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Summary
Establishing the origin of mitochondria and plastids is vital to know 2 founding occasions within the origin and early evolution of eukaryotes. Latest advances within the exploration of microbial range and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids through the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Right here, we strongly help these placements by analyzing the machineries for meeting of iron–sulfur ([Fe–S]) clusters, an important perform in eukaryotic cells that’s carried out in mitochondria by the ISC equipment and in plastids by the SUF equipment. We assessed the taxonomic distribution of ISC and SUF in representatives of main eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins present an early branching of mitochondria inside Alphaproteobacteria, proper after the emergence of Magnetococcales. Comparable analyses with the SUF equipment place main plastids as sister to Gloeomargarita inside Cyanobacteria. Our outcomes add to the rising proof of an early emergence of main organelles and present that the evaluation of important machineries of endosymbiotic origin present a strong sign to resolve historical and elementary steps in eukaryotic evolution.
Quotation: Garcia PS, Barras F, Gribaldo S (2023) Parts of iron–Sulfur cluster meeting machineries are strong phylogenetic markers to hint the origin of mitochondria and plastids. PLoS Biol 21(11):
e3002374.
https://doi.org/10.1371/journal.pbio.3002374
Educational Editor: Filipa L. Sousa, Universitat Wien, AUSTRIA
Acquired: February 28, 2023; Accepted: October 10, 2023; Printed: November 8, 2023
Copyright: © 2023 Garcia et al. That is an open entry article distributed below the phrases of the Artistic Commons Attribution License, which allows unrestricted use, distribution, and replica in any medium, offered the unique creator and supply are credited.
Information Availability: All related knowledge are inside the paper and its Supporting Info recordsdata.
Funding: This work was supported by the European Union’s Horizon 2020 analysis and innovation program below grant 722361 (wage of PSG) and the Agence Nationale de la Recherche ANR-10-LABX- 62-IBEID to FB and SG. The funders had no function in examine design, knowledge assortment and evaluation, choice to publish, or preparation of the manuscript.
Competing pursuits: The authors have declared that no competing pursuits exist.
Endosymbiosis occasions had been necessary steps within the origin and early evolution of eukaryotes and notably people who gave rise to mitochondria and first plastids from Alphaproteobacteria and Cyanobacteria, respectively [1–3]. Latest phylogenomic analyses have steered a basal placement of mitochondria with Alphaproteobacteria and that the long-time assumed branching with the Rickettsiales is probably going attributable to a compositional bias pushed by convergent AT-rich genomes [4–8]. In regards to the placement of plastids, a number of analyses have supported the basal place of plastids [9,10] and, extra just lately, as sister to the newly sequenced cyanobacterium Gloeomargarita lithophora [11–13].
Iron–sulfur [Fe–S] clusters are very historical protein cofactors important for all times and are concerned in lots of organic processes [14,15]. Our current analyses have reconstructed the taxonomic distribution and evolution of the characterised machineries, SUF and ISC, in Micro organism [16]. In eukaryotes, SUF and ISC function in plastids and mitochondria, respectively [17], and catalyze related biochemical steps however contain totally different proteins (Figs 1A and 2A). The elements of the ISC equipment are encoded by nuclear genes and are translocated to mitochondria to synthesize [Fe–S] clusters [18]. The SUF elements are additionally largely encoded by nuclear genes, to the exception of SufB and SufC, which may be encoded in plastid genomes [19,20]. From earlier phylogenetic analyses of some elements, it’s typically accepted that these machineries originated from the two endosymbionts [17,21–24]. Nevertheless, the phylogenetic sign introduced by these techniques as a complete has not been used to analyze the location of mitochondria and plastids.
Fig 1.
(A) Schematic view of [Fe–S] cluster biosynthesis by the ISC system and the corresponding elements. (B) Taxonomic distribution of the ISC and SUF techniques mapped on the Alphaproteobacteria reference tree (IQ-TREE, LG+R10+C60+PMSF. IF2+RpoB+RpoC. 3,429 amino acid positions, 1,193 sequences). Dots at branches point out ultrafast-bootstrap values ≥ 95%. The dimensions bar signifies common variety of substitutions per web site. (C) Abstract of the location of mitochondria utilizing totally different approaches and fashions. Two different positions are indicated and reported in (D). (D) Bayesian phylogeny from the concatenated ISC dataset together with alphaproteobacterial and eukaryote homologues (IscA+IscS+HscA+Fdx+CyaY, Phylobayes, GTR+CAT, 1,306 amino acid positions, 149 sequences). Dots at branches point out posterior possibilities ≥ 0.95. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out the taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
Fig 2.
