scholarly journals Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus

2019 ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

AbstractHuanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphapro-teobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

scholarly journals Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
Causative Agent ◽  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

ABSTRACT Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”

scholarly journals Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates

mSystems ◽  
2021 ◽  
Author(s):  
Wangxiao Zhou ◽  
Ye Jin ◽  
Yanzi Zhou ◽  
Yuan Wang ◽  
Luying Xiong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Health Issues ◽  
Content Type ◽  
Genome Wide Analysis ◽  
Genome Wide

Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage.

scholarly journals De novo assembly and functional annotation of Citrus aurantifolia transcriptome from Candidatus Liberibacter asiaticus infected and non-infected trees

Data in Brief ◽  
2020 ◽  
Vol 29 ◽  
pp. 105198 ◽  
Author(s):  
Ángela Paulina Arce-Leal ◽  
Rocío Bautista ◽  
Edgar A. Rodríguez-Negrete ◽  
Miguel Ángel Manzanilla-Ramírez ◽  
José Joaquín Velázquez-Monreal ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Functional Annotation ◽  
De Novo ◽  
Candidatus Liberibacter Asiaticus ◽  
Citrus Aurantifolia ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

scholarly journals Comparative Genomic Analysis Reveals a Critical Role of De Novo Nucleotide Biosynthesis for Saccharomyces cerevisiae Virulence

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0122382 ◽  
Author(s):  
Roberto Pérez-Torrado ◽  
Silvia Llopis ◽  
Benedetta Perrone ◽  
Rocío Gómez-Pastor ◽  
Bernhard Hube ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Critical Role ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Nucleotide Biosynthesis

scholarly journals Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation

2021 ◽  
Vol 12 ◽  
Author(s):  
Felipe Cabarcas ◽  
Ana Luz Galvan-Diaz ◽  
Laura M. Arias-Agudelo ◽  
Gisela María García-Montoya ◽  
Juan M. Daza ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Cryptosporidium Hominis ◽  
Stool Samples ◽  
Metagenomic Assembly ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India

2019 ◽  
Vol 8 (27) ◽  
Author(s):  
Amrita Salim ◽  
Pradeesh Babu ◽  
Keerthi Mohan ◽  
Manju Moorthy ◽  
Devika Raj ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type ◽  
E Coli

ABSTRACT We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.

scholarly journals Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal PathogenicEscherichia coli(ExPEC) Lineages

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Sabiha Shaik ◽  
Amit Ranjan ◽  
Sumeet K. Tiwari ◽  
Arif Hussain ◽  
Nishant Nandanwar ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
E Coli ◽  
Extended Spectrum ◽  
Tract Infections ◽  
St131 Clone

ABSTRACTEscherichia colisequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenicE. coli(ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producingE. coliclones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131E. colistrains with 40 genomes from three other STs, including ST38 (n =12), ST405 (n =10), and ST648 (n =18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification ofE. colistrains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.IMPORTANCEE. coli, particularly the ST131 extraintestinal pathogenicE. coli(ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzesE. coliST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemicE. coliST131 clone.

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