scholarly journals Comparative analysis of essential genes in prokaryotic genomic islands

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Xi Zhang ◽  
Chong Peng ◽  
Ge Zhang ◽  
Feng Gao
Keyword(s):  
Comparative Analysis ◽  
Essential Genes ◽  
Genomic Islands

scholarly journals Genome Mining and Comparative Analysis of Streptococcus intermedius Causing Brain Abscess in a Child

Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 22 ◽  
Author(s):  
Elio Issa ◽  
Tamara Salloum ◽  
Balig Panossian ◽  
David Ayoub ◽  
Edmond Abboud ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Metal Ions ◽  
Genome Evolution ◽  
Brain Abscess ◽  
Survival Rates ◽  
Genome Mining ◽  
Genomic Islands ◽  
Polymorphism Analysis ◽  
Streptococcus Intermedius ◽  
Pan Genome

Streptococcus intermedius (SI) is associated with prolonged hospitalization and low survival rates. The genetic mechanisms involved in brain abscess development and genome evolution in comparison to other members of the Streptococcus anginosus group are understudied. We performed a whole-genome comparative analysis of an SI isolate, LAU_SINT, associated with brain abscess following sinusitis with all SI genomes in addition to S. constellatus and S. anginosus. Selective pressure on virulence factors, phages, pan-genome evolution and single-nucleotide polymorphism analysis were assessed. The structural details of the type seven secretion system (T7SS) was elucidated and compared with different organisms. ily and nanA were both abundant and conserved. Nisin resistance determinants were found in 47% of the isolates. Pan-genome and SNPs-based analysis didn’t reveal significant geo-patterns. Our results showed that two SC isolates were misidentified as SI. We propose the presence of four T7SS modules (I–IV) located on various genomic islands. We detected a variety of factors linked to metal ions binding on the GIs carrying T7SS. This is the first detailed report characterizing the T7SS and its link to nisin resistance and metal ions binding in SI. These and yet uncharacterized T7SS transmembrane proteins merit further studies and could represent potential therapeutic targets.

scholarly journals Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Dexi Bi ◽  
Jiayi Zheng ◽  
Ruting Xie ◽  
Yin Zhu ◽  
Rong Wei ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Genetic Features ◽  
Clonal Distribution ◽  
Structural Modulation

ABSTRACT AbaR-type genomic islands (AbaRs) are prevalent and associated with multiple antimicrobial resistance in Acinetobacter baumannii. AbaRs feature varied structural configurations involving different but closely related backbones with acquisition of diverse mobile genetic elements (MGEs) and antimicrobial resistance genes. This study aimed to understand the structural modulation patterns of AbaRs. A total of 442 intact AbaRs, including nonresistance but closely related islands, were mapped to backbones Tn6019, Tn6022, Tn6172/Tn6173, and AbGRI1-0 followed by alien sequence characterization. Genetic configurations were then examined and compared. The AbaRs fall into 53 genetic configurations, among which 26 were novel, including one Tn6019-type, nine Tn6022-type, three Tn6172/Tn6173-type, nine AbGRI1-type, and four new transposons that could not be mapped to the known backbones. The newly identified genetic configurations involved insertions of novel MGEs like ISAcsp2, ISAba42, ISAba17, and ISAba10, novel structural modulations driven by known MGEs such as ISCR2, Tn2006, and even another AbaR, and different backbone deletions. Recombination events in AbGRI1-type elements were also examined by identifying hybrid sequences from different backbones. Moreover, we found that the content and context features of AbaRs including the profiles of the MGEs driving the plasticity of these elements and the consequently acquired antimicrobial resistance genes, insertion sites, and clonal distribution displayed backbone-specific patterns. This study provides a comprehensive view of the genetic features of AbaRs. IMPORTANCE AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii. These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structural diversity is far from complete. In this study, we performed a large-scale comparative analysis of AbaRs, including nonresistance but closely related islands. Our findings offered a comprehensive and interesting view of their genetic features, which allowed us to correlate the structural modulation signatures, antimicrobial resistance patterns, insertion loci, as well as host clonal distribution of these elements to backbone types. This study provides insights into the evolution of these elements, explains the association between their antimicrobial resistance gene profiles and clonal distribution, and could facilitate establishment of a more proper nomenclature than the term “AbaR” that has been variously used.

scholarly journals Comparative Analysis of Mobilizable Genomic Islands

2012 ◽  
Vol 195 (3) ◽  
pp. 606-614 ◽  
Author(s):  
A. Daccord ◽  
D. Ceccarelli ◽  
S. Rodrigue ◽  
V. Burrus
Keyword(s):  
Comparative Analysis ◽  
Genomic Islands

scholarly journals Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Mostafa Y. Abdel-Glil ◽  
Uwe Fischer ◽  
Dieter Steinhagen ◽  
Una McCarthy ◽  
Heinrich Neubauer ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Genetic Relatedness ◽  
Critical Role ◽  
Genome Structure ◽  
The United States ◽  
Genomic Islands ◽  
Stable Set ◽  
Whole Genome ◽  
Yersinia Ruckeri

