(A and B) Maximum-likelihood trees of 28 strains of Pantoea agglomerans and closely related species, constructed using concatenated sequences of six protein-coding.

Slides:

Advertisements

Similar presentations

Methods for Phylogenetics and Evolutionary analysis Jianpeng Xu University of Nebraska-Omah a.

Advertisements

Supplementary Fig. S1. 16S RNA Neighbor-joining (NJ) tree of Brevibacterium metallicus sp. nov. NM2E3 T (in bold) and related species of genus Brevibacterium.

Choosing the most parsimonious tree

How many …?. What shape can you see? I can see some _____. Q1 Q1 stars.

Experimental design for high‐throughput characterization of synthetic human gut microbiome consortia Experimental design for high‐throughput characterization.

West Nile virus outbreak in Israel in 2015: phylogenetic and geographic characterization in humans and mosquitoes Y. Lustig, Z. Kaufman, B. Mannasse,

Survival of mice after infection with M

A. Papa, K. Dumaidi, F. Franzidou, A. Antoniadis

F. Aujoulat, H. Marchandin, I. Zorgniotti, A. Masnou, E. Jumas-Bilak

Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus.

Usutu virus infections in humans: a retrospective analysis in the municipality of Modena, Italy A. Grottola, M. Marcacci, S. Tagliazucchi, W. Gennari,

Distribution of TMEM173 in vertebrates.

Volume 9, Issue 9, Pages (September 2016)

(a) Subtree of the MetaPalette output tree for the Iowa prairie metagenome using organisms from the genus Bradyrhizobium. (a) Subtree of the MetaPalette.

Phylogenetic tree of perA A2-domain DNA sequence.

Comparative phylogenetic analysis of sapoviruses based on complete RdRp and VP1 nucleotide sequences. Comparative phylogenetic analysis of sapoviruses.

Genomes with Fe-S cluster assembly-related genes.

Whole genome-based phylogenetic analysis of Rickettsiae

Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene V. Sistek, M.

Maximum likelihood (ML) unrooted tree based on the full-length 16S rRNA genes (A) and 31 conserved single-copy genes (B) showing the phylogenetic position.

(A, left) Radial cladogram based on RAxML-based maximum-likelihood phylogeny (500 bootstraps, gamma distribution model, and LG+F substitution model) constructed.

Phylogenetic tree based on 16S rRNA gene sequence comparisons over 1,260 aligned bases showing the relationship between species of the genus Actinomyces.

Phylogenetic tree constructed by the neighbor-joining method, showing the position of Peptostreptococcus species within Clostridium rRNA clusters XI, XIII,

Phylogenetic tree of 38 Pseudomonas type strains, based on the V3-V5 region sequence of the 16S rRNA gene (V3 primer, positions 442 to 492; and V5 primer,

Genetic diversity of Legionella pneumophila inferred from rpoB and dotA sequences K.S. Ko, H. Miyamoto, H.K. Lee, M.-Y. Park, K. Fukuda, B.J. Park, Y.-H.

Phylogenetic diversity of archaeal lineages in the great ape gut microbiome. Phylogenetic diversity of archaeal lineages in the great ape gut microbiome.

Species diversity within the P. fluorescens species complex.

Neighbor-joining dendrogram based on concatenated gene fragments of adk, atpG, frdB, mdh, pgi, and recA (2,712 nucleotides), comparing the type strains.

F.M. Cohan Clinical Microbiology and Infection

Maximum likelihood phylogeny of USA500 and other CC8 strains.

Relative abundances of Propionibacterium species in different skin areas determined by 16S rRNA gene sequence analysis of 10 individuals. Relative abundances.

K. S. Ko, T. Kuwahara, L. Haehwa, Y. -J. Yoon, B. -J. Kim, K. -H

Phylogenetic tree. Phylogenetic tree. Shown are circle phylogram relationships for known genotypes of HRV-A, HRV-B, and HRV-C. The tree was calculated.

bHLH-PAS protein family structure and phylogeny.

NP sequence alignment of human H1N1 strains and phylogenetic analysis of representative NP from pandemic and seasonal H1N1 strains. NP sequence alignment.

Core genome phylogeny of V. anguillarum strains.

Phylogenetic analyses of alphacoronaviruses based on complete genome and ORF1ab protein sequence. Phylogenetic analyses of alphacoronaviruses based on.

Neighbor-joining tree based on nifH for 20 organisms along with the maximum-likelihood sequence obtained from aligning the soil data to the gene sequence.

Rooted neighbor-joining tree inferred from the concatenated MLST typing scheme sequences (CAP59, GPD1, LAC1, SOD1, URA5, and PLB1 genes and IGS) of 10.

Phylogenetic tree of 38 Pseudomonas type strains, based on a concatenated nine-gene MLST analysis. Phylogenetic tree of 38 Pseudomonas type strains, based.

Phylogenetic comparison among selected Pasteurella multocida and Haemophilus influenzae species with completed genome sequences. Phylogenetic comparison.

