scholarly journals Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate ofPantoea vagansPV989

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Lei Xu ◽  
Min Yin ◽  
Tingyuan Zhu ◽  
Yabo Liu ◽  
Yuanyuan Ying ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Erwinia Amylovora ◽  
Variable Region ◽  
Fruit Trees ◽  
Natural Environments ◽  
Negative Bacterium ◽  
Phage Integrase ◽  
Comparative Genomics Analysis ◽  
Large Plasmids ◽  
Pantoea Vagans

Pantoea vagans, a gram-negative bacterium from the genusPantoeaand familyEnterobacteriaceae, is present in various natural environments and considered to be plant endophytes. We isolated thePantoea vagansPV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molecule, it also harboured three large plasmids. A comparative genomics analysis was performed for the smallest plasmid, pPV989-94. It can be divided into four regions, including three conservative regions related to replication (R1), transfer conjugation (R2), and transfer leading (R3), and one variable region (R4). Further analysis showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 ofErwinia amylovorastrains isolated from fruit trees. These three plasmids share three conservative regions (R1, R2, and R3). Interestingly, a fragment (R4′) in R4, mediated by phage integrase and phage integrase family site-specific recombinase and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was unique in pPV989-94. Homologues of R4′were found in other plasmids or chromosomes, suggesting that horizontal gene transfer (HGT) occurred among different bacteria of various species or genera. The acquired functional genes may play important roles in the adaptation of bacteria to different hosts or environmental conditions.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

scholarly journals In Vitro Evaluation of Five Antimicrobial Peptides against the Plant Pathogen Erwinia amylovora

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 554
Author(s):  
Rafael J. Mendes ◽  
Laura Regalado ◽  
João P. Luz ◽  
Natália Tassi ◽  
Cátia Teixeira ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Antimicrobial Peptides ◽  
Erwinia Amylovora ◽  
Growth Curves ◽  
Fruit Trees ◽  
Membrane Permeabilization ◽  
Control Measures ◽  
Minimal Bactericidal Concentration ◽  
Pome Fruit

Fire blight is a major pome fruit trees disease that is caused by the quarantine phytopathogenic Erwinia amylovora, leading to major losses, namely, in pear and apple productions. Nevertheless, no effective sustainable control treatments and measures have yet been disclosed. In that regard, antimicrobial peptides (AMPs) have been proposed as an alternative biomolecule against pathogens but some of those AMPs have yet to be tested against E. amylovora. In this study, the potential of five AMPs (RW-BP100, CA-M, 3.1, D4E1, and Dhvar-5) together with BP100, were assessed to control E. amylovora. Antibiograms, minimal inhibitory, and bactericidal concentrations (minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC), growth and IC50 were determined and membrane permeabilization capacity was evaluated by flow cytometry analysis and colony-forming units (CFUs) plate counting. For the tested AMPs, the higher inhibitory and bactericidal capacity was observed for RW-BP100 and CA-M (5 and 5–8 µM, respectively for both MIC and MBC), whilst for IC50 RW-BP100 presented higher efficiency (2.8 to 3.5 µM). Growth curves for the first concentrations bellow MIC showed that these AMPs delayed E. amylovora growth. Flow cytometry disclosed faster membrane permeabilization for CA-M. These results highlight the potential of RW-BP100 and CA-M AMPs as sustainable control measures against E. amylovora.

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

2017 ◽  
Vol 39 (12) ◽  
pp. 1307-1316 ◽  
Author(s):  
Xunbiao Liu ◽  
Qianqian Zhang ◽  
Xinyao Xia ◽  
Xiuyuan Liu ◽  
Lei Ge ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationships ◽  
Comparative Genomics Analysis

scholarly journals Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Huihui Du ◽  
Rendong Fang ◽  
Tingting Pan ◽  
Tian Li ◽  
Nengzhang Li ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Pasteurella Multocida ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Insertion Sequences ◽  
Capsular Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Comparative Genomics Analysis

The Pasteurella multocida capsular type A isolates can cause pneumonia and bovine respiratory disease (BRD). In this study, comparative genomics analysis was carried out to identify the virulence genes in two different virulent P. multocida capsular type A isolates (high virulent PmCQ2 and low virulent PmCQ6). The draft genome sequence of PmCQ2 is 2.32 Mbp and contains 2,002 protein-coding genes, 9 insertion sequence (IS) elements, and 1 prophage region. The draft genome sequence of PmCQ6 is 2.29 Mbp and contains 1,970 protein-coding genes, 2 IS elements, and 3 prophage regions. The genome alignment analysis revealed that the genome similarity between PmCQ2 and PmCQ6 is 99% with high colinearity. To identify the candidate genes responsible for virulence, the PmCQ2 and PmCQ6 were compared together with that of the published genomes of high virulent Pm36950 and PmHN06 and avirulent Pm3480 and Pm70 (capsular type F). Five genes and two insertion sequences are identified in high virulent strains but not in low virulent or avirulent strains. These results indicated that these genes or insertion sequences might be responsible for the virulence of P. multocida, providing prospective candidates for further studies on the pathogenesis and the host-pathogen interactions of P. multocida.

scholarly journals First Report and Comparative Genomics Analysis of a blaOXA-244–Harbouring Escherichia coli Isolate Recovered in American Continent

2019 ◽  
Author(s):  
Deisy J Abril ◽  
Ingrid Gisell Bustos Moya ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Diego Fernando Josa Montero ◽  
Zayda Lorena Corredor Rozo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Genomic Island ◽  
Genomic Analysis ◽  
American Continent ◽  
Incompatibility Group ◽  
Coli Isolate ◽  
First Report ◽  
E Coli ◽  
Comparative Genomics Analysis

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harbouring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harbouring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38 and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbour resistance genes. The blaOXA-244 gene was chromosomally-encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. For our knowledge this is the first report of a blaOXA-244–harbouring Escherichia coli isolate in American continent.Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently on the American continent.

scholarly journals Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Michael T. Leonard ◽  
Jennie R. Fagen ◽  
Connor M. McCullough ◽  
Austin G. Davis-Richardson ◽  
Michael J. Davis ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Comparative Genomics Analysis
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