydiae, Bacillariophyceae)
38	Putative folylpolyglutamate synthase gi\|46447260	99
39	Transketolase gi\|46447148	70	Dictyostelium sister to [B], [V G CB]

39 proteins were identified by ML analyses. The proteins are grouped according to the observed tree topologies in the maximum likelihood analyses. The bootstrap support (ML) for the indicated clades is given. For 20 genes (in bold letters) this is to our knowledge the first detailed phylogenetic analysis. See Additional File 2 for an extended version of Table 1 including tree topologies. ¹⁾The accession number and annotation for the gene from Protochlamydia is given. n. a. not applicable, A Apicomplexa, B Bacillariophyta, C Chlamydiae except Protochlamydia, CB Cyanobacteria, CP Chlorophyta, F Firmicutes, G Glaucoplantae, P Protochlamydia, R Rhodoplantae, SP Streptophyta, V Viridiplantae.
Becker et al. BMC Evolutionary Biology 2008 8:203 doi:10.1186/1471-2148-8-203