(A) Schematic view of [Fe–S] cluster biosynthesis by the SUF system and the corresponding elements. (B) Taxonomic distribution of the ISC and SUF techniques mapped on the Cyanobacteria reference tree (IQ-TREE, LG+R10+C60+PMSF. IF2+RpoB+RpoC. 3,026 amino acid positions, 107 sequences). Dots on the branches point out ultrafast-bootstrap values ≥ 95%. The dimensions bar signifies common variety of substitutions per web site. (C) Abstract of the location of mitochondria utilizing totally different approaches and fashions. Three different positions are indicated and reported in (D). (D) Bayesian phylogeny from the concatenated SUF dataset together with cyanobacterial and eukaryote homologues (SufB+SufC+SufD+SufS) (Phylobayes, GTR+CAT, 1,565 amino acid positions, 112 sequences). Dots at branches point out posterior possibilities ≥ 0.95. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out the taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
We used our current datasets [16] to investigate intimately the taxonomic distribution of the ISC and SUF machineries in 1,191 genomes protecting the present range of Alphaproteobacteria (for a listing of taxa, see S1 Desk). The presence of ISC and SUF homologues in Alphaproteobacteria is patchy, ISC being recognized largely within the basal lineages (Magnetococcales, Marine Proteobacteria 1, MC1) and in Rickettsiales, whereas it’s absent in a lot of the different Alphaproteobacteria which have the SUF system (Fig 1B and S2 Desk). The sample of mutual exclusion between ISC and SUF has been noticed in different bacterial teams, particularly Gammaproteobacteria [16]. A phylogeny based mostly on concatenation of 5 core ISC proteins (IscS, HscA, Fdx, CyaY, and IscA, 1,306 amino acid positions) is essentially in step with the reference Alphaproteobacteria phylogeny, exhibiting the monophyly of all main orders (S1 Fig). These outcomes point out that the ISC system was current within the ancestor of Alphaproteobacteria and was inherited primarily vertically, whereas it was subsequently misplaced in lots of lineages throughout diversification of this phylum. This distribution de facto excludes an origin of the mitochondrial ISC from many lineages.
We then investigated the presence of the SUF and ISC techniques in 66 genomes protecting the principle eukaryotic phyla [25] (for a listing of taxa, see S3 Desk). Homologues of the 8 ISC equipment elements had been recognized in most eukaryotic taxa—aside from IscX—and are encoded in nuclear genomes (S4 Desk). Preliminary single-gene tree analyses allowed to obviously establish the eukaryotic orthologues of mitochondrial origin by their branching with Alphaproteobacteria (S1 Information). We subsequently added these ISC elements within the Alphaproteobacteria dataset to analyze their placement. Bayesian evaluation utilizing the CAT+GTR mannequin helps the monophyly of eukaryotic sequences (PP = 1) and their deep branching, simply after Magnetococcales (PP = 0.82). These outcomes strengthen the Alphaproteobacteria-deep speculation, though the place of eukaryotes is extra basal than beforehand noticed [4,6], branching earlier than the Marine Proteobacteria 1 group (Fig 1C and 1D). Furthermore, the inner topology of Alphaproteobacteria agrees with the reference phylogeny of this phylum, notably with Rickettsiales branching after Magnetococcales and sister to all remaining Alphaproteobacteria (Fig 1D).
We investigated the robustness of the Alphaproteobacteria-deep placement by analyzing the ISC dataset with a panel of different fashions and methodologies (Fig 1C). An ML phylogeny with the LG+R8+C60+PMSF mannequin certainly exhibits Eukaryotes as sister group of Rickettsiales, though with low help (bootstrap worth (BV) = 48%) (Fig 1C, place #2 in Fig 1D, S2 Fig). Furthermore, the inner phylogeny of Alphaproteobacteria exhibits incongruencies with each the reference phylogeny of the phylum and the alphaproteobacterial ISC concatenation tree, notably with the cut up of the Rickettsiales in 2 teams (S2 Fig), which strongly counsel the presence of a tree reconstruction artefact utilizing this mannequin when eukaryotic sequences are included.
