scholarly journals A Genomic Survey of Signalling in the Myxococcaceae

2020 ◽  
Vol 8 (11) ◽  
pp. 1739
Author(s):  
David E. Whitworth ◽  
Allison Zwarycz
Keyword(s):  
Core Genome ◽  
Gene Gain ◽  
Fruiting Body Formation ◽  
Two Component System ◽  
Genome Sequences ◽  
The Core ◽  
Accessory Genes ◽  
Two Component ◽  
Gain Loss ◽  
Core Genes

As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.

scholarly journals Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility

2020 ◽  
Vol 38 (1) ◽  
pp. 2-15 ◽  
Author(s):  
Julien Martinez ◽  
Lisa Klasson ◽  
John J Welch ◽  
Francis M Jiggins
Keyword(s):  
Cytoplasmic Incompatibility ◽  
Gene Gain ◽  
Evolutionary Models ◽  
Loss Of Function ◽  
Genome Sequences ◽  
Life And Death ◽  
Selfish Genes ◽  
Wolbachia Genome ◽  
The Cross ◽  
Gain Loss

Abstract Cytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.

scholarly journals Comparative analysis of probiotic bacteria based on a new definition of core genome

2018 ◽  
Vol 16 (03) ◽  
pp. 1840012 ◽  
Author(s):  
Maria Satti ◽  
Yasuhiro Tanizawa ◽  
Akihito Endo ◽  
Masanori Arita
Keyword(s):  
Stress Responses ◽  
Core Genome ◽  
Public Library ◽  
Orthologous Gene ◽  
Orthologous Group ◽  
Probiotic Properties ◽  
The Core ◽  
Significant Difference ◽  
Definition Of ◽  
Core Genes

The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of “core genome”, core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories “amino acid transport and metabolism” representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.

scholarly journals Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 63 ◽  
Author(s):  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Core Genome ◽  
Position Effect ◽  
Genome Structure ◽  
Enrichment Analysis ◽  
Gene Clusters ◽  
Gene Cassette ◽  
Etiologic Agent ◽  
Functional Genes ◽  
The Core ◽  
Core Genes

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.

scholarly journals Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations

2017 ◽  
Author(s):  
Andries J van Tonder ◽  
James E Bray ◽  
Keith A Jolley ◽  
Sigríður J Quirk ◽  
Gunnsteinn Haraldsson ◽  
...  
Keyword(s):  
Bacterial Population ◽  
Core Genome ◽  
Bacterial Species ◽  
Essential Point ◽  
Genetic Lineages ◽  
The Core ◽  
Pan Genome ◽  
Single Dataset ◽  
Genomic Regions ◽  
Core Genes

AbstractBackgroundUnderstanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.ResultsThe analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.ConclusionsSome subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.

scholarly journals Pan-genome of Novel Pantoea stewartii subsp. indologenes Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

2021 ◽  
Author(s):  
Gaurav Agarwal ◽  
Ronald D. Gitaitis ◽  
Bhabesh Dutta
Keyword(s):  
Gene Transfer ◽  
Core Genome ◽  
Foxtail Millet ◽  
Evaluation Study ◽  
Full Spectrum ◽  
The Core ◽  
Pan Genome ◽  
Pantoea Stewartii ◽  
Comparative Phylogenetic Analysis ◽  
Core Genes

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onion and millets or on millets only, respectively. In the current study we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n= 4) and pv. setariae (n=13)]. The full spectrum of the pan-genome contained 7,030 genes. Among these, 3,546 (present in genomes of all 17 strains) were the core genes that were a subset of 3,682 soft-core genes (present in ≥16 strains). The accessory genome included 1,308 shell genes and 2,040 cloud genes (present in ≤ 2 strains). The pan-genome showed a clear liner progression with >6,000 genes, suggesting the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison to core genome SNP-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study including four other Pantoea species namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfers observed between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes including seven cluster of genes associated with the pathogenicity phenotype on onion. One of the clusters contain 11 genes with known functions and are found to be chromosomally located.

scholarly journals Adding context to the pneumococcal core genes – a bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae

2021 ◽  
Author(s):  
Flemming Damgaard Nielsen ◽  
Jakob Møller-Jensen ◽  
Mikkel Girke Jørgensen
Keyword(s):  
Streptococcus Pneumoniae ◽  
Core Genome ◽  
Biological Function ◽  
Bioinformatic Analysis ◽  
Bacterial Pathogenicity ◽  
The Core ◽  
Intergenic Regions ◽  
Crucial Information ◽  
Genetic Context ◽  
Core Genes

AbstractWhole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.

scholarly journals Real-Time Sequencing To Decipher the Molecular Mechanism of Resistance of a Clinical Pan-Drug-Resistant Acinetobacter baumannii Isolate from Marseille, France

2012 ◽  
Vol 57 (1) ◽  
pp. 592-596 ◽  
Author(s):  
Jean-Marc Rolain ◽  
Seydina M. Diene ◽  
Marie Kempf ◽  
Gregory Gimenez ◽  
Catherine Robert ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Molecular Mechanisms ◽  
Multidrug Resistant ◽  
Drug Resistant ◽  
Two Component System ◽  
Genome Sequences ◽  
Component System ◽  
Content Type ◽  
Two Component ◽  
Baumannii Isolate

