Fig 1.
Maximum likelihood phylogenomic tree inferred from concatenated alignments of 120 single-copy amino acid sequences in Genome Taxonomy Database (GTDB).
Genomic sequences were obtained from the NCBI RefSeq database under the corresponding assembly accession number. Bootstrap values are represented by the nodes as filled circle (>90%) and empty circle (>50%). Corynebacterium diphtheria NCTC11397T (GCF_001457455) was used as an outgroup. Scale bar, 0.05 substitutions per amino acid position. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated for the following genomes: 1. DK17T, 2. R. jostii RHA1, 3. R. opacus ATCC 51881T, 4. R. opacus R7, 5. R. wratislaviensis NBRC100605T, 6. R. koreensis DSM 44498T, 7. R. pseudokoreensis R79T, 8. R. jostii NBRC 16295T.
Fig 2.
Comparative genome analysis of DK17T with closely related Rhodococcus strains.
(a) UpSet plot represents the core, unique, and accessory genes between Rhodococcus genomes. (b) The proportion of shared genes.
Table 1.
Differential physiological properties of the strain DK17T and phylogenetically closely related Rhodococcus species. Strains: 1, DK17T; 2, R. jostii RHA1 [65]; 3, R. opacus KCTC 9811T [91]; 4, R. wratislaviensis N805T [5]; 5, R. jostii IFO 16295T [92].
Table 2.
Cellular fatty acid composition of the strain DK17T and phylogenetically closely related Rhodococcus species. Strains: 1, DK17T; 2, R. jostii RHA1; 3, R. opacus KCTC 9811T; 4, R. wratislaviensis N805T; 5, R. jostii IFO 16295T. Data for DK17T, R. jostii RHA1, and R. opacus KCTC 9811Tare from the present study, while data for the other strains are from previously published sources4-5.
Fig 3.
Biosynthetic gene clusters (BGCs) in Rhodococcus strains.
NRPS, non-ribosomal peptides synthase; NAPAA, non-alpha-poly amino acid; T1PKS, type I polyketide synthase.
Fig 4.
Comparison of the genetic organization of the akb gene cluster.
The plot was visualized using the syntenyPlotteR package (v1.0.0) in R (v4.3.3). Putative genes are colored by dark gray and pseudogenes are shown in a dashed arrow shape. akbS and akbT, two-component regulatory genes; akbA1a-akbA2a and akbA1b-akbA2b, o-xylene dioxygenase—two sets of large and small oxygenase subunits; akbA3, a gene for ferredoxin component; akbA4, a gene for ferredoxin reductase component; akbB, cis-dihydrodiol dehydrogenase; akbC, meta-cleavage 2,3-dioxygenase; akbD, hydrolase; akbE, hydratase; akbF, aldolase.