Phylogenetic genome by recombination bacterial recombination genetic. Medical search. Frequent questions

The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. (jci.org)
Whole-genome sequencing (WGS) of M. tuberculosis and related mycobacteria is now routine, allowing comparisons across time and space. (jci.org)
Whole genome sequencing was attempted for specimens with cycle threshold values <30. (cdc.gov)
Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. (cdc.gov)
We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). (peerj.com)
It requires not only finding the nucleotide sequence of small pieces of the genome, but also ordering those small pieces together into the whole genome. (learner.org)
Two general strategies have been used in the sequencing of large genomes: clone-based sequencing and whole genome sequencing (Fig. 1). (learner.org)

In common with multilocus enzyme organism's wide distribution, high levels of genetic and anti- electrophoresis, MLST indexes variation in housekeeping genic diversity, and a lack of representative population sam- genes, which evolve slowly as they are under stabilizing selec- ples (9). (cdc.gov)
The recently reported phage genomes range up to 735 kb in length and encode a diversity of genes involved in transcription and translation, as well as genes that may augment host metabolism 2 . (nature.com)
Augmentation of bacterial energy generation by auxiliary metabolic genes has been reported for phages with smaller genomes. (nature.com)
Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. (mbl.edu)
We are now using advanced optical mapping technology to reproduce these maps in the absence of genetic variation, in order to disentangle the role of chromosome structure from the potential for genetic incompatibilities ("speciation genes") skewing our results. (drexel.edu)
We have developed a novel method for mapping genes in bacteria, exploiting natural transformation in combination with genome-wide deep sequencing. (drexel.edu)
Selection for recombinants that acquired the trait, followed by genome-wide profiling of donor-specific allele frequencies, we can rapidly identify the relevant genes. (drexel.edu)
We are applying a variety of genomic methods to identifying putative virulence genes, including machine learning and phylogenetic correlated evolution methods. (drexel.edu)
Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. (frontiersin.org)
The sheer number of non-human genes represented by the human microbiota - there are millions in our "extended genome" 2) compared to the nearly 23,000 in the human genome - implies we have just begun to fathom the full extent to which bacteria work to facilitate their own survival. (mpkb.org)
7) The human gut alone contains on average: 40,000 bacterial species, 8) 9 million unique bacterial genes and 100 trillion microbial cells. (mpkb.org)
9) According to Asher Mullard, "Between them [the bacteria in our bodies], they harbor millions of genes, compared with the paltry 20,000 estimated in the human genome. (mpkb.org)
13) The combined genetic contributions of these microbes - in excess of 1,000,000 protein-coding genes - provide traits not encoded in our own genomes. (mpkb.org)
Genes in the human microbiota far outnumber those in the human genome. (mpkb.org)
Bacterial genomes, in contrast to eukaryotic genomes, usually maintain constant genome sizes [9, 10], suggesting that while horizontal gene transfer (HGT) increases the genome size by adding new genes, selection maintains the genome size by removing deleterious, non-functional or non-useful genes [11-13]. (researchsquare.com)
Recombination decreases linkage disequilibrium among genes, allowing selection and the related Hill-Robertson effect to operate in specific genes and avoiding the purged of genetic diversity along with the genome [22, 23]. (researchsquare.com)
In presence of phylogenetically distant genomes, due to the variability introduced in gene duplication and transmission, the task of recognizing homologous genes becomes even more difficult. (biomedcentral.com)
Homologous genes can be distinguished into paralogous, when homology occurs within the same genome, or orthologous, when homology occurs between different genomes. (biomedcentral.com)
On the contrary, "horizontal" transmission occurs between genomes of organisms of different lineages, involving one or few genes. (biomedcentral.com)
Genes present in every genome are core genes of the pan-genome and they may be involved in essential living functionalities. (biomedcentral.com)
Singleton genes are present only in one genome and represent some genome-specific functionality. (biomedcentral.com)
The variations make the task of recognizing homologous genes difficult, especially when ancestor genomes are no more available. (biomedcentral.com)
The amount of variations affecting dispensable genes varies and the similarity between homologous sequences tends to decrease according to their phylogenetic distance. (biomedcentral.com)
Recently, a multilocus sequence analysis approach was proposed to reconstruct phylogenetic histories of bacterial clonal complexes by using concatenated sequences of housekeeping genes when within-loci and between-loci recombinations are infrequent ( 5 ). (cdc.gov)
It also highlights the importance of HGT in the evolutionary history of CHS and describes bacterial chs genes for the first time. (biomedcentral.com)
Indeed, the flexible genome provided evidence as L-population strains encoded flexible genes related to biofilm formation and the biosynthesis of MSHA for chitin adhesion. (microbomics.com)
The acquisition of habitat-specific flexible genes can lead to ecological specialization, which further depresses recombination between the incipient populations. (microbomics.com)
All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. (biomedcentral.com)
Although some scientists expected to find at least 100,000 genes coding for proteins, only about 30,000-35,000 of such genes appear to be in the human genome. (learner.org)