ABSTRACTWe compare the whole-genome sequences of two multidrug-resistant clinicalAcinetobacter baumanniiisolates recovered in the same patient before (ABIsac_ColiS susceptible to colistin and rifampin only) and after (ABIsac_ColiR resistant to colistin and rifampin) treatment with colistin and rifampin. We decipher all the molecular mechanisms of antibiotic resistance, and we found mutations in therpoBgene and in the PmrAB two-component system explaining resistance to rifampin and colistin in ABIsac_ColiR, respectively.

scholarly journals Identification of Multiple Replication Stages and Origins in the Nucleopolyhedrovirus of Anticarsia gemmatalis

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 648
Author(s):  
Solange A.B. Miele ◽  
Carolina S. Cerrudo ◽  
Cintia N. Parsza ◽  
María Victoria Nugnes ◽  
Diego L. Mengual Gómez ◽  
...  
Keyword(s):  
Core Genome ◽  
Anticarsia Gemmatalis ◽  
Replication Machinery ◽  
Host Proteins ◽  
Viral Dna ◽  
The Core ◽  
Plasmid Library ◽  
Close Proximity ◽  
Multiple Replication ◽  
Core Genes

To understand the mechanism of replication used by baculoviruses, it is essential to describe all the factors involved, including virus and host proteins and the sequences where DNA synthesis starts. A lot of work on this topic has been done, but there is still confusion in defining what sequence/s act in such functions, and the mechanism of replication is not very well understood. In this work, we performed an AgMNPV replication kinetics into the susceptible UFL-Ag-286 cells to estimate viral genome synthesis rates. We found that the viral DNA exponentially increases in two different phases that are temporally separated by an interval of 5 h, probably suggesting the occurrence of two different mechanisms of replication. Then, we prepared a plasmid library containing virus fragments (0.5–2 kbp), which were transfected and infected with AgMNPV in UFL-Ag-286 cells. We identified 12 virus fragments which acted as origins of replication (ORI). Those fragments are in close proximity to core genes. This association to the core genome would ensure vertical transmission of ORIs. We also predict the presence of common structures on those fragments that probably recruit the replication machinery, a structure also present in previously reported ORIs in baculoviruses.

scholarly journals Selection-based model of prokaryote pangenomes

2019 ◽  
Author(s):  
Maria Rosa Domingo-Sananes ◽  
James O. McInerney
Keyword(s):  
Low Frequency ◽  
Gene Content ◽  
Gene Gain ◽  
Genotype By Environment ◽  
Fitness Effects ◽  
Accessory Genes ◽  
Large Numbers ◽  
Gene By Environment Interactions ◽  
Gain And Loss ◽  
Core Genes

AbstractThe genomes of different individuals of the same prokaryote species can vary widely in gene content, displaying different proportions of core genes, which are present in all genomes, and accessory genes, whose presence varies between genomes. Together, these core and accessory genes make up a species’ pangenome. The reasons behind this extensive diversity in gene content remain elusive, and there is an ongoing debate about the contribution of accessory genes to fitness, that is, whether their presence is on average advantageous, neutral, or deleterious. In order to explore this issue, we developed a mathematical model to simulate the gene content of prokaryote genomes and pangenomes. Our model focuses on testing how the fitness effects of genes and their rates of gene gain and loss would affect the properties of pangenomes. We first show that pangenomes with large numbers of low-frequency genes can arise due to the gain and loss of neutral and nearly neutral genes in a population. However, pangenomes with large numbers of highly beneficial, low-frequency genes can arise as a consequence of genotype-by-environment interactions when multiple niches are available to a species. Finally, pangenomes can arise, irrespective of the fitness effect of the gained and lost genes, as long as gene gain and loss rates are high. We argue that in order to understand the contribution of different mechanisms to pangenome diversity, it is crucial to have empirical information on population structure, gene-by-environment interactions, the distributions of fitness effects and rates of gene gain and loss in different prokaryote groups.

scholarly journals Transcriptomic Analysis of Aggregatibacter actinomycetemcomitans Core and Accessory Genes in Different Growth Conditions

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 282 ◽  
Author(s):  
Tjokro ◽  
Kittichotirat ◽  
Torittu ◽  
Ihalin ◽  
Bumgarner ◽  
...  
Keyword(s):  
Gene Pool ◽  
Expression Patterns ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Growth Conditions ◽  
Genomic Islands ◽  
Accessory Gene ◽  
The Core ◽  
Accessory Genes ◽  
Core Genes

Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in some but not all strains) and a core gene pool (found in all strains). The functions of the accessory genes (genomic islands and non-island accessory genes) are largely unknown. We hypothesize that accessory genes confer critical functions for A. actinomycetemcomitans in vivo. This study examined the expression patterns of accessory and core genes of A. actinomycetemcomitans in distinct growth conditions. We found similar expression patterns of island and non-island accessory genes, which were generally lower than the core genes in all growth conditions. The median expression levels of genomic islands were 29%–37% of the core genes in enriched medium but elevated to as high as 63% of the core genes in nutrient-limited media. Several putative virulence genes, including the cytolethal distending toxin operon, were found to be activated in nutrient-limited conditions. In conclusion, genomic islands and non-island accessory genes exhibited distinct patterns of expression from the core genes and may play a role in the survival of A. actinomycetemcomitans in nutrient-limited environments.

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