On condition that ISC elements are all nuclear encoded, the “Rickettsiales-sister” placement is unlikely to be attributable to a convergent compositional bias towards AT-rich genomes between Rickettsiales and mitochondria. An AminoGC plot (S3A Fig) exhibits that the GC bias of eukaryotic sequences just isn’t notably related neither to Rickettsiales or Magnetoccocales. The removing of compositional heterogeneous websites by a stationary-based methodology resulted in a tree in step with the Bayesian tree, putting once more Eukaryotes on the base of Alphaproteobacteria, and after the Magnetococcales, though with low help (BV = 23%), however exhibits an accurate inner phylogeny of Alphaproteobacteria (Figs 1C and S4). An AminoGC plot of the trimmed dataset exhibits a diminished distinction between the teams, suggesting that decreasing the GC bias between clades would possibly take away the inaccurate placement of Eukaryotes with Rickettsiales (S3B Fig). Surprisingly, even though nucleic sequences are normally extra immediate to compositional bias, an ML tree obtained from the nucleic acid model of the unique alignment (GTR mannequin) additionally strongly helps the “Alphaproteobacteria-deep” placement (BV = 100%), though with a poorly resolved inner topology of Alphaproteobacteria (S5 Fig). A %GC plot of this dataset exhibits an identical sample as the complete protein dataset (S3C Fig).
Altogether, these outcomes counsel that sequence compositional bias is no less than partially liable for the location of Eukaryotes with the Rickettsiales, in settlement with current analyses [4,6,7]. This tree reconstruction artefact may be counterbalanced both by eradicating compositional heterogeneous positions or through the use of the GTR mannequin, whereas ML web site heterogeneous fashions similar to LG+C60+PMSF fail to sort out this subject.
We then used the identical strategy to analyze the origin of plastids by analyzing the SUF system (Fig 2). We used the dataset from our earlier examine [16], originating from 95 genomes protecting the present range of Cyanobacteria (for a listing of taxa, see S5 Desk). Whereas the SUF system is essentially current in most genomes, the ISC system is absent (Fig 2B and S6 Desk). An ML tree obtained from concatenation of the 4 most conserved SUF markers (SufB, SufC, SufD, and SufS, 1,561 amino acid positions) is essentially in step with the reference Cyanobacteria phylogeny, besides a couple of misplacements probably attributable to particular intra-phylum HGTs (S6 Fig). We didn’t embrace Gloeobacter within the dataset as we’ve got just lately proven that its authentic SUF was changed by one laterally acquired from different micro organism [16].
Amongst Eukaryotes, SUF homologues are current solely in photosynthetic lineages, both nuclear or plastid encoded (S4 Desk). Preliminary single-gene tree analyses allowed us to establish the eukaryotic orthologues of plastid origin by their branching with Cyanobacteria (S1 Information). When included within the cyanobacterial dataset, Bayesian evaluation (CAT+GTR) (Fig 2D) and ML evaluation (LG+C60+PMSF) with out and with stationary-based trimming (S7 and S8 Figs, respectively) help a deep placement of plastids inside Cyanobacteria (place #1 in Fig 2C and 2D), in settlement with earlier analyses [9,10]. Apparently, these timber favor the location of plastids as sister to Gloeomargarita lithophora (PP = 0.65, BV = 70%, BV = 54%), strengthening current knowledge [11–13]. Puzzlingly, ML evaluation with nucleic acids (S9 Fig) infers a extremely incongruent tree the place Eukaryotes will not be monophyletic and department with totally different cyanobacterial clades (positions #2 and #2’ in Fig 2C and 2D), which strongly signifies that this tree just isn’t dependable. Lastly, our knowledge properly verify the impartial acquisition of a main plastid within the amoeba Paulinella microspora from a member of Prochlorococcales [26,27] (Figs 2D and S7–S9).