We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
High levels of recombination could confound studies of the gonococcal populations, especially if the studies are based on few genetic loci within strains as compared to the entire genomes. (peerj.com)
However, the Pa Loc is variably present, even among closely related strains, and thus resembles a mobile genetic element. (whiterose.ac.uk)
Methods Bacterial strains, plasmids and media Bacterial strains and plasmids used are shown in Table 1. (mirnainhibitor.com)
Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. (pacb.com)
Following the observations that Vibrio strains appeared to have preferences for particle size, a study lead by Shapiro sought to identify the genomic mechanisms of divergence potentially leading to bacterial speciation [3]. (microbomics.com)
Utilizing 20 genomes from large (L) or small (S) particles sizes (proxy for habitat), they first found evidence for differentiation among closely-related strains. (microbomics.com)
Evidence for high recombination within-habitat strains led the authors to inquiry how these populations may be differentiating. (microbomics.com)
The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. (biomedcentral.com)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. (asm.org)
The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. (asm.org)
A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans. (asm.org)

A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes. (wikipedia.org)
Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes. (wikipedia.org)
These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. (nature.com)
[4] Wilkins further grouped the species concepts into seven basic kinds of concepts: (1) agamospecies for asexual organisms (2) biospecies for reproductively isolated sexual organisms (3) ecospecies based on ecological niches (4) evolutionary species based on lineage (5) genetic species based on gene pool (6) morphospecies based on form or phenotype and (7) taxonomic species, a species as determined by a taxonomist. (atozwiki.com)
In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. (mdpi.com)
Therefore, bacteria can present very different genomic compositions even within a species, with HGT creating a flexible genome and natural selection purging or maintaining it [10, 14]. (researchsquare.com)
MLST studies showed that local populations of a bacterial species typically consist of discrete clusters of multilocus sequence types called "clonal complexes," rather than a multitude of randomly assorted genotypes ( 2 ). (cdc.gov)
Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species. (peerj.com)
Most, if not all of these transfers seem to be the result of a gene being transferred from the mitochondrial genome of one species to that of another. (biomedcentral.com)
By 2003 biologists had sequenced genomes from about one hundred different species. (learner.org)
The polymorphism observed in the organization of the subtelomeric region in the genome of two Penicillium species within the high homogeneous Penicillium subgenus is for the first time reported and perhaps can be employed in future phylogenetic studies. (scielo.br)

