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Pan-genome

Tìm thấy 20+ kết quả cho từ khóa "Pan-genome"

Comparative genomics and pangenomeoriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

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Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T.. Genome sequence of the emerging plant pathogen Dickeya solani strain RNS 08.23.3.. Estimating the size of the bacterial pan-genome.. Draft genome sequence of a highly virulent strain of the plant pathogen Dickeya solani, IFB0099.

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

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The resulting core genome of the complete dataset (Pan All), the subsets Pan Subsp_pallidum and Pan Subsp_perte- nue, have the following tg(θ) values, respectively. Concerning the Singletons of the complete dataset (Pan All) and the subsets Pan Subsp_.

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.

Comparative genome characterization of the periodontal pathogen Tannerella forsythia

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In an additional run, orthologs were required to be present in at least 80% of the T. forsythia genomes to become part of a relaxed form of the core genome, sometimes referred to as “soft core genome”. All these Perl scripts are part of the GET_HO- MOLOGUES pipeline.. Based on the results of the pan-genome analysis, puta- tive pathogenicity islands were detected as follows:. Genes that were found to be present in at least eight of the ten T.

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

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The results showed that the pan- genome size of all 80 strains of L. The pan-genome size of the 14 strains of L. gasseri was 2834 genes, and the exponential value of deduced mathematical function is <.

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

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Analysis of the core and pan-genome of a population of Salmonella and Citrobacter strains offered a reliable de- lineation of the fuzzy taxonomic boundaries between these closely related bacteria. As the most stable portion of the pan-genome, the core genome encodes character- istics common to all members of a species [28, 29]..

Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae

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The core, flex, and pan-genomes of isolate genomes were classified to determine the functional composition of the conserved and unique genes. S3), and the curve of the pan-genome plot and the Heaps law model (alpha = 0.47) indicated an open-pan genome amongst these isolates..

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

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Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. On the catabolism of amino acids in the yeast Dekkera bruxellensis and the implications for industrial fermentation processes. In: Proceedings of the convention-institute of brewing asia pacific section, vol.

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

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To analyze genomic features among strains in the Rhizo- bium genus occupying diverse niches, we used the 50 available Rhizobium genomes (Additional file 1: Table S1) to probe the evolution of the gene repertoire through pan-genome analysis. The core genome represented 39.93 to 47.59% of the repertoire of protein-coding genes in each strain.

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

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Accession numbers, metadata and genome characteristics of the 73 Streptomyces isolates. 16S rRNA tree of Streptomyces isolates with bootstrap values.. Pan-genome analysis of the 73 Streptomy- ces genomes estimated using Roary.. Biosynthetic gene clusters (BGCs) of all genomes of Streptomyces estimated using antiSMASH.. Pan-genome analyses of Streptomyces sp.. We also thank the students in the Northup lab at the University of New Mexico for assisting with our bat netting efforts..

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

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Analysis of the pan-genome curve using a power-law regression model confirmed that the pan-genome was open (B pan = 0.5), as the curve did not approach a constant as more genomes were selected..

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.

Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA

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Based on the variability of the ST93-IV accessory genes over time and location we attempted to identify clade 1 or 2 specific subclades. 2 Principal Component Analysis of pan-genome gene matrix of ST93-IV isolates. Non Bacteraemia Isolates N.

Evolutionary relationships among bifidobacteria and their hosts and environments

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Given that previous studies have shown evidence that species isolated from bees, like B. 2A|The pan-genome of the 129 bifidobacteria strains is summarized in a pie chart showing the core genes (438), the soft genes (115), the shell genes (1802), and the cloud genes (24,550). 2B|Pan- genome alignment of 129 bifidobacteria strains is depicted by combining the phylogenetic tree inferred by RAxML 8.2.10 and the pan-genome heatmap showing gene presence (royal blue) or absence (white) in each of the strains

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

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The pan genomes of the hybrid assemblies of S. Typhimurium with mediocre-quality long reads were similar to that of the reference genome, while SPAdes and Unicycler were more tolerant of low-quality long reads than MaSuRCA for the pan-genome analysis. Oxford Nanopore sequencing can generate long reads that span repetitive regions in bacterial genomes, thus resulting in less fragmented or even complete ge- nomes.

Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

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Genome sequence of the Chlamydophila abortus variant strain LLG. Unity in variety--the pan-genome of the Chlamydiae. specificity of the modified Gimenez staining on smears and comparison of the sensitivity of isolation in eggs and three different cell cultures

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.

Comparative genomics of whole-cell pertussis vaccine strains from India

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Circular diagram of pan-genome of vaccine strains (J445, J4445, J446, J448, BP165) and clinical strains (BPD1, BPD2) and reference strain Tohama-I. pertussis vaccine strains (J445, J4445, J446, J448, BP165) and clinical strains (BPD1, BPD2) and reference strain Tohama-I. The plot shows that progression of the pan (orange) and core (purple) genomes. Among the 2038 loci of the cgMLST scheme, 57 (BPD1).

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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Identifying Streptococcus pneumoniae genes associated with invasive disease using pangenome-based whole genome sequence typing. Cornick JE, Chaguza C, Harris SR, Yalcin F, Senghore M, Kiran AM, et al.. Region-specific diversification of the highly virulent serotype 1. Streptococcus pneumoniae. Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, et al.. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

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To further examine the credibility of the CNVRs de- tected in this study, we compared the CNV genes with those in the Goat Pan-genome database (hereafter re- ferred to as Pangoat for simplicity) and a previous study [7] that used SNP data from the ADAPTmap project (see details in Methods). 2 Summary of the copy number variable genes identified in the seven goat populations. a Comparison of the identified copy number variable genes with two other large-scale datasets.