The origins of mitochondria and plastids is a troublesome query to handle phylogenetically, because of the antiquity of such occasions and the potential biases in composition and evolutionary patterns arising from profound diversifications that occurred through the endosymbiosis course of. Latest advances in genomic protection from Alphaproteobacteria and Cyanobacteria, along with enchancment of phylogenomics approaches and evolutionary fashions, have allowed to make clear the timing and origin of those endosymbioses. We present right here that the [Fe–S] cluster biosynthesis ISC and SUF machineries present a strong extra dataset to deduce the origin of organelles. 4 standards concur to the pertinence of utilizing these machineries: (i) they had been inherited from Alphaproteobacteria and Cyanobacteria on the origin of Eukaryotes and first photosynthetic lineages, respectively; (ii) they perform an important mobile perform; (iii) most of their elements are encoded within the nucleus, lowering the issue of compositional biases; and (iv) being a part of a extremely built-in course of, they had been probably subjected to related evolutionary constraints.
The complexity of the big protein households, together with the ISC and SUF elements, might have prevented their choice in earlier large-scale automated analyses looking for organelle orthologues. Due to this fact, an identical strategy specializing in the detailed evaluation of different elementary eukaryotic techniques of mitochondrial and plastid origin, coupled with improve in genomic protection from deep branches of the Alphaproteobacteria and Cyanobacteria, will certainly present additional key data on our most historical previous.
Materials and strategies
Genome databases
We used a database of 10,865 archaeal and bacterial proteomes, which we just lately assembled for our survey of [Fe–S] biosynthesis machineries in prokaryotes [16]. The database incorporates 1,188 proteomes annotated as Alphaproteobacteria (S1 Desk) and 95 proteomes annotated as Cyanobacteria (S5 Desk). For the current evaluation, we added 3 alphaproteobacterial Metagenome Assembled Genomes from the Martijn examine (one equivalent to MarineAlpha4 and two to MarineProteo1) [4]. We additionally assembled a database of 66 Eukaryote proteomes gathered from the NCBI and representing the foremost eukaryotic superphyla (TSAR, Amorphea, Excavates, Cryptista, Haptista, Archaeplastida) [25] (S3 Desk). We additionally included 4 plastid genomes from Glaucophyta (Cyanophora paradoxa, Gloeochaete wittrockiana, Glaucocystis incrassata, Cyanoptyche gloeocystis).
Meeting of datasets
Datasets of prokaryotic homologues of IscA, IscS, IscU, IscX, CyaY, HscA, HscB, Fdx, SufB, SufC, SufD, SufE, SufS, SufT, SufU had been already assembled as described in [16]. Right here, for eukaryote sequences, we used the identical process. Briefly, we used HMM profiles of every part from [16] to carry out an HMM search utilizing HMMER v3.2.1 [28] on the eukaryotic database, choosing hits with an e-value < 0.01. These hits had been then added to the prokaryotic homologue datasets. Sequences had been aligned utilizing MAFFT v7.419 [29] (auto choice), the alignments had been manually curated to get rid of nonhomologous sequences, and preliminary phylogenies had been inferred utilizing FASTTREE v2.1.10 [30] (LG+G4) and with and with out trimming utilizing BMGE v1.12 [31] (BLOSUM30). For every part, eukaryotic orthologue subfamilies had been delineated manually based mostly on the branching of sequences inside Cyanobacteria or Alphaproteobacteria, taxonomic distribution, area composition, and size of sequences. We didn’t discover any homologs of the archaeal SMS system [16], to the exception of SmsB and SmsC, that are fused in the identical ORF within the genome of Blastocystis sp. ATCC 50177, as beforehand reported [32]. The SufB and SufC of the 4 Glaucophyta plastid genomes had been recognized utilizing tBLASTn [33] and added manually. All preliminary timber used for the delineation of eukaryote orthologue teams can be found in S1 Information.