Further advantages are characterization of C. jejuni isolates has relied on serologic that the data are electronically portable, enabling comparison typing schemes since the 1980s (10,11), but the data available of isolates via the Internet without exchange of biological from these techniques have not resolved the epidemiology of materials, and amenable to analysis by phylogenetic and popu- lation genetic techniques (19,20). (cdc.gov)
These factors were evaluated in various phylogenetic groups (phylotypes) of E. coli isolates. (biomedcentral.com)
Phylogenetic analyses and annotation of the regions spanning the Pa Loc were performed using C. difficile population-representative genomes chosen from a collection of 1,693 toxigenic (Pa Loc present) and non toxigenic (Pa Loc absent) isolates. (whiterose.ac.uk)
Teodorovic S, Braverman JM, Elmendorf HG: Unusually low levels of genetic variation among Giardia lamblia selleckchem isolates. (mirnainhibitor.com)
In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. (researchsquare.com)
To resolve phylogenetic relationships among isolates, we sequenced 68 isolates from Europe and North America at 1 chromosomal locus (16S-23S ribosomal RNA spacer) and 3 plasmid loci ( ospC , dbpA , and BBD14). (cdc.gov)
The genetic homogeneity of ospC -A isolates was confirmed by sequences at 6 additional chromosomal housekeeping loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)

See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
In 1986 Nobel laureate Renato Dulbecco laid down the gauntlet to the scientific community to sequence the complete human genome. (learner.org)
Like the conquest of space, sequencing the human genome required the development of wholly new technologies. (learner.org)
The human genome, containing more than three billion nucleotides, is vast. (learner.org)
The capstone, of course, was the completion of the human genome sequence. (learner.org)
In 2001 two rival teams jointly announced the completion of a draft sequence of the entire human genome, consisting of more than three billion nucleotides. (learner.org)
One major surprise emerged from the sequencing of the human genome. (learner.org)
We should think of the human genome as a database of critical information that serves as a tool for exploring the workings of the cell and, ultimately, understanding how a complex living organism functions. (learner.org)

The intestines of many feral and commercially reared birds, approach, which exploits recent technical developments in livestock, domestic pets, and animals are asymptomatically high-throughput nucleotide sequence determination and com- colonized by this bacterium, which is widely distributed in the bines them with conceptual advances in bacterial population environment and food. (cdc.gov)
the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
While the genome sequence was already transformative at the time, the past 25 years of progress have substantially increased its impact on TB taxonomy, drug discovery, resistance mechanisms, epidemiology, vaccine development, and pathogenesis. (jci.org)
Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
Paralogy is linked to sequence duplication within the same genome. (biomedcentral.com)
Computer based sequence similarity searches of the nucleic acid databases are considered to be a more accurate method to identify retrotransposon families and estimate TE content and distribution in rice genome [ 28 - 31 ]. (biomedcentral.com)
Multilocus sequence typing (MLST) is the use of DNA sequences at multiple housekeeping loci to characterize genetic variations of natural populations of a bacterial pathogen ( 1 , 2 ). (cdc.gov)
Sequence variability at ospC is the highest among known genomic loci and is strongly linked to variations at other genome-wide loci, with occasional recombinant genotypes caused by plasmid exchanges ( 16 - 19 ). (cdc.gov)
The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. (pacb.com)
Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. (pacb.com)
Draft genome sequence of Micromonospora sp. (pacb.com)
Complete genome sequence of Kosakonia oryzae type strain Ola 51(T). (pacb.com)
Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. (pacb.com)
Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata , respectively. (biomedcentral.com)
The sequence information provides a starting point from which the real research into the thousands of diseases that have a genetic basis can begin. (learner.org)

Comparative analyses of the sequenced genomes have also led to discovery of many conserved insertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. (wikipedia.org)
Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria. (wikipedia.org)
Comparative genomics analyses have shown a wide range of genomic variation within bacteria from different phylogenetic groups [1-3]. (researchsquare.com)
Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). (biomedcentral.com)
Analyses of the core and flexible genome support these conclusions as they identified core regions more frequently recombined within-habitat than between-habitat. (microbomics.com)
Our search relied primarily on phylogenetic analyses, but also involved scrutiny of each potential case (including generation of new gene sequences from phylogenetically relevant taxa) to rule out artifacts and various types of homoplasy. (biomedcentral.com)

The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. (nature.com)
We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. (nature.com)
How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune defenses is unknown. (elifesciences.org)
The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding. (pacb.com)

