A Phylogenetic Characterization of the Microbiome of the Ponerine Ants (Hymenoptera: Formicidae: Ponerinae)

2021 ◽  
Author(s):  
Narayan Hin-Lun Wong
Keyword(s):  
Phylogenetic Characterization ◽  
Ponerine Ants

DETECTION AND PHYLOGENETIC CHARACTERIZATION OF HEPATITIS E VIRUS GENOTYPE 3 IN A CAPTIVE WILD BOAR IN THAILAND

2012 ◽  
Vol 43 