Table 3.
ANI and AF comparisons for sub-Antarctic strains with type strains of R. erythropolis and R. qingshengii (panel A) and the closest neighbours of strains 1163 and 1168 (panel B), highlighting species identity between strains of R. erythropolis (orange shading) or R. qingshengii (green shading).
| Panel A | |||||||||
| Strain No. | Species | Provenance | Pairwise ANI and AF (%) a | ||||||
| CCM 2595 |
NBRC
15567 |
TUHH-12 | JCM 15477 | Djl-6-2 | 1139 | 1159 | |||
| CCM 2595 | R. erythropolis | NCBI reference genome for the species | 98.83 AF = 88.64 |
95.55 AF = 64.79 |
95.60 AF = 79.47 |
95.57 AF = 85.27 |
95.67 AF = 81.41 |
98.86 AF = 84.01 |
|
| NBRC 15567 = JCM 3201 b | R. erythropolis | Type strains, https://lpsn.dsmz.de | 98.83 AF = 99.99 |
95.49 AF = 65.56 |
95.49 AF = 81.12 |
95.54 AF = 85.42 |
95.53 AF = 82.11 |
98.78 AF = 84.47 |
|
| TUHH-12 | R. qingshengii | NCBI-cited genome publication for this species (2015) | 95.547 AF = 72.99 |
95.49 AF = 71.14 |
98.58 AF = 68.04 |
98.77 AF = 72.62 |
98.73 AF = 69.10 |
95.43 AF = 68.31 |
|
| JCM 15477 c | R. qingshengii | Type strain, https://lpsn.dsmz.de | 95.60 AF = 89.60 |
95.49 AF = 88.16 |
98.57 AF = 68.11 |
98.83 AF = 89.45 |
98.67 AF = 85.23 |
95.47 AF = 83.86 |
|
| Djl-6-2 | R. qingshengii | Related to original isolate djl-6 type strain, https://lpsn.dsmz.de | 95.57 AF = 85.47 |
95.54 AF = 85.32 |
98.79 AF = 66.68 |
98.82 AF = 82.23 |
98.91 AF = 82.90 |
95.53 AF = 80.41 |
|
| 1139 | Rhodococcus sp. | This study | 95.66 AF = 89.01 |
95.52 AF = 86.46 |
98.73 AF = 67.09 |
98.67 AF = 82.59 |
98.91 AF = 87.35 |
95.56 AF = 83.34 |
|
| 1159 | Rhodococcus sp. | This study | 98.86 AF = 92.59 |
98.78 AF = 89.77 |
95.44 AF = 66.72 |
95.48 AF = 81.83 |
95.54 AF = 85.57 |
95.55 AF = 83.95 |
|
| Panel B | |||||||||
| Strain | Species | Provenance | Pairwise ANI and AF (%) | ||||||
| PAMC 28707 | 1163 | 1168 | |||||||
| PAMC 28705 PAMC 28707 | Rhodococcus sp. (identical strains) | Published genome Korean Polar Research Institute (IMG/M) | 94.50 AF = 84.60 |
93.58 AF = 74.36 |
|||||
| 1163 | Rhodococcus sp. | This study | 94.50 AF = 80.13 |
93.75 AF = 74.20 |
|||||
| 1168 | Rhodococcus sp. | This study | 93.55 AF = 79.27 |
93.74 AF = 83.80 |
|||||
a Average nucleotide identity (ANI) and alignment fraction (AF) were calculated using the IMG/M pairwise ANI tool; shading in panel A shows identity between species. b Genome BLAST (NCBI) indicated that these two strains are identical. c There are two genome sequences in IMG/M for the type strain JCM 15477: genome ID 2744054616 (NCBI GCF_001646745.1) was used for ANI pairwise comparisons here; ANI analysis of JCM 15477 genome ID 2734481946 (NCBI GCA_001313445.1) showed >99% ANI similarity but < 35% AF with genome ID 2744054616 and other strains named as R. qingshengii (Table S1).