Comparison of the core genome and Pa Loc phylogenies demonstrated aneventful evolutionary history, with distinct Pa Loc variants acquired clade specifically after divergence. (whiterose.ac.uk)

More recent studies have also suggested high rates of recombination within the Neisseria genus ( Didelot & Maiden, 2010 ). (peerj.com)

In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. (nature.com)
Bacteriophages (phages), viruses that infect and replicate within bacteria, are important in both natural and human microbiomes because they prey on bacterial hosts, mediate horizontal gene transfer, alter host metabolism and redistribute bacterially derived compounds via host cell lysis 1 . (nature.com)
Using genomics to investigate the mechanism, consequences and evolution of genetic recombination, especially in pathogenic bacteria. (drexel.edu)
This pathway, called "natural transformation," is a major mechanism of gene transfer across bacteria and has a profound effect on genome evolution, including spreading antibiotic resistances and other virulence determinants. (drexel.edu)
In several ongoing collaborations, we are investigating how the genomes of bacteria isolated from patients with chronic infections change over time. (drexel.edu)
based methods for culturing bacteria have drastically underrepresented the size and diversity of bacterial populations. (mpkb.org)
Background In bacteria, pan-genomes are the result of the evolutionary 'tug of war' between selection and horizontal gene transfer (HGT). (researchsquare.com)

Most studies employ comparative genomics by collating closely-related genomes from various databases. (microbomics.com)

LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. (biomedcentral.com)

MLST is especially suitable for the investigation of Elucidation of the epidemiology of this zoonosis is compli- diverse bacterial populations that have weakly clonal popula- cated by the sporadic nature of the disease (8), along with the tion structures (13,16,17). (cdc.gov)
The long-term goal of this research is to apply statistical genomic approaches developed by human geneticists to the identification of bacterial virulence factors that contribute to disease in natural populations. (drexel.edu)
On the one hand, homologous recombination homogenizes populations, keeping them genetically cohesive in a closed pan-genome [16, 17]. (researchsquare.com)
In order to expand our understanding of how recombination might influence virus variation during the course of adaptation, we focused on large DNA viruses, in which rapidly evolving populations can simultaneously harbor both adaptive gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus. (elifesciences.org)
Remaining to be tested are how such factors as natural selection, low recombination rate, and genetic drift due to geographic structuring contribute to the formation and maintenance of these clonal complexes in natural bacterial populations ( 3 , 4 ). (cdc.gov)
Further, these SNPs contain low within-habitat diversity suggesting these regions are a result from recent recombination and have subsequently swept through the populations, coined gene-specific sweeps. (microbomics.com)

In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. (researchsquare.com)
However, if there is a selective pressure towards local adaptation, the genetic diversity introduced by HGT will be purged, resulting in a closed pan-genome and clonal lineages [14]. (researchsquare.com)
The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. (who.int)

Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses. (nature.com)
suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. (researchsquare.com)

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. (nature.com)
Phages with very large genomes were recently reported from a man-made lake that covers a deposit of methane-generating tailings from an oil sands mine in Canada 2 . (nature.com)

Exchanges and losses of the Pa Loc DNA have also occurred, via long homologous recombination events involving flanking chromosomal sequences. (whiterose.ac.uk)
On the other hand, non-homologous recombination brings new genetic material, offering new evolutionary opportunities for diversification and generating an open pan-genome [18-21]. (researchsquare.com)

Resistance against β-lactam agents can occur via (i) mutation or expression of alternative penicillin-binding proteins (PBPs) as the drug target, (ii) downregulation of porins to reduce the bacterial permeability against β-lactams, (iii) over-expression of efflux systems which are membrane transport proteins to export drug substrates and (iv) production of β-lactamases that hydrolyze the β-lactam amide [ 6 ]. (biomedcentral.com)
The estimated ratio of recombination to mutation ( r / m = 2.2) from our data set indicates an appreciable level of recombination occurring in the population. (peerj.com)
2007). Here, we report the unusual genetic behavior of a quantitative gain-of-function CNGC mutation ( brush ) in Lotus japonicus resulting in a leaky tetrameric channel. (elifesciences.org)

