Journal: International journal of systematic and evolutionary microbiology
Article Title: Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi .
doi: 10.1099/ijsem.0.006679
Figure Lengend Snippet: Fig. 1. Core-genome maximum-likelihood (ML) trees based on concatenated sequence alignments of conserved genes (left, 409 gene markers) or proteins (right, 323 protein markers). The analysis includes the type strains of all Rhodococcus species with genome assemblies available at the NCBI as of January 2024 (acc. nos. in Table S1, available in the online Supplementary Material). Rhodococcoides fascians from an early diverging branch of the rhodococcal radiation [11] was used as an outgroup. The tree was midpoint rooted because of the uncertain position of Rhodococcus antarcticus 75T [53] within the genus Rhodococcus. Branch support is given for 1000 ultrafast bootstrap replicates (IQtree UFBoot). The large case numbers on the nt-based tree indicate the main Rhodococcus sublineages as defined in ref. [11]. The trees are entirely congruent with our previous ML phylogenies based on Mycobacteriales or Nocardiaceae core-genome alignments (the latter incorporating a larger strain representation than the type’s) [11]. The only exception is that Rhodococcus rhodnii ATCC 33071T and Rhodococcus triatomae DSM 44892T form here an independent branch at the root of the monophyletic line of descent containing sublineages 3 and 4 instead of being part of the sublineage 4 radiation (see ref. [11]).
Article Snippet: To determine the phylogenetic position and relationships of PAM 2766T, we generated a core- genome phylogeny using all available genome assemblies for the type strains of each species of the genus Rhodococcus (as emended by Val- Calvo and VázquezBoland 2023 [11, 39]) with status name ‘correct’ in the LPSN repository (https://lpsn.dsmz.de/genus/rhodococcus, accessed January 2024) (Table S1).
Techniques: Sequencing
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![Fig. 1. Core-genome maximum-likelihood (ML) trees based on concatenated sequence alignments of conserved genes (left, 409 gene markers) or proteins (right, 323 protein markers). The analysis includes the type strains of all <t>Rhodococcus</t> species with genome assemblies available at the NCBI as of January 2024 (acc. nos. in Table S1, available in the online Supplementary Material). Rhodococcoides fascians from an early diverging branch of the rhodococcal radiation [11] was used as an outgroup. The tree was midpoint rooted because of the uncertain position of Rhodococcus antarcticus 75T [53] within the genus Rhodococcus. Branch support is given for 1000 ultrafast bootstrap replicates (IQtree UFBoot). The large case numbers on the nt-based tree indicate the main Rhodococcus sublineages as defined in ref. [11]. The trees are entirely congruent with our previous ML phylogenies based on Mycobacteriales or Nocardiaceae core-genome alignments (the latter incorporating a larger strain representation than the type’s) [11]. The only exception is that Rhodococcus rhodnii ATCC 33071T and Rhodococcus triatomae DSM 44892T form here an independent branch at the root of the monophyletic line of descent containing sublineages 3 and 4 instead of being part of the sublineage 4 radiation (see ref. [11]).](https://pub-med-unpaywalled-images-cdn.bioz.com/pub_med_ids_ending_with_3668/pm40063668/pm40063668__page4_image1.jpg)
![Fig. 2. Unrooted core-genome ML tree of Rhodococcus monophyletic sublineage no. 2 containing R. equi and R. parequi PAM 2766T. The analysis includes a selection of R. equi strains representative of the genomic diversity of the species [29] (acc. nos. in Table S1). Based on a concatenated alignment of 828 core genes identified using Get-Homologues v22082022 [40] (orthologues identified with the COG and OrthoMCL clustering algorithms intersect using the settings minimal coverage 75% and maximum E-value 1e−05). Substitution model was GTR+F+ASC+R3. Branch support for each node is 100 (1000 ultrafast bootstrap replicates using IQtree UFBoot).](https://pub-med-unpaywalled-images-cdn.bioz.com/pub_med_ids_ending_with_3668/pm40063668/pm40063668__page5_image1.jpg)