For the concatenation, we chosen the markers based mostly on totally different standards. Markers that weren’t broadly distributed (IscX in eukaryotes, SufU and SufT in Cyanobacteria) had been eradicated. We additionally discarded HscB and IscU as they didn’t type clear monophyletic teams in preliminary timber. Lastly, in eukaryotes, 2 homologues of IscA (ISA1 and ISA2 belonging to the big ATC-II and ATC-I protein subfamilies, respectively [22]), SufE and SufS, had been recognized. For IscA (ISA) and SufS, we chosen the paralogues distributed equally to different ISC/SUF elements and which department with Alphaproteobacteria and Cyanobacteria, respectively, within the preliminary phylogenies (ISA1 and SufS1 in S4 Desk). We discarded the entire SufE household, because it included 2 clades (SufE1 and SufE2 in S4 Desk) both containing a number of paralogues or not broadly conserved in Eukaryotes. Though the ATC-II household is shared by the ISC and SUF techniques (IscA and SufA) in Alphaproteobacteria, we chosen IscA for the ISC concatenation as we noticed that it’s in neighborhood of the remainder of ISC system [16] and follows the reference tree of Alphaproteobacteria group.
Lastly, alignments and every protein household dataset had been aligned utilizing MAFFT v7.419 [29] (LINSI choice) and trimmed utilizing BMGE v1.12 [31] (entropy threshold = 0.95, minimal size = 1, matrix = BLOSUM30) and particular person duplicated sequences (paralogues, isoforms, meeting artifacts) had been eliminated after visible inspection of timber/alignments. The nucleic sequences had been back-aligned on amino acid sequences by changing every amino acid in its respective codon by a customized script (S2 Information). For trimming of the nucleic alignments, we used the -t CODON choice of BMGE. For the concatenations, we saved a taxon if it possessed n(markers) ≥ 3 for each ISC and SUF, aside from Rhodophyta and Glaucophyta (SUF) for which we retained the one 2 detected markers. The extremely divergent sequences from amitochondriate eukaryotes (Metanomada and Entamoeba) had been eliminated to keep away from tree reconstruction artefacts.
For the reference timber of Alphaproteobacteria and Cyanobacteria, we assembled supermatrices utilizing IF2, RpoB, and RpoC as markers with the identical process as described above.
Phylogenetic inference
The ML phylogenies of ISC and SUF techniques based mostly on protein sequences had been inferred utilizing IQ-TREE v1.6.10 [34], with the most effective mannequin based on BIC standards and with the PMSF methodology (posterior imply web site frequency) choice with 60 combination classes [35], with the beginning phylogenies inferred by homogeneous fashions. To evaluate the robustness of branches, 100 nonparametric bootstrap replicates had been used. The tree of SUF was rooted utilizing Nitrosomonadales and Balneolaeota, as SUF was anciently acquired by horizontal gene switch from these organisms [16] (S7 Desk). SUF homologues from Gloeobacter had been eliminated as the unique system was changed on this bacterium by HGT from different micro organism [16]. The ML phylogenies based mostly on nucleic sequences had been inferred utilizing IQ-TREE, with the GTR/SYM fashions. The Bayesian phylogenies had been inferred utilizing Phylobayes v4.1c [36], with the GTR+CAT mannequin. For ISC, 4 chains had been run for round 99,000 iterations every. The convergence between chains was examined utilizing bpdiff with a sampling of 1,885 and 1,878 timber (each 50 timber) and a burn-in of 5,000. Two chains with a maxdiff < 0.15 (0.13) had been used to deduce the consensus tree. The opposite maxdiff outcomes correspond to decrease however acceptable convergence (0.23, 0.25, 0.22, 0.32, 0.32). For SUF, 4 chains had been run for round 86,000 iterations every. The convergence between chains was examined utilizing bpdiff with a sampling of 14,259 and 14,235 timber (each 5 timber) and a burn-in of 15,000. Two chains with a maxdiff ≈ 0.3 (0.3079) had been used to deduce the consensus tree. The remainder of the opposite maxdiff outcomes correspond to nonconvergent runs (0.75, 0.45, 0.87, 0.58, 0.60).
The ML reference phylogenies of Alphaproteobacteria and Cyanobacteria had been inferred utilizing IQ-TREE v1.6.10 [34], with the most effective mannequin based on BIC standards and with the PMSF methodology (posterior imply web site frequency) choice with 60 combination classes [35] with the beginning phylogenies inferred by homogeneous fashions. To evaluate the robustness of branches, 1,000 fast-bootstrap replicates had been used. The 2 reference timber had been rooted utilizing as outgroup different Proteobacteria and Melainabacteria, respectively (S7 Desk).
Supporting data
S1 Fig.
