TABLE 2.
Inter-clade and intra-strain recombination in examined samples and in previously determined whole genome sequences of TPA.
|
Intra-strain recombination |
Inter-clade recombination |
||||||||||||||
| Strain | Year of isolation | rrn1/rrn21 | TP08582 | tprC/D3 | tprG4 | TP01365 | TP03266 | TP04627 | TP04838 | TP04889 | TP086510 | tprC11 | tprG12 | tprJ13 | |
| Nichols-like | Nichols (CP004010.2) | 1912 | Ile/Ala | R7R4R6 | D | G1 | – | – | – | – | – | – | C | – | – |
| strains | Chicago (CP001752.1) | 1951 | Ile/Ala | R7R4R6 | D | G1 | – | – | – | – | – | – | C | – | – |
| previously | DAL-1 (CP003115.1) | 1991 | Ile/Ala | R7R4R6 | D | G1 | – | – | – | – | – | – | C | – | – |
| described | SEA81-4 (CP003679.1) | 2014 | ? | R3R4R5 | D2 | G2 | – | – | – | – | – | Nichols/TEN | C | – | Nichols/TEN or TPE |
| Nichols-like | CW82 (CP34972) | 2016 | Ala/Ile | R7R4R5 | D2 | G2 | Nichols/SS14 | – | – | – | – | – | C3 | – | – |
| strains in this | CW65 (CP34918) | 2014 | Ile/Ala | R7R4R5 | D2 | G2 | – | – | – | – | – | – | C4 | – | – |
| study | CW83 (CP34917) | 2015 | Ile/Ala | R7R4R6 | D2 | G2 | – | – | – | Nichols/TEN | – | – | C3 | – | – |
| CW59 (CP34919) | 2012 | Ile/Ala | R7R4R6 | D2 | G2 | – | – | Nichols/TEN or TPE | – | – | Nichols/TEN | C3 | – | Nichols/TEN or TPE | |
| CW86 (CP34914) | 2013 | Ile/Ala | R7R4R6 | D2 | G2 | – | – | Nichols/TEN or TPE | – | – | Nichols/TEN | C3 | – | – | |
| SS14-like | SS14 (CP004011.1) | 1977 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – |
| strains | Mexico A (CP003064.1) | 1953 | Ala/Ile | R7R4R6 | D2 | G1 | – | SS14/TEN | – | – | SS14/TEN | – | C2 | – | – |
| previously | Phi-1 (CP035193) | 1988 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – |
| described | Grady (CP035104) | 1980s | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – |
| UZ1974 (CP028438.1) | 2012 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – | |
| SS14-like | CW30 (CP034921) | 2014 | Ile/Ala | R7R4R6 | D2 | – | – | – | – | – | – | – | C2 | SS14/Nichols | – |
| strains in this | CW84 (CP34916) | 2015 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – |
| study | CW85 (CP34915) | 2016 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – |
| CW87 (CP34913) | 2016 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – | |
| CW88 (CP34912) | 2017 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – | |
| CW56 (CP34920) | 2013 | Ile/Ala | R7R4R6 | D2 | G1 | – | – | – | – | – | – | C2 | – | – | |
1Intra-genomic rearrangements of rrn spacer patterns (Ile/Ala) (Čejková et al., 2013; Figure 3). 2Intra-genomic rearrangements of modular structure of TP0856 and TP0858 (Strouhal et al., 2018; Figure 3). 3Intra-genomic recombination of tprC and tprD. Also described in Kumar et al. (2018). 4Intra-genomic recombination of tprG and tprJ (Figure 3). 5The inter-clade recombination of the TP0136 gene (Figure 4), reported also in Grillová et al. (2018c) and predicted in Arora et al. (2016). 6The inter-clade recombination of the TP0326 gene, as described in Pětrošová et al. (2012) and predicted in Arora et al. (2016). 7,8The inter-clade recombination of the TP0462 and TP0483 genes (Figure 4). 9The inter-clade recombination of the TP0488 gene, as described in Pětrošová et al. (2012). 10–13The inter-clade recombination of the TP0865, as predicted in Arora et al. (2016), tprC, tprG, and tprJ genes (Figure 4). Inter-clade and intra-strain recombination events are highlighted in gray.