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Core genome

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Impact of homologous recombination on core genome phylogenies

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Impact of homologous recombination on core genome phylogenies. Background: Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.. Results: In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates.

The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis

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While this small selection allows for the sequencing of the genes even in bacteria, from which whole genome sequences are not possible to acquire, it still lacks the discrimin- atory power of the gene-by-gene comparison methods.. In contrast, the core genome (cg) MLST system uses all the coding sequences that can be found in the majority of the strains.

The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis

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Considering this rule, the core genome of the subset Subsp_pertenue have higher num- ber of core genes (1038-number of core genes) after stabilization, whereas, the complete dataset haS the smallest number of core genes (318-number of core genes). The core genes of the complete dataset, the subsets Pan Subsp_pallidum and Pan Subsp_pertenue, of T. Moreover, the majority of the core genome of all the strains were classified as “poorly charac- terized” (Additional file 1: Table S2A-C)..

Comparative genome characterization of the periodontal pathogen Tannerella forsythia

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Therefore, criteria are specified which demand core genes to be present in at least 80% or 90% of the studied genomes, respectively. ATCC KS16, UB4, UB20, UB22, 9610, WW11663, WW10960, and 92A2, we assessed a core genome of the species comprising 1864 genes, when requiring a core gene to be present in each strain without exception. 90% of the strains contained 2043 genes.

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

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Similarly, 2796 genes consisted of the core gen- ome of 5 acidophilic species. Comparison of these two core genomes led to the identification of at least 89 genes that were specific to the core genome of non-acidophilic species (subset 1), whereas about 340 genes were exclu- sively present in acidophilic core genome only (subset 2).. Despite the similarities in the enrichment of KEGG path- ways in both core genomes, a significant difference in these two subsets was observed.

Comparative analysis of genome of Ehrlichia sp. HF, a model bacterium to study fatal human Ehrlichiosis

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Comparative core genome alignment and phylogenetic analysis reveal that Ehrlichia sp. The genome sequencing and analysis, including com- parative virulence factor analysis of Ehrlichia sp. Culture Isolation of Ehrlichia sp. Spleen and blood samples were collected from Ehrlichia sp. Morulae of Ehrlichia sp. The mouse LD 50 of Ehrlichia sp. General features of the Ehrlichia sp. The complete genome of Ehrlichia sp. genome was rotated to the replication origin of Ehrlichia sp.

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

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Nucleotide diversity (Tajima ’ s D) and recombinant events across the length of the core genome alignment. fastidiosa in Costa Rica (orange), subsp. fastidiosa : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. pauca : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among

Similar yet different: Phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

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The point of the curve at which additional number of genes incorporated into the core genome relative to the num- ber of analyzed genomes begins to plateau indicates the value needed for complete core genome representation for all included genomes.. Phylogenetic trees based on variations in the amino acid sequences encoded by the core genome were con- structed using the tree module of centreseq [27].

Stratified reconstruction of ancestral Escherichia coli diversification

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This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli core genome in 1023 genes, representing about 20% of the complete genome.

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): Antimicrobial use/misuse selects for resistance and drives evolution

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Reference strain WHO O [19] is included in the tree. 4 Phylogenomic tree with the size of the core genome for the three separate eras. a Phylogenomic tree including the size of the core genome for the preantibiotic, golden, and postmodern era consisting of and 1542 genes, respectively, using the Roary pan genome pipeline. b The proportion of the genes for each era is divided into core, soft-core, shell, and cloud genes, which are changing over time and the core genome length is increasing from 0.91

Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

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A resistance gene for tellurite is also present in the core-genome specific to B. is the presence of the lxa locus. Overall, Burkholderia sp. When mining in the core-genome of Burkholderia sp. nov., but also the core genome of the third identity clade, we detected two genes supporting a clear adapta- tion to the plant environment. In the same genomic cluster, a gene coding for a phenylacetaldoxime dehydratase was also found.

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

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We conducted further phylogenetic analysis based on the core genome of the five YLY strains and all other se- quenced and assembled Yarrowia-like genomes available thus far: Y. In addition to the nuclear genome, the mitochondrial genome was assembled into a single contig for each of the five YLY strains.

Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco

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The average length of the genome of the serotype 1 strains from Morocco was 2,227,119 bp. This genome size is greater than the size of the reference strain of serotype 1, S. In our study, 1685 CDS were highlighted as core gen- ome in all 80 isolates analyzed which corresponds on 79.7% of the total genome translation. The quantification of the bacterial core genome may vary among different isolates collections.

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

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The rest of the clades dis- played closed pan-genome patterns (i.e., alpha values >. 2 Core gene phylogeny of the 1254 orthologs. In the case of the generalist Clade II, we found sub- structure. Regarding the posterior distribution of the effective population size, it was far smaller in the Sub-clades (Sub-clade A N e = 55,938. Of these ortholog gene families, 297 belonged to the flexible genome, while 70 are part of the core genome.

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus

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The core genome only represented 45.3 to 52.8% of the gene content of each strain, illustrating a relatively high degree of gen- omic diversity. This core gene ratio was much lower than that of the actinobacterial species Streptomyces albidoflavus (65.3 to 73.0%, recalculated with the same clustering algorithm and parameters, intraspecies ANI >. Furthermore, the cloud genes contained more than half of the pan-genome (4210 genes, 52.1%;.

Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

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Comparison of the d total number of genes, e accessory genes and f singleton genes in the pan-genome of each species. Using the core genome alignment of each of the three species, we tested for evidence of recombination using the.. The Splitstree analysis shows the reticulations in the phylogenetic relationships between strains of each species (Fig. 4 A phylogenetic network of the core genome of Streptomyces species 20, 29 and 38 generated using SplitsTree4.

Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China

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Interestingly, almost two thirds of the SNPs (n = 437) lo- cated in the core genes were nonsynonymous, which was very different from the SNPs located on the whole genome. SNPs present in the core genome were used to infer the phylogenetic relationship of the 71 sequenced ST87 strains using the maximum likelihood method (Fig. Six of the 10 clades contained strains from the same geographic source.

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

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The pan-genome of the Pseudomonas_K group genomes comprised 20,296 genes belonging to 6805 Microscope gene Families (MICFAM) [44, 45]. Pan- and core-genome size evolutions were estimated with the four available genomes of the Pseudomonas_K group and the genome of strain OF001.

The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

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Core genome and plasmidome of the quorum-quenching bacterium. Analysis of the 7.6-kb cryptic plasmid pNC500 from Rhodococcus rhodochrous B-276 and construction of Rhodococcus – E. Enantioselective hydrolysis of β -hydroxy nitriles using the whole cell biocatalyst Rhodococcus rhodochrous ATCC BAA-870. Enantioselective biocatalytic hydrolysis of β -aminonitriles to β -amino-amides using Rhodococcus rhodochrous ATCC BAA-870. Sizing of the Rhodococcus sp.

Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

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Functional core-genome groups containing the least number of coding sequences belong to the ‘cell motility’, ‘mobilome’, and ‘secondary metabolite biosynthesis’ groups. prophages, transposons’ group showed the lowest pro- portion between the number of core-genes vs the num- ber of pan-genes, with only 5 sequences in the core- genome versus 137 in the pan-genome, illustrating ex- ceptional diversity even across these highly related strains.