scholarly journals A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence

2019 ◽  
Author(s):  
Nathan A. Wyatt ◽  
Jonathan K. Richards ◽  
Robert S. Brueggeman ◽  
Timothy L. Friesen
Keyword(s):  
Genomic Analysis ◽  
Effector Proteins ◽  
Comparative Genomic ◽  
Pyrenophora Teres ◽  
Structural Variations ◽  
Evolution Of Virulence ◽  
Reference Quality ◽  
Genomic Characterization ◽  
Genomic Regions

AbstractPyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.

scholarly journals A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

2020 ◽  
Vol 33 (2) ◽  
pp. 173-188 ◽  
Author(s):  
Nathan A. Wyatt ◽  
Jonathan K. Richards ◽  
Robert S. Brueggeman ◽  
Timothy L. Friesen
Keyword(s):  
Genomic Analysis ◽  
Effector Proteins ◽  
Comparative Genomic ◽  
Pyrenophora Teres ◽  
Structural Variations ◽  
Evolution Of Virulence ◽  
Reference Quality ◽  
Genomic Characterization ◽  
Genomic Regions ◽  
Subtelomeric Regions

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.

scholarly journals Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants

2019 ◽  
Vol 10 ◽  
Author(s):  
João Pedro Rueda Furlan ◽  
Otávio Guilherme Gonçalves de Almeida ◽  
Elaine Cristina Pereira De Martinis ◽  
Eliana Guedes Stehling
Keyword(s):  
Antimicrobial Resistance ◽  
Metal Tolerance ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

scholarly journals Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

2019 ◽  
Vol 366 (17) ◽  
Author(s):  
Chrystine Zou Yi Yan ◽  
Christopher M Austin ◽  
Qasim Ayub ◽  
Sadequr Rahman ◽  
Han Ming Gan
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Illumina Miseq ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Phylogenomic Analysis ◽  
Genomic Characterization ◽  
Genomic Resource ◽  
Acute Hepatopancreatic Necrosis Disease ◽  
Genomic Regions

ABSTRACT The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections

2020 ◽  
Vol 76 (1) ◽  
pp. 91-100
Author(s):  
Jorge Arca-Suárez ◽  
Cristina Lasarte-Monterrubio ◽  
Bruno-Kotska Rodiño-Janeiro ◽  
Gabriel Cabot ◽  
Juan Carlos Vázquez-Ucha ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Molecular Mechanisms ◽  
Genomic Analysis ◽  
Resistance Mechanisms ◽  
Comparative Genomic ◽  
Development Of Resistance ◽  
Structural Impact ◽  
Genetic Context

Abstract Background The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning. Objectives Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections. Methods Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes. Results The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold. Conclusions Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.

scholarly journals Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

2020 ◽  
Vol 8 (3) ◽  
pp. 366
Author(s):  
Jarred Yasuhara-Bell ◽  
Mohammad Arif ◽  
Grethel Y. Busot ◽  
Rachel Mann ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
The United States ◽  
Grass Species ◽  
Comparative Genomic ◽  
Underrepresented Populations ◽  
System A ◽  
Genome Wide ◽  
The Family ◽  
Study Support ◽  
Genomic Regions

Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.

scholarly journals Complete-Genome Sequencing and Comparative Genomic Characterization of an IMP-4 Producing Citrobacter freundii Isolate from Patient with Diarrhea

2020 ◽  
Vol Volume 13 ◽  
pp. 1057-1065
Author(s):  
Xiaohui Chi ◽  
Jing Guo ◽  
Yanzi Zhou ◽  
Tingting Xiao ◽  
Hao Xu ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome ◽  
Comparative Genomic ◽  
Citrobacter Freundii ◽  
Complete Genome Sequencing ◽  
Genomic Characterization

scholarly journals Comparative Genomic Characterization of Three Streptococcus parauberis Strains in Fish Pathogen, as Assessed by Wide-Genome Analyses

PLoS ONE ◽  
2013 ◽  
Vol 8 (11) ◽  
pp. e80395 ◽  
Author(s):  
Seong-Won Nho ◽  
Jun-ichi Hikima ◽  
Seong Bin Park ◽  
Ho Bin Jang ◽  
In Seok Cha ◽  
...  
Keyword(s):  
Comparative Genomic ◽  
Fish Pathogen ◽  
Genomic Characterization ◽  
Streptococcus Parauberis ◽  
Genome Analyses

scholarly journals Comparative genomic characterization of citrus-associated Xylella fastidiosa strains

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 474 ◽  
Author(s):  
Vivian S da Silva ◽  
Cláudio S Shida ◽  
Fabiana B Rodrigues ◽  
Diógenes CD Ribeiro ◽  
Alessandra A de Souza ◽  
...  
Keyword(s):  
Xylella Fastidiosa ◽  
Comparative Genomic ◽  
Genomic Characterization

Comparative Genomic Analysis for Identification and Characterization of Common Genes among Parasitic Nematodes

2016 ◽  
Vol 28 (2) ◽  
pp. 259-267
Author(s):  
Vimalraj Mani ◽  
◽  
Kang-Hyun Choi ◽  
Parthiban Subramanian ◽  
Chang-Muk Lee ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Identification And Characterization
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