MLST analysis of Bacillus strains of this study and related species of the B. cereus sensu lato group. MLST analysis of Bacillus strains of this study.

(a) Mycetoma aspect of the patient in the right forearm.

Phylogenetic network with concatenated 16S rRNA, 23S rRNA, groEL, rpoB, and dnaK sequences (3,009 unambiguously aligned base pairs), including 71 Coxiella-like.

Phylogenetic analysis of AquK2P.

Phylogenetic analysis of K. quasipneumoniae subsp

Genogroup and genotypes of GI, GII, GIII, GIV, and GV sapovirus strains based on complete VP1 nucleotide sequences. Genogroup and genotypes of GI, GII,

Genetic relationships of Haemophilus and Aggregatibacter species, using Escherichia coli as an outgroup. Genetic relationships of Haemophilus and Aggregatibacter.

Phylogenetic tree representation of a neighbor-joining analysis of several species of piroplasms. Phylogenetic tree representation of a neighbor-joining.

Hector H. García et al. Clin. Microbiol. Rev. 2002; doi: /CMR

Fig. 1 Maximum likelihood tree relating the Denisova 2 mtDNA to other ancient and present-day mtDNAs. Maximum likelihood tree relating the Denisova 2 mtDNA.

Dendrogram of the genus Serratia, constructed using the neighbor-joining method in MicroSeq software. 16S rRNA gene sequences of type strains of the species,

Phylogenetic analyses showing the relationship between Ruminococcus, Blautia, and Clostridium on the basis of the sequences of the 16S region for each.

Distance tree of ITS2 rRNA gene sequences of 54 strains belonging to species known as black-grain mycetoma agents. Distance tree of ITS2 rRNA gene sequences.

Roberta B. Carey et al. Clin. Microbiol. Rev. 2018; doi: /CMR

S protein sequence-based phylogenetic analyses of alphacoronaviruses.

(A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt and representative CDV sequences obtained from GenBank.

Synteny and Phylogeny of Putative GRMZM2G Orthologs.

Phylogenetic tree based on predominant 16S rRNA gene sequences obtained by C4–V8 Sutterella PCR from AUT-GI patients, Sutterella species isolates, and.

Molecular phylogenetic analysis of RNA polymerase II largest-subunit protein sequences from various trichomonads, including D. fragilis. Molecular phylogenetic.

Phylogenetic trees for fusion (F) and attachment (G) genes of selected HMPV isolates. Phylogenetic trees for fusion (F) and attachment (G) genes of selected.

Maximum likelihood nucleotide tree of the bla OXA-51-like genes intrinsic to A. baumannii. Maximum likelihood nucleotide tree of the blaOXA-51-like genes.

Phylogenetic tree of the complete genomes of 27 representative human (black) and camel (red) MERS-CoV strains rooted by NeoCoV (KC ). Phylogenetic.

Relationship of partial rpoB gene sequences inferred by the neighbor-joining method for Canadian study strains of C. pyruviciproducens. Relationship of.

Dendrogram relationships by 16S rRNA gene similarity of the A

Dendrogram clustering the MALDI-TOF MSP obtained from at least 20 mass spectra of strains belonging to the C. haemulonii complex species and related species.

This figure shows the six phenotypes observed during CLI induction testing of S. aureus by disk diffusion. This figure shows the six phenotypes observed.

Tree depicting the phylogenetic relationships of all strains included in this study. Tree depicting the phylogenetic relationships of all strains included.

16S rRNA-based phylogeny of sponge-associated cyanobacteria and chloroplasts. 16S rRNA-based phylogeny of sponge-associated cyanobacteria and chloroplasts.

Unrooted neighbor-joining tree of 16S rRNA gene sequences from low-G+C-content gram-positive bacteria, obtained from clone libraries. Unrooted neighbor-joining.

Presentation transcript:

(A and B) Maximum-likelihood trees of 28 strains of Pantoea agglomerans and closely related species, constructed using concatenated sequences of six protein-coding genes (fusA, gyrB, leuS, pyrG, rplB, and rpoB) (A) and 16S rRNA sequences (B) based on the general time-reversible model of nucleotide substitution, which was inferred to be the most likely using MODELTEST. (C) Split decomposition analysis tree of the 20 strains of P. agglomerans and 2 P. agglomerans-like strains. (A and B) Maximum-likelihood trees of 28 strains of Pantoea agglomerans and closely related species, constructed using concatenated sequences of six protein-coding genes (fusA, gyrB, leuS, pyrG, rplB, and rpoB) (A) and 16S rRNA sequences (B) based on the general time-reversible model of nucleotide substitution, which was inferred to be the most likely using MODELTEST. (C) Split decomposition analysis tree of the 20 strains of P. agglomerans and 2 P. agglomerans-like strains. Circles and triangles represent P. agglomerans groups I and II, respectively. The two P. agglomerans-like strains, PA5 and SB547, are in the rectangle. The numbers at the nodes are bootstrap values higher than 80%, obtained after 1,000 replicates. Alexis Delétoile et al. J. Clin. Microbiol. 2009; doi:10.1128/JCM.01916-08