Table 3.
Pairwise alignment fractions (A) and average nucleotide identities (B) for M. kansasii subtypes and outgroup species.
| Subtype/groupa | M. kansasii I | M. kansasii II+ | M. kansasii II | M. persicum | M. kansasii III | M. kansasii IV | M. kansasii V | M. kansasii VI | MTBC | M. tuberculosis | M. africanum | M. bovis | M. caprae | M. microti | M. conspicuum | M. gastri | M. marinum | M. riyadhense | M. szulgai |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | |||||||||||||||||||
| M. kansasii I | 0.69–1.0 | ||||||||||||||||||
| M. kansasii II+ | 0.65–0.9 | 0.89–0.99 | |||||||||||||||||
| M. kansasii II | 0.65–0.89 | 0.89–0.99 | 0.91–0.99 | ||||||||||||||||
| M. persicum | 0.65–0.9 | 0.89–0.99 | 0.89–0.99 | 0.92–0.99 | |||||||||||||||
| M. kansasii III | 0.64–0.87 | 0.75–0.86 | 0.75–0.85 | 0.76–0.86 | 0.85–0.99 | ||||||||||||||
| M. kansasii IV | 0.63–0.85 | 0.78–0.84 | 0.78–0.84 | 0.79–0.84 | 0.74–0.84 | 0.97 | |||||||||||||
| M. kansasii V | 0.61–0.89 | 0.75–0.88 | 0.75–0.88 | 0.77–0.87 | 0.73–0.89 | 0.81–0.88 | 0.85–0.98 | ||||||||||||
| M. kansasii VI | 0.64–0.87 | 0.8–0.86 | 0.8–0.85 | 0.8–0.86 | 0.74–0.84 | 0.76–0.82 | 0.75–0.86 | 0.9–0.98 | |||||||||||
| MTBC | 0.4–0.75 | 0.48–0.75 | 0.48–0.75 | 0.49–0.74 | 0.47–0.74 | 0.52–0.75 | 0.51–0.74 | 0.49–0.74 | 0.9–1.0 | ||||||||||
| M. tuberculosis | 0.41–0.73 | 0.5–0.73 | 0.5–0.73 | 0.51–0.72 | 0.48–0.73 | 0.54–0.73 | 0.53–0.72 | 0.5–0.72 | 0.91–0.99 | 0.95–0.99 | |||||||||
| M. africanum | 0.4–0.74 | 0.5–0.74 | 0.5–0.74 | 0.51–0.73 | 0.48–0.73 | 0.54–0.74 | 0.53–0.73 | 0.49–0.73 | 0.92–0.99 | 0.93–0.97 | 0.96–0.99 | ||||||||
| M. bovis | 0.4–0.75 | 0.49–0.75 | 0.49–0.75 | 0.5–0.74 | 0.47–0.74 | 0.53–0.75 | 0.52–0.74 | 0.49–0.74 | 0.9–1.0 | 0.91–0.97 | 0.93–0.98 | 0.96–1.0 | |||||||
| M. caprae | 0.4–0.73 | 0.5–0.73 | 0.5–0.73 | 0.51–0.72 | 0.48–0.73 | 0.54–0.73 | 0.53–0.73 | 0.49–0.72 | 0.92–0.97 | 0.93–0.97 | 0.95–0.97 | 0.94–0.97 | –* | ||||||
| M. microti | 0.4–0.7 | 0.48–0.7 | 0.48–0.7 | 0.49–0.7 | 0.47–0.7 | 0.52–0.7 | 0.51–0.7 | 0.49–0.69 | 0.9–0.94 | 0.91–0.93 | 0.92–0.93 | 0.9–0.94 | 0.92–0.92 | –* | |||||
| M. conspicuum | 0.45–0.6 | 0.55–0.59 | 0.55–0.58 | 0.55–0.59 | 0.53–0.59 | 0.56–0.6 | 0.54–0.62 | 0.56–0.59 | 0.43–0.65 | 0.45–0.64 | 0.44–0.64 | 0.44–0.65 | 0.44–0.63 | 0.43–0.62 | –* | ||||
| M. gastri | 0.6–0.84 | 0.74–0.83 | 0.74–0.83 | 0.75–0.82 | 0.72–0.84 | 0.82–0.86 | 0.79–0.86 | 0.73–0.81 | 0.54–0.75 | 0.57–0.73 | 0.56–0.74 | 0.56–0.75 | 0.56–0.73 | 0.54–0.7 | 0.54–0.6 | –* | |||