Sequences shared by a subset of genomes are referred as dispensable and they represent variable features. (biomedcentral.com)
In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. (biomedcentral.com)

[5] The eukaryote Monocercomonoides is known to have completely lost its mitochondria, [6] and the multicellular organism Henneguya salminicola is known to have retained mitochondrion-related organelles in association with a complete loss of their mitochondrial genome. (wikipedia.org)

It also introduces the student to the continuity of life from genetic and molecular perspectives. (uaeu.ac.ae)
This includes: the kingdom systems of classification and the three main taxonomy domains, binomial nomenclature, phylogenetic and how molecular data are revolutionizing taxonomy. (uaeu.ac.ae)

Diversification into the phylogenetic tree happens much more rapidly via sexual reproduction than it does by way of asexual reproduction. (wikizero.com)

The discord stems from the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-content between members of several orders. (wikipedia.org)
Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. (nature.com)
Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. (elifesciences.org)
Gene duplication is long recognized as a potential source of genetic innovation ( Ohno, 1970 ). (elifesciences.org)
Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. (biomedcentral.com)
The retrieval of a complete gene distribution among a class of genomes is an NP-hard problem because computational costs increase with the number of analyzed genomes, in fact, all-against-all gene comparisons are required to completely solve the problem. (biomedcentral.com)
There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. (biomedcentral.com)
Comparative genetic maps within the grass family indicate extensive regions of conserved gene content and orders [ 16 ]. (biomedcentral.com)
Previously, a study from the Polz/Alm research groups at MIT identified diverse phylogenetic clusters using the partial hsp60 gene. (microbomics.com)
A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. (biomedcentral.com)
This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36 , without the level and length of similarity normally expected to support recombination. (biomedcentral.com)
The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the exclusion of heterokont and alveolate plastids. (biomedcentral.com)
Moreover, the bacterial gene has replaced the native plastid rpl36 gene by an uncertain mechanism that appears inconsistent with existing models for the recombinational basis of gene conversion. (biomedcentral.com)
Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
Despite the initial enthusiasm and multiple clinical trials, there is still no FDA-approved gene therapy for CF. This review details the history of CF gene therapy and outlines the progress toward the development of a genetic treatment for all people with CF. The cover image is a 3D rendering of a newborn pig lung CT image (image reconstructed by Carley Stewart). (mdpi.com)

Genetic variability arises from mutations and recombination , while organisms themselves are mobile, leading to geographical isolation and genetic drift with varying selection pressures . (atozwiki.com)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)

Our primary model system is the human bacterial pathogen Haemophilus influenzae , an important agent of ear infections (otitis media) in children, as well as lung infections associated with chronic respiratory conditions. (drexel.edu)
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland. (who.int)

Stable integration of the Pa Loc is suggested by its single chromosomal location and the clade specificity of its different genetic variants. (whiterose.ac.uk)
The genetic organization of the clade 3 Pa Loc was unique in containing a stably integrated novel trans poson (designated Tn6218), variants of which were found at multiple chromosomal locations. (whiterose.ac.uk)
The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. (researchsquare.com)

One special type of plasmid used for genome sequencing is a bacterial artificial chromosome (BAC) , which can contain DNA fragments of about 150 kb. (learner.org)
The genome of T. maritima consists of a single circular 1.8 megabase chromosome encoding for 1877 proteins. (eol.org)

The topics covered include the appearance of the first genetic material, the origins of cellular life, evolution and development, selection and adaptation, and genome evolution. (cshlpress.com)
AMR evolution should be considered in the context of the genetic structure of the N. gonorrhoeae population. (peerj.com)
Genome Biology and Evolution, 6 (1). (whiterose.ac.uk)
Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. (peerj.com)