(A) Reference tree of Alphaproteobacteria possessing an ISC system (IF2+RpoB+RpoC). IQ-TREE, LG+F+R7+C60+PMSF, 3,483 amino acid positions, 96 sequences. Numbers at branches point out ultrafast-bootstrap values. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. (B) ML Phylogeny of alphaproteobacterial ISC (IscA+IscS+HscA+Fdx+CyaY). IQ-TREE, LG+R7+C60+PMSF, 1,275 amino acid positions, 97 sequences. Numbers at branches point out nonparametric bootstrap values. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s001
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S2 Fig. ML phylogeny of alphaproteobacterial and eukaryote ISC (IscA+IscS+HscA+Fdx+CyaY).
IQ-TREE, LG+R8+C60+PMSF, 1,306 amino acid positions, 149 sequences. Numbers at branches point out nonparametric bootstrap values. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s002
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S3 Fig. Boxplot of AminoGC and %GC distribution amongst sequences for the ISC concatenation.
(A) AminoGC for protein concatenation. (B) AminoGC for protein concatenation after stationary-based trimming. (C) %GC for nucleic protein concatenation. The AminoGC was calculated by the script prune_ali.pl from Martijn and colleagues [4]. Center bar: median; hinges: first and third quartiles; whiskers: largest worth no additional than 1.5 (interquartile vary); dots: particular person factors; large dots: outliers. The higher bars correspond to the two-tailed Mann–Whitney U take a look at end result (H0 = no distinction between the two teams). N.S.: p > 0.05, *: p < 1 × 10−3, **: p < 1 × 10−5.
https://doi.org/10.1371/journal.pbio.3002374.s003
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S4 Fig. ML phylogeny of alphaproteobacterial and eukaryote ISC with stationary-based trimming.
IQ-TREE, LG+R6+C60+PMSF, 532 amino acid positions, 149 sequences. Numbers at branches point out the nonparametric bootstrap values. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s004
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S5 Fig. ML nucleic acid phylogeny of alphaproteobacterial and eukaryote ISC (IscA+IscS+HscA+Fdx+CyaY).
IQ-TREE, GTR+F+R8, 4,128 nucleic positions, 149 sequences. Numbers on the branches point out nonparametric bootstrap values. The dimensions bar signifies common variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s005
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S6 Fig. ML phylogeny of cyanobacterial SUF rooted with an exterior group (SufB+SufC+SufD+SufS).
IQ-TREE, LG+F+R10+C60+PMSF. 1,561 amino acid positions, 167 sequences. The numbers on the branches point out the ultrafast-bootstrap values. The dimensions bar signifies the typical variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s006
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S7 Fig. ML phylogenies of cyanobacterial and eukaryote SUF (SufB+SufC+SufD+SufS).
(A) ML phylogeny of cyanobacterial and eukaryote SUF rooted with an exterior group (with out stationary-based trimming). IQ-TREE, LG+R10+C60+PMSF. 1,553 amino acid positions, 188 sequences. The numbers on the branches point out the nonparametric bootstrap values. The dimensions bar signifies the typical variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. (B) ML phylogeny of cyanobacterial and eukaryote SUF (with out stationary-based trimming). IQ-TREE, LG+R8+C60+PMSF. SufB+SufC+SufD+SufS. 1,565 amino acid positions, 112 sequences. The numbers on the branches point out the nonparametric bootstrap values. The dimensions bar signifies the typical variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s007
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S8 Fig. ML phylogeny of cyanobacterial and eukaryote SUF (with stationary-based trimming).
IQ-TREE, LG+R6+C60+PMSF. SufB+SufC+SufD+SufS. 813 amino acid positions, 112 sequences. The numbers on the branches point out the nonparametric bootstrap values. The dimensions bar signifies the typical variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s008
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S9 Fig. ML nucleic phylogeny of cyanobacterial and eukaryote SUF.
IQ-TREE, SYM+R8. SufB+SufC+SufD+SufS. 4,809 nucleic positions, 112 sequences. The numbers on the branches point out the nonparametric bootstrap values. The dimensions bar signifies the typical variety of substitutions per web site. Numbers on the ideas point out taxonomy IDs from NCBI. The information underlying this Determine may be present in S1 Information.
https://doi.org/10.1371/journal.pbio.3002374.s009
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