Table 1. Minimal List of Candidate HGTs between Chlamydiales and Archaeplastida
EggnogDescriptionPfamRefSeqBootstrapTopology
COG0037Predicted ATPase of the PP-loop superfamily implicated in cell cycle controlPF01171gi1675203090G
COG0039Malate/lactate dehydrogenasesPF00056gi1560510090G
COG0042tRNA-dihydrouridine synthasePF01207gi4640085490G
COG0144tRNA and rRNA cytosine-C5-methylasesPF01189gi29762039090R+Gl
COG0162Tyrosyl-tRNA synthetasePF00579gi1583495290G+R
COG0217Uncharacterized conserved proteinPF01709gi4640060390G+R
COG0275Predicted S-adenosylmethionine–dependent methyltransferase involved in cell envelope biogenesisPF01795gi4639958690G
COG03043-Oxoacyl-(acyl-carrier-protein) synthasePF00109gi29853795090G+R
COG0306Phosphate/sulfate permeasesPF01384gi1560542575G
COG0324tRNA δ(2)-isopentenylpyrophosphate transferasePF01715gi4640051890G
COG0448*GlgC; ADP-Glc pyrophosphorylaseagi297375973NAG
COG0517FOG: CBS domainPF01380gi4640105790G
COG0527AspartokinasesPF00696gi29737639790Gl
COG0545FKBP-type peptidyl-prolyl cis-trans isomerase1PF00254gi28149780275R
COG0547Anthranilate phosphoribosyltransferasePF00591gi12376321690G+R
COG0564Pseudouridylate synthases, 23S RNA-specificPF00849gi28149810775R
COG0566rRNA methylasesPF00588gi4639941690G
COG0574Phosphoenolpyruvate synthase/pyruvate phosphate dikinasePF02896gi28149903790Gl
COG0588Phosphoglycerate mutase 1PF00300gi1583472090G
COG0590Cytosine/adenosine deaminasesPF00383gi28149882175G+R
COG07206-Pyruvoyl-tetrahydropterin synthasePF01242gi29737639890R+Gl
COG0812UDP-N-acetylmuramate dehydrogenasePF02873gi1583483890G
COG0821Enzyme involved in the deoxyxylulose pathway of isoprenoid biosynthesisPF04551gi4640001575G
COG1054Predicted sulfur transferasePF00581gi4639965390G+Gl
COG1092Predicted SAM-dependent methyltransferasesPF10672gi28150014675Gl
COG1164Oligoendopeptidase FPF01432gi4640045390R
COG11652-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthasePF02776gi33648269975R
COG1169Isochorismate synthasePF00425gi33648269890R
COG1181d-Ala-d-Ala ligase and related ATP-grasp enzymesPF01820gi4639967390G
COG118716S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthasesPF00849gi27028488890G
COG1212CMP-2-keto-3-deoxyoctulosonic acid synthetasePF02348gi28150049475G
COG12183-Phosphoadenosine 5-phosphosulfate (PAPS) 3-phosphatasePF00459gi33469558275G
COG1477Membrane-associated lipoprotein involved in thiamine biosynthesisPF02424gi33341021390R
COG1496Uncharacterized conserved proteinPF02578gi4640114375Gl
COG1523GlgX; type II secretory pathway, pullulanase PulA and related glycosidasesPF00128gi4640038190G+R+Gl
COG1576Uncharacterized conserved proteinPF02590gi4640098375R
COG1611Predicted Rossmann fold nucleotide binding proteinPF03641gi4639985690Gl
COG1878Predicted metal-dependent hydrolasePF04199gi33648362175G
COG19474-Diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate synthasePF00288gi4640086490G+R+Gl
COG2217Cation transport ATPasePF00122gi1583472590G+R
COG2265SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferasePF05958gi4640127390G+R
COG3914Predicted O-linked N-acetylglucosamine transferase, SPINDLY familyPF00534gi33648090875R
euNOG050122-C-Methyl-d-erythritol 4-phosphate cytidylyltransferasePF01128gi4644596175G+R+Gl
KOG4197FOG: PPR repeatPF01535gi336482601NAG
NOG04817Putative uncharacterized proteingi28149947390G
NOG04985Protein involved in glycerolipid metabolismPF12695gi2983455390R
NOG05008Glycerol-3 proteinPF01553gi46400593NAG+R+Gl
NOG87709Glycosyltransferase family A (GT-A)PF01704gi46399599NAG+Gl
  • The Archaeplastida are named as follows: G, Chloroplastida; R, Rhodophyta; and Gl, Glaucophyta. These candidate HGTs were identified using an automated phylogenomic procedure that took as the selection criterion monophyly of Chlamydiales and Archaeplastida to the exclusion of any other clade (except algae that contain secondary plastids, such as chromalveolates and euglenids) with bootstrap values ≥90 or ≥75%. Trees that only contained Chlamydiales and Archaeplastida are marked with “NA.” This list does not contain examples of chlamydial gene transfers that have a complex gene history, such as GlgA (this work) and the ATP translocator that has been previously described. The trees listed here are available in the same order in Supplemental Data Set 1 online. It should be noted that the putative gene functions result from an automated annotation procedure and should be interpreted with caution.

  • a The automated annotation GlgC-ADP-Glc pyrophosphorylase is justified by the presence of a GlgC-like domain within an otherwise unknown protein. This protein found in prasinophytes, stramenopiles, and chlamydiales does not define a classical and functional ADP-Glc pyrophosphorylase.