We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. (frontiersin.org)
During the infection process, bacteriophages can transfer foreign DNA to their host (including virulence factors), integrate into the host genome, and/or kill their host through cell lysis ( Chen and Novick, 2009 ). (frontiersin.org)

We have generated high-resolution genome-wide maps of transformation, finding massive variation in rates at different chromosomal loci. (drexel.edu)
This variation range has been explained in part by the wide ecological niche occupied by different bacterial groups [4-8]. (researchsquare.com)
A major goal in evolutionary biology is to understand the origin and maintenance of genetic variation and diversity. (microbomics.com)

1. What factors control transformation frequency across the genome? (drexel.edu)

Genome Biol , 11(12), R119. (mbl.edu)

We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)

Bacterial DNAs are constantly detected in atherosclerotic plaques (APs), suggesting that a combination of chronic infection and inflammation may have roles in AP formation. (bvsalud.org)
Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment. (nature.com)
Neisseria gonorrhoeae , a Gram-negative bacterium, causes gonorrhea, the most common bacterial sexually transmitted infection (STIs), causing more than 106 million cases per year globally ( World Health Organization (WHO), 2012 ). (peerj.com)
We have used this method to map an operon involved in intracellular invasion of airway epithelial cells, a trait with implications for chronic infection, bacterial persistence, and trafficking of cells to different body sites. (drexel.edu)
One such bacterial infection caused by a phytopathogen Erwinia amylovora ( Zwet and Keil, 1979 ) is called fire blight and mainly affects ornamental plants of the Rosaceae family. (frontiersin.org)

In theory, speciation is dependent on 1) selection leading to ecological differentiation and 2) barriers to recombination. (microbomics.com)

The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. (mdpi.com)
Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. (who.int)

In hermaphroditic reproduction, each of the two parent organisms required for the formation of a zygote can provide either the male or the female gamete, which leads to advantages in both size and genetic variance of a population. (wikizero.com)

90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus , Methylocystis and Methylobacter spp. (nature.com)

A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations. (biomedcentral.com)

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. (cdc.gov)

Sexual reproduction derives from recombination , where parent genotypes are reorganized and shared with the offspring. (wikizero.com)

To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa , we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. (biomedcentral.com)

Human Microbiome The bacterial community in the human body. (mpkb.org)

Similar to the Apollo project that met President Kennedy's goal of a manned lunar landing by 1970, the genome project also succeeded - beyond the dreams of the scientists who proposed it. (learner.org)

We examined the consequences of CTCF depletion in immortalised human and mouse cells using shRNA knockdown and CRISPR/Cas9 genome editing and examined the growth and development of heterozygous Ctcf ( Ctcf +/- ) mice. (preprints.org)

In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. (nature.com)

At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. (jci.org)

The M. tuberculosis genome has ushered in a quarter century of substantial clinical and public health advancements. (jci.org)
In this paper, we describe the genetic analysis of four IMPase homologues of M. tuberculosis. (mirnainhibitor.com)

Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. (biomedcentral.com)

Anatomy9

Organisms6

Diseases3

Chemicals and Drugs43

Analytical, Diagnostic and Therapeutic Techniques and Equipment15

Phenomena and Processes90

Disciplines and Occupations2

Information Science4

Health Care1

Whole-genome7

Genes31

Strains13

Species11

Isolates7

Human Genome8

Sequence15

Analyses6

Mechanisms4

Core genome1

High rates of recombination1

Bacteria7

Genomics1

Eukaryotic genomes1

Populations6

Clonal3

Lineages2

Large genomes2

Homologous recombination2

Mutation3

Sequences2

Mitochondrial genome1

Molecular2

Diversification1

Gene15

Mutations2

Pathogen2

Clade3

Chromosome2

Evolution4

Virulence2

Variation3

Transformation1

Biol1

Comparative1

Infection5

Speciation1

Distinct2

Organisms1

Phylogenetically1

Similarity1

20191

Genotypes1

Evolutionary history1

Microbiome1

19701

CRISPR1

Patterns1

Insights1

Tuberculosis2

Hosts1