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.
| Gene | Functional Category | Strains Group |
Observations | Reference | |||
|---|---|---|---|---|---|---|---|
| Ocular | Nonprevalent Genital | Prevalent Genital | LGV | ||||
| CT037 | HP | = | R | Ψ | Ψ | A/2497, A/363, A/5291, and A/7249 are smaller than the nonprevalent genital serovars. | This study |
| CT052 | Coproporphyrinogen III oxidase | > | > | = | R | This study | |
| CT058 | Putative inclusion membrane protein | Ψ | = | = | R | A/Har13 and C/TW-3 are not Ψs. | Almeida et al. 2012 |
| CT101 | Inclusion membrane protein | = | Ψ | Ψ | R | E/Bour, E/11023, and D/UW3 are not Ψs. | Almeida et al. 2012; This study |
| CT105 | T3S effector | Ψ | = | = | R | Borges et al. 2012 | |
| CT106 | Predicted pseudouridine synthetase family | = | > | > | R | This study | |
| CT160 | HP | > | > | > | R | B/Jali20 is a Ψ, and F(s)/70 is smaller. | This study |
| CT161 | HP | = | < | < | R | B/Jali20 and E/SotonE8 are Ψs. | This study |
| CT162 | HP | < | < | < | R | E/SotonE8, F(s)/70, J/6276, Ia/SotonIa1, and Ia/SotonIa3 are Ψs. | This study |
| CT171 | Tryptophan synthase (alpha chain) | Ψ | = | = | R | B/TZ is not a Ψ. | Caldwell et al. 2003 |
| CT172 | HP | < | << | << | R | This study | |
| CT234 | Membrane transport protein from the major facilitator superfamily | = | = | < | R | This study | |
| CT300 | Putative inclusion membrane protein | R | = | = | Ψ | Almeida et al. 2012 | |
| CT358 | HP | > | > | > | R | B/Jali20 is smaller. | Almeida et al. 2012; Thomson et al. 2008 |
| CT373 | HP | R | = | = | Ψ | Giles et al. 2009; This study | |
| CT374 | Arginine/ornithine antiporter | Ψ | = | = | R | Giles et al. 2009; This study | |
| CT392 | HP | > | > | > | R | This study | |
| CT441 | Tail-specific protease | < | < | = | R | Ia/SotonIa1, Ia/SotonIa3, and J/6276 have the size of the LGV and prevalent genital serovars sequences. | This study |
| CT470 | HP | = | = | > | R | This study | |
| CT473 | HP | = | = | Ψ | R | This study | |
| CT480.1 | HP | > | > | > | R | G/9301, G/9768, G/11074, J/6276, Ia/SotonIa1, and Ia/SotonIa3 are smaller than the remainder strains’ sequences. | This study |
| CT522 | S3 ribosomal protein | = | = | < | R | This study | |
| CT605 | HP | > | > | = | R | This study | |
| CT793 | HP | > | > | > | R | G/9301, G/11074, and G/9768 are Ψs. | This study |
| CT807 | Glycerol-3-P acyltransferase | < | < | = | R | This study | |
| CT809 | HP | < | < | = | R | This study | |
| CT833 | Initiation factor 3 | < | < | < | R | This study | |
| CT852 | YhgN family | < | < | < | R | This study | |
| CT868 | Membrane thiol protease (predicted) | > | > | > | R | This 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.