| M. marinum | 0.5–0.68 | 0.63–0.68 | 0.64–0.67 | 0.63–0.68 | 0.6–0.68 | 0.63–0.68 | 0.62–0.72 | 0.63–0.66 | 0.48–0.74 | 0.5–0.73 | 0.5–0.73 | 0.49–0.74 | 0.5–0.73 | 0.48–0.7 | 0.55–0.55 | 0.62–0.7 | –* | ||
| M. riyadhense | 0.5–0.66 | 0.61–0.65 | 0.61–0.65 | 0.62–0.65 | 0.58–0.66 | 0.64–0.65 | 0.63–0.7 | 0.61–0.64 | 0.53–0.77 | 0.55–0.75 | 0.55–0.76 | 0.54–0.77 | 0.55–0.75 | 0.53–0.72 | 0.55–0.59 | 0.65–0.68 | 0.59–0.63 | –* | |
| M. szulgai | 0.5–0.69 | 0.62–0.68 | 0.63–0.67 | 0.62–0.68 | 0.59–0.68 | 0.62–0.68 | 0.62–0.73 | 0.63–0.67 | 0.47–0.73 | 0.49–0.71 | 0.49–0.72 | 0.48–0.73 | 0.49–0.72 | 0.47–0.68 | 0.59–0.6 | 0.61–0.7 | 0.62–0.62 | 0.66–0.71 | –* |
| B | |||||||||||||||||||
| M. kansasii I | 98.82–100.0 | ||||||||||||||||||
| M. kansasii II+ | 93.2–94.22 | 99.66–99.99 | |||||||||||||||||
| M. kansasii II | 93.2–94.22 | 99.66–99.99 | 99.66–99.98 | ||||||||||||||||
| M. persicum | 93.25–94.16 | 99.68–99.99 | 99.68–99.99 | 99.7–99.99 | |||||||||||||||
| M. kansasii III | 93.23–93.78 | 92.71–92.91 | 92.76–92.87 | 92.71–92.91 | 99.61–100.0 | ||||||||||||||
| M. kansasii IV | 92.9–93.3 | 93.8–93.93 | 93.8–93.89 | 93.81–93.93 | 92.62–92.81 | 99.87–99.9 | |||||||||||||
| M. kansasii V | 93.96–94.22 | 94.72–94.91 | 94.72–94.91 | 94.73–94.91 | 93.61–93.77 | 94.38–94.51 | 98.9–99.99 | ||||||||||||
| M. kansasii VI | 90.48–90.88 | 88.55–88.73 | 88.55–88.71 | 88.58–88.73 | 90.4–90.53 | 88.82–88.96 | 89.18–89.34 | 99.66–99.94 | |||||||||||
| MTBC | 81.52–81.79 | 81.6–81.79 | 81.6–81.79 | 81.64–81.78 | 81.57–81.81 | 81.85–81.98 | 81.88–82.04 | 81.04–81.22 | 99.83–100.0 | ||||||||||
| M. tuberculosis | 81.52–81.72 | 81.6–81.71 | 81.6–81.7 | 81.64–81.71 | 81.57–81.74 | 81.85–81.97 | 81.88–82.0 | 81.04–81.15 | 99.83–99.96 | 99.88–99.96 | |||||||||
| M. africanum | 81.56–81.74 | 81.66–81.78 | 81.66–81.77 | 81.69–81.78 | 81.65–81.77 | 81.89–81.97 | 81.9–82.01 | 81.07–81.18 | 99.87–99.98 | 99.87–99.94 | 99.92–99.98 | ||||||||
| M. bovis | 81.56–81.76 | 81.66–81.79 | 81.66–81.79 | 81.69–81.78 | 81.66–81.81 | 81.91–81.98 | 81.93–82.04 | 81.07–81.22 | 99.87–100.0 | 99.87–99.94 | 99.9–99.95 | 99.95–100.0 | |||||||
| M. caprae | 81.57–81.71 | 81.64–81.73 | 81.64–81.7 | 81.68–81.73 | 81.65–81.74 | 81.91–81.95 | 81.9–81.99 | 81.08–81.14 | 99.83–99.96 | 99.83–99.89 | 99.88–99.93 | 99.94–99.96 | –* | ||||||
| M. microti | 81.65–81.79 | 81.65–81.74 | 81.65–81.71 | 81.7–81.74 | 81.68–81.8 | 81.94–81.97 | 81.9–82.01 | 81.06–81.18 | 99.89–99.94 | 99.89–99.91 | 99.92–99.94 | 99.9–99.93 | 99.9–99.9 | –* | |||||
