There are great disparities in the genome G + C% content and amino acid compositions of the Rickettsiales, Pelagibacterales (including alphaproteobacterium HIMB59) and Holosporales with all other …
All branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A maximum-likelihood tree inferred under the LG + PMSF(ES60)+F + R6 model and from the untreated dataset which is …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated.
Branch support values are 1.0 posterior probabilities unless annotated. (A) Bayesian consensus tree inferred from the full dataset which is highly compositionally heterogeneous. (B) Bayesian …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A tree that results from the analysis of the untreated dataset. (B) A tree that results from the analysis of a dataset …
In this tree, derived from an analysis using a model that does not account for compositional heterogeneity across sites, the Geminicoccaceae has a more derived placements within the Rhodospirillales …
Magnetococcales in gray; Rickettsiales in brown; Pelagibacterales in maroon; Holosporales in light blue; Rhizobiales in green; Caulobacterales in orange; Rhodobacterales in red; Sneathiellales in …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A maximum-likelihood tree, inferred under the LG + PMSF(ES60)+F + R6 model, to place the Holosporaceae in the absence of …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A tree that results from the analysis of the untreated dataset. () A tree that results from the analysis of a dataset …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A tree that results from the analysis of the untreated dataset. (B) A tree that results from the analysis of a dataset …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A tree that results from the analysis of the untreated dataset. (B) A tree that results from the analysis of a dataset …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated. (A) A tree that results from the analysis of the untreated dataset. (B) A tree that results from the analysis of a dataset …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated.( A) A tree that results from the analysis of the untreated dataset. (B) A tree that results from the analysis of a dataset …
Branch support values are 1.0 posterior probabilities unless annotated. (A) Bayesian consensus tree inferred to place the Holosporales in the absence of the Rickettsiales and the Pelagibacterales …
Branch support values are 100% SH-aLRT and 100% UFBoot unless annotated.
Branch support values are 1.0 posterior probabilities unless annotated.
See Supplementary file 1 as well.
Species | ‘Candidatus Finniella inopinata’ | Stachyamoeba-associated rickettsialean | Peranema-associated rickettsialean |
---|---|---|---|
Genome size | 1,792,168 bp | 1,738,386 bp | 1,375,759 bp |
N50 | 174,737 bp | 1,738,386 bp | 28,559 bp |
Contig number | 28 | 1 | 125 |
Gene number† | 1741 | 1588 | 1223 |
A + T% content | 56.58% | 67.01% | 59.13% |
Family | 'Candidatus Paracaedibacteraeae' | Rickettsiaceae | ‘Candidatus Midichloriaceae’ |
Order | Holosporales | Rickettsiales | Rickettsiales |
Completeness‡ | 94.96% | 97.12% (=100%) | 92.08% |
Redundancy‡ | 0.0% | 0.0% | 2.1% |
†as predicted by Prokka v.1.13 (rRNA genes were searched with BLAST).
‡as estimated by Anvi’o v.2.4.0 using the Campbell et al., 2013 marker gene set.
Class 1. Alphaproteobacteria Garrity et al., 2005 |
Subclass 1. Rickettsidae Ferla et al., 2013 emend. Muñoz-Gómez et al. 2019 (this work) |
Order 1. Rickettsiales Gieszczkiewicz, 1939 emend. Dumler et al., 2001 |
Family 1. Anaplasmataceae Philip, 1957 Family 2. 'Candidatus Midichloriaceae' Montagna et al., 2013 Family 3. Rickettsiaceae Pinkerton, 1936 |
Subclass 2. Caulobacteridae Ferla et al., 2013 emend. Muñoz-Gómez et al. 2019 |
Order 1. Rhodospirillales Pfennig and Trüper, 1971 emend. Muñoz-Gómez et al. 2019 |
Family 1. Acetobacteraceae (ex Henrici 1939) Gillis and De Ley, 1980 Family 2. Rhodospirillaceae Pfennig and Trüper, 1971 emend. Muñoz-Gómez et al. 2019 Family 3. Azospirillaceae fam. nov. Muñoz-Gómez et al. 2019 Family 4. Holosporaceae Szokoli et al., 2016 Family 5. Rhodovibriaceae fam. nov. Muñoz-Gómez et al. 2019 Family 6. Geminicoccaceae Proença et al., 2018 |
Order 2. Sneathiellales Kurahashi et al., 2008 |
Order 3. Sphingomonadales Yabuuchi and Kosako, 2005 |
Order 4. Pelagibacterales Grote et al., 2012 |
Order 5. Rhodobacterales Garrity et al., 2005 |
Order 6. Caulobacterales Henrici and Johnson, 1935 |
Order 7. Rhizobiales Kuykendall, 2005 |
Class 2. Magnetococcia Parks et al., 2018 |
Order 1. Magnetococcales Bazylinski et al., 2013 |
A 16S rRNA gene maximum-likelihood tree of the Rickettsiales and Holosporales that phylogenetically places the three endosymbionts whose genomes were sequenced in this study.
(1) ‘Candidatus Finniella inopinata’ endosymbiont of Viridiraptor invadens strain Virl02, (2) an alphaproteobacterium associated with Peranema trichophorum strain CCAP 1260/1B, and (3) an alphaproteobacterium associated with Stachyamoeba lipophora strain ATCC 50324. Branch support values are SH-aLRT and UFBoot.
Supplementary tables.
(A) Ultrafast bootstrap (UFBoot) variation for several clades discussed in this study as compositionally biased sites, according to ɀ, are progressively removed in steps of 10%. (B) Ultrafast bootstrap (UFBoot) variation for several clades discussed in this study as the fastest sites are progressively removed in steps of 10%. (C) GenBank assembly accession numbers for the 120 alphaproteobacterial and outgroup genomes used in this study. (D) A list of the least compositionally heterogeneous genes out of the 200 single-copy and vertically inherited genes used in this study. (E) Model fit of amino acid replacement matrices as components of simple models that do not account for compositional heterogeneity across sites. Models are ordered from lowest to highest BIC. -LnL: log-likelihood; df: degrees of freedom or number of free parameters; AIC: Akaike information criterion; AICc: corrected Akaike information criterion; BIC: Bayesian information criterion. (F) Model fit of amino acid replacement matrices as components of complex models that account for compositional heterogeneity across sites. Models are ordered from lowest to highest BIC. -LnL: log-likelihood; df: degrees of freedom or number of free parameters; AIC: Akaike information criterion; AICc: corrected Akaike information criterion; BIC: Bayesian information criterion. (G) Model fit of LG + ES60+F for which the model component that accounts for rate heterogeneity across sites varies. Models are ordered from lowest to highest BIC. -LnL: log-likelihood; df: degrees of freedom or number of free parameters; AIC: Akaike information criterion; AICc: corrected Akaike information criterion; BIC: Bayesian information criterion. (H) Several summary statistics for the PhyloBayes MCMC chains run for each analysis under the CAT-Poisson+Γ4.