atcc 27335 strain  (ATCC)

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Genomic characteristics of the 27 studied S. intermedius strains

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: Plasmid Preparation, Infection

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Genome sequencing details of the 13 S. intermedius strains from our study

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: Sequencing, Concentration Assay, Extraction

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Circular representation of the 27 studied S. intermedius genomes. Genomic sequences were aligned using strain ATCC 27335 as reference. The alignment gaps tend to coincide with the regions of low G + C contents. The rings, from the inside out, display the size in kbp; GC skew; G + C content; followed by genomes as listed in the left legend

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: Genomic Sequencing

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: 16S rRNA-based phylogenetic relationships of S. intermedius strains using the Maximum Likelihood method with Kimura 2-parameter. The scale bar indicates the evolutionary distance between the sequences determined by a 0.005 substitution per nucleotide position. Numbers at the nodes indicate bootstrap values obtained from 1,000 replicates

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Clustered gene presence/ absence and accessory genome distribution calculated by pangenome analysis among the 27 studied S. intermedius strains. Left: core-genome phylogeny; the three clusters in the dendrogram are delineated by red lines; right: heatmap of core genes

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Phylogenetic tree of S. intermedius strains based upon SNPs extracted from the core genome. Sequences were aligned using ClustalW with default parameters and phylogenetic inferences obtained using the Maximum likelihood method within the MEGA, version 7, software. Nodes indicate bootstrap support from 1000 replicates.

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: Software

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Differential distribution of COG functional categories in S. intermedius : a proportion of six classes of functional categories in strain-specific and core genes; b functional categories in strain-specific and core genes; c functional categories in the 27 S. intermedius strains. Category abbreviations are as follows: C, energy production and conversion; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; X, mobilome: prophages, transposons; A, RNA processing and modification; B, chromatin structure and dynamics; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; D, cell cycle control, cell division, chromosomal partitioning; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Z, cytoskeleton; R, general function predicted only; S, function unknown

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: Functional Assay, Modification, Control, Membrane, Transduction

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Plot representing the numbers of new and unique genes found as each isolate of S. intermedius is added

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Fitted curves indicating the characteristics of core- and pan-genomes from 27 studied S. intermedius strains. a curve showing the relationship between the core genome and the number of genomes, b curve showing the relationship between the pan-genome and the number of genomes. As the number of genomes sequenced increased, the pan-genome size increased, whereas the core-genome size decreased, thus indicating an open pan-genome model. The gradual extension of the pangenome with addition of new genomes describes an open pan-genome model of S. intermedius. The number of genes that each strain contains is documented from comprehensive statistical analysis given earlier in Table

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Unique Virulence-associated genes detected in the 27 studied S. intermedius genomes

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: Antimicrobial resistance genes of studied S. intermedius strains

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques:

Journal: BMC Genomics

Article Title: Pangenome analysis and virulence profiling of Streptococcus intermedius

doi: 10.1186/s12864-021-07829-2

Figure Lengend Snippet: CRISPR elements found in studied S. intermedius strains

Article Snippet: A circular comparison of genomes was obtained using the online GView Server ( https://server.gview.ca/ ) with S. intermedius strain ATCC 27,335 as reference genome [ ].

Techniques: CRISPR