Table 3 C. trachomatis known and putative pseudogenes for a particular disease group and genes that present differences in gene length among strains from different disease groups
GeneFunctional CategoryStrains GroupObservationsReference
OcularNonprevalent GenitalPrevalent GenitalLGV
CT037HP=RΨΨA/2497, A/363, A/5291, and A/7249 are smaller than the nonprevalent genital serovars.This study
CT052Coproporphyrinogen III oxidase>>=RThis study
CT058Putative inclusion membrane proteinΨ==RA/Har13 and C/TW-3 are not Ψs.Almeida et al. 2012
CT101Inclusion membrane protein=ΨΨRE/Bour, E/11023, and D/UW3 are not Ψs.Almeida et al. 2012; This study
CT105T3S effectorΨ==RBorges et al. 2012
CT106Predicted pseudouridine synthetase family=>>RThis study
CT160HP>>>RB/Jali20 is a Ψ, and F(s)/70 is smaller.This study
CT161HP=<<RB/Jali20 and E/SotonE8 are Ψs.This study
CT162HP<<<RE/SotonE8, F(s)/70, J/6276, Ia/SotonIa1, and Ia/SotonIa3 are Ψs.This study
CT171Tryptophan synthase (alpha chain)Ψ==RB/TZ is not a Ψ.Caldwell et al. 2003
CT172HP<<<<<RThis study
CT234Membrane transport protein from the major facilitator superfamily==<RThis study
CT300Putative inclusion membrane proteinR==ΨAlmeida et al. 2012
CT358HP>>>RB/Jali20 is smaller.Almeida et al. 2012; Thomson et al. 2008
CT373HPR==ΨGiles et al. 2009; This study
CT374Arginine/ornithine antiporterΨ==RGiles et al. 2009; This study
CT392HP>>>RThis study
CT441Tail-specific protease<<=RIa/SotonIa1, Ia/SotonIa3, and J/6276 have the size of the LGV and prevalent genital serovars sequences.This study
CT470HP==>RThis study
CT473HP==ΨRThis study
CT480.1HP>>>RG/9301, G/9768, G/11074, J/6276, Ia/SotonIa1, and Ia/SotonIa3 are smaller than the remainder strains’ sequences.This study
CT522S3 ribosomal protein==<RThis study
CT605HP>>=RThis study
CT793HP>>>RG/9301, G/11074, and G/9768 are Ψs.This study
CT807Glycerol-3-P acyltransferase<<=RThis study
CT809HP<<=RThis study
CT833Initiation factor 3<<<RThis study
CT852YhgN family<<<RThis study
CT868Membrane thiol protease (predicted)>>>RThis study
  • The differences in sequence length shown only refer to differences in termination between strains. Genes with discordant 5′ annotation, for which the correct start codon lacks confirmation, were not included. The differences in length do not contemplate indel events. LGV, lymphogranuloma venereum. Ψ, sequences considered as pseudogenes; R, the sequence whose size was used for reference purposes. LGV sequences were used by default except for LGV pseudogenes; =, gene of the same size as the reference; >, gene larger than the reference; <, gene smaller than the reference; <<, gene with the smallest size. Three sequence sizes were observed for CT172, depending on the disease group.