scholarly journals Genomic Analysis of Curtobacterium Flaccumfaciens Reveals the Differences Between Pathogenic and Nonpathogenic Strains

2021 ◽  
Author(s):  
Qingde Li ◽  
Lianjun Sun
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Pectate Lyase ◽  
Economic Losses ◽  
Positive Bacterium ◽  
Citrate Cycle ◽  
The Core ◽  
Genomic Level ◽  
Genes Encoding ◽  
Genome Phylogeny

Abstract Purpose Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens. KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.

scholarly journals In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9643 ◽  
Author(s):  
Carlos Leonardo Araújo ◽  
Iago Blanco ◽  
Luciana Souza ◽  
Sandeep Tiwari ◽  
Lino César Pereira ◽  
...  
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Structural Features ◽  
Corynebacterium Pseudotuberculosis ◽  
Economic Losses ◽  
Hypothetical Proteins ◽  
Protein Protein Interaction ◽  
The Core ◽  
Virulence Potential

Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

scholarly journals Draft genomes of 12 host-adapted and environmental isolates ofPseudomonas aeruginosaand their positions in the core genome phylogeny

2013 ◽  
Vol 71 (1) ◽  
pp. 20-25 ◽  
Author(s):  
Lewis Stewart ◽  
Amy Ford ◽  
Vartul Sangal ◽  
Julie Jeukens ◽  
Brian Boyle ◽  
...  
Keyword(s):  
Core Genome ◽  
Environmental Isolates ◽  
The Core ◽  
Genome Phylogeny

scholarly journals Genome-Wide Analysis of Ruminant Staphylococcus aureus Reveals Diversification of the Core Genome

2008 ◽  
Vol 190 (19) ◽  
pp. 6302-6317 ◽  
Author(s):  
Nouri L. Ben Zakour ◽  
Daniel E. Sturdevant ◽  
Sergine Even ◽  
Caitriona M. Guinane ◽  
Corinne Barbey ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Core Genome ◽  
Allelic Variation ◽  
Genomic Variation ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Extensive Variation ◽  
Genes Encoding ◽  
Genome Content

ABSTRACT Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus, we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of S. aureus host adaptation.

scholarly journals Comparative Genomics of Leuconostoc carnosum

2021 ◽  
Vol 11 ◽  
Author(s):  
Francesco Candeliere ◽  
Stefano Raimondi ◽  
Gloria Spampinato ◽  
Moon Yue Feng Tay ◽  
Alberto Amaretti ◽  
...  
Keyword(s):  
Amino Acids ◽  
Core Genome ◽  
Meat Products ◽  
Genome Comparison ◽  
The Core ◽  
Functional Potential ◽  
Pathway Reconstruction ◽  
Genes Encoding ◽  
Food Matrices ◽  
Leuconostoc Carnosum

Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1–4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.

scholarly journals PANINI: Pangenome Neighbor Identification for Bacterial Populations

2017 ◽  
Author(s):  
Khalil Abudahab ◽  
Joaquín M. Prada ◽  
Zhirong Yang ◽  
Stephen D. Bentley ◽  
Nicholas J. Croucher ◽  
...  
Keyword(s):  
Machine Learning ◽  
Core Genome ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Diverse Populations ◽  
Data Set ◽  
Bacterial Populations ◽  
Accessory Genome ◽  
The Core ◽  
Link Type

ABSTRACTThe standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, in the current era of population genomics, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here we introduce PANINI, a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding. PANINI is browser-based and integrates with the Microreact platform for rapid online visualisation and exploration of both core and accessory genome evolutionary signals together with relevant epidemiological, geographic, temporal and other metadata. Several case studies with single-and multi-clone pneumococcal populations are presented to demonstrate ability to identify biologically important signals from gene content data. PANINI is available at http://panini.wgsa.net/ and code at http://gitlab.com/cgps/panini

scholarly journals Evidence of Extensive Homologous Recombination in the Core Genome ofRickettsia

2009 ◽  
Vol 2009 ◽  
pp. 1-5 ◽  
Author(s):  
Jinyu Wu ◽  
Tonghai Yu ◽  
Qiyu Bao ◽  
Fangqing Zhao
Keyword(s):  
Homologous Recombination ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Phylogenetic Network ◽  
Genomic Analysis ◽  
Intracellular Bacteria ◽  
The Core ◽  
Evolutionary Genomic ◽  
The Impact

The important role of homologous recombination has been extensively demonstrated to be fundamental for genetic variation in bacterial genomes. In contrast to extracellular or facultative intracellular bacteria, obligate intracellular bacteria are considered to be less prone to recombination, especially for their core genomes. InRickettsia, only antigen-related genes were identified to have experienced homologous recombination. In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome ofRickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently duringRickettsiaevolution. 28% ofRickettsiacore genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into the substantial role of recombination in the evolution of the intracellular pathogenic bacteriaRickettsia.

scholarly journals Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 661 ◽  
Author(s):  
Nadezhda Chernysheva ◽  
Evgeniya Bystritskaya ◽  
Anna Stenkova ◽  
Ilya Golovkin ◽  
Olga Nedashkovskaya ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Active Enzyme ◽  
Comparative Genomic ◽  
The Core ◽  
Pan Genome ◽  
Carbohydrate Active Enzyme ◽  
Pharmaceutical Industries

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

scholarly journals Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis

2016 ◽  
Vol 3 (3) ◽  
Author(s):  
James R. Johnson ◽  
Gregg Davis ◽  
Connie Clabots ◽  
Brian D. Johnston ◽  
Stephen Porter ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Core Genome ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
The Core ◽  
Genome Phylogeny ◽  
Genome Level ◽  
Repeated Infections

Abstract Background.  Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods.  Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results.  In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions.  Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.

scholarly journals Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

2021 ◽  
Vol 9 (2) ◽  
pp. 348
Author(s):  
Florian Tagini ◽  
Trestan Pillonel ◽  
Claire Bertelli ◽  
Katia Jaton ◽  
Gilbert Greub
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Mycobacterium Kansasii ◽  
Type Vii Secretion ◽  
A Genome ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Immunosuppressed Patients ◽  
Type Vii Secretion System ◽  
Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

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