| M. conspicuum | 80.79–80.97 | 80.88–81.09 | 80.91–81.06 | 80.88–81.09 | 80.81–81.0 | 81.05–81.12 | 81.06–81.19 | 80.39–80.47 | 81.23–81.33 | 81.26–81.33 | 81.23–81.29 | 81.26–81.32 | 81.3–81.32 | 81.27–81.28 | –* | ||||
| M. gastri | 92.13–92.39 | 92.89–93.04 | 92.94–93.03 | 92.89–93.04 | 92.1–92.27 | 95.15–95.18 | 93.64–93.76 | 88.73–88.79 | 81.85–81.95 | 81.88–81.91 | 81.85–81.89 | 81.86–81.91 | 81.9–81.91 | 81.93–81.95 | 81.12–81.14 | –* | |||
| M. marinum | 81.37–81.53 | 81.29–81.48 | 81.29–81.46 | 81.32–81.48 | 81.33–81.57 | 81.64–81.67 | 81.71–81.79 | 80.96–81.01 | 80.34–80.47 | 80.34–80.43 | 80.35–80.43 | 80.39–80.47 | 80.39–80.41 | 80.41–80.43 | 79.81–79.84 | 81.61–81.62 | –* | ||
| M. riyadhense | 81.63–81.83 | 81.63–81.78 | 81.63–81.72 | 81.66–81.78 | 81.66–81.86 | 81.99–82.04 | 82.03–82.12 | 81.19–81.25 | 82.5–82.61 | 82.54–82.59 | 82.5–82.56 | 82.55–82.61 | 82.54–82.55 | 82.55–82.56 | 81.2–81.23 | 82.06–82.07 | 80.39–80.41 | –* | |
| M. szulgai | 81.06–81.35 | 81.18–81.49 | 81.18–81.49 | 81.18–81.25 | 81.11–81.45 | 81.34–81.43 | 81.37–81.46 | 80.69–80.77 | 81.13–81.25 | 81.16–81.22 | 81.13–81.19 | 81.18–81.25 | 81.17–81.2 | 81.21–81.22 | 80.82–80.82 | 81.41–81.42 | 80.06–80.06 | 83.19–83.21 | –* |
Each M. kansasii subtype was represented by a group of 2–31 strains (genomes). The M. kansasii II group included 7 strains (2193, NLA001001128, B11073207, B11063838, 1010001469, H47, and H48); the M. persicum group included 4 strains [AFPC-000227 (T) (Shahraki et al., 2017), MK4, MK15, and MK42 (Tagini et al., 2019)]; the M. kansasii II+ group incorporated strains of both M. kansasii II and M. persicum groups (11 strains in total). The M. kansasii groups III, V, and VI included strains of respective genotypes collected for this study as well as strains which had elsewhere been designated as M. pseudokansasii (MK21, MK35, and MK142), M. innocens (MK13), and M. attenuatum (MK41, MK136, MK191), accordingly (Tagini et al., 2019). In addition, genomes of six M. tuberculosis, five M. africanum, five M. bovis, and single M. caprae, M. microti, M. conspicuum, M. gastri, M. marinum, M. riyadhense, and M. szulgai strains were analyzed. The MTBC contained genomes of all the aforesaid M. tuberculosis, M. africanum, M. bovis, M. caprae, and M. microti strains (18 strains in total). See Supplementary Table 6.
The values were not given, since only one genome sequence per species was analyzed; AF/ANI values calculated within the groups of strains (genomes) are indicated in bold. The AF and gANI values of 0.6 and 96.5, respectively, were identified as minimum thresholds to assign a genome pair to the same species.