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

2007 ◽  
Vol 279 (1) ◽  
pp. 87-94 ◽  
Author(s):  
Xiaodong Gong ◽  
Shaohua Fan ◽  
Amy Bilderbeck ◽  
Mingkun Li ◽  
Hongxia Pang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Essential Genes ◽  
Escherichia Coli K12 ◽  
Nonessential Genes

scholarly journals Towards the identification of essential genes using targeted genome sequencing and comparative analysis

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Adam M Gustafson ◽  
Evan S Snitkin ◽  
Stephen CJ Parker ◽  
Charles DeLisi ◽  
Simon Kasif
Keyword(s):  
Comparative Analysis ◽  
Genome Sequencing ◽  
Essential Genes

scholarly journals Complete genome sequence of fish-pathogenic Aeromonas hydrophila HX-3 and a comparative analysis: insights into virulence factors and quorum sensing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lei Jin ◽  
Yu Chen ◽  
Wenge Yang ◽  
Zhaohui Qiao ◽  
Xiaojun Zhang
Keyword(s):  
Comparative Analysis ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Aeromonas Hydrophila ◽  
Complete Genome ◽  
Virulent Strain ◽  
Genomic Islands ◽  
Circular Chromosome

Abstract The gram-negative, aerobic, rod-shaped bacterium Aeromonas hydrophila, the causative agent of motile aeromonad septicaemia, has attracted increasing attention due to its high pathogenicity. Here, we constructed the complete genome sequence of a virulent strain, A. hydrophila HX-3 isolated from Pseudosciaena crocea and performed comparative genomics to investigate its virulence factors and quorum sensing features in comparison with those of other Aeromonas isolates. HX-3 has a circular chromosome of 4,941,513 bp with a 61.0% G + C content encoding 4483 genes, including 4318 protein-coding genes, and 31 rRNA, 127 tRNA and 7 ncRNA operons. Seventy interspersed repeat and 153 tandem repeat sequences, 7 transposons, 8 clustered regularly interspaced short palindromic repeats, and 39 genomic islands were predicted in the A. hydrophila HX-3 genome. Phylogeny and pan-genome were also analyzed herein to confirm the evolutionary relationships on the basis of comparisons with other fully sequenced Aeromonas genomes. In addition, the assembled HX-3 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database (76.03%), Gene Ontology database (18.13%), and Kyoto Encyclopedia of Genes and Genome pathway database (59.68%). Two-component regulatory systems in the HX-3 genome and virulence factors profiles through comparative analysis were predicted, providing insights into pathogenicity. A large number of genes related to the AHL-type 1 (ahyI, ahyR), LuxS-type 2 (luxS, pfs, metEHK, litR, luxOQU) and QseBC-type 3 (qseB, qseC) autoinducer systems were also identified. As a result of the expression of the ahyI gene in Escherichia coli BL21 (DE3), combined UPLC-MS/MS profiling led to the identification of several new N-acyl-homoserine lactone compounds synthesized by AhyI. This genomic analysis determined the comprehensive QS systems of A. hydrophila, which might provide novel information regarding the mechanisms of virulence signatures correlated with QS.

Identification of genomic islands in the genome ofBacillus cereusby comparative analysis withBacillus anthracis

2003 ◽  
Vol 16 (1) ◽  
pp. 19-23 ◽  
Author(s):  
Ren Zhang ◽  
Chun-Ting Zhang
Keyword(s):  
Comparative Analysis ◽  
Integration Site ◽  
Gc Content ◽  
Genomic Islands ◽  
Gene Gain ◽  
Abrupt Changes ◽  
Phage Protein ◽  
Recombinase Gene ◽  
A Site ◽  
Genomic Gc Content

Horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. The availability of both complete genome sequences of Bacillus cereus and B. anthracis provides the possibility to perform comparative analysis based on their genomes. By using a windowless method to display the distribution of the genomic GC content of B. cereus and B. anthracis, we have found three genomic islands in the genome of B. cereus, i.e., BCGI-1, BCGI-2, and BCGI-3, respectively, which are absent in the genome of B. anthracis. All the genomic islands have abrupt changes in GC content compared with that of surrounding regions. BCGI-1 has many conserved features of genomic islands, e.g., a Val-tRNA gene is utilized as the integration site, and a site-specific recombinase gene is located at the 3′ end. BCGI-2 has a large percentage of phage protein, suggesting a phage-related recombination is involved. BCGI-3 contains a ferric anguibactin transport system, which is likely to be involved in the iron transport that enables the bacterium to overcome the iron limitation in the host. In addition, BCGI-3 also contains a cluster of genes related to lantibiotics, which may play a role during the evolution of the genome. Furthermore, the integrations of the genomic islands, BCGI-1 and BCGI-3, result in deletions of DNA sequence fragments; therefore, such integrations lead to both gene gain and gene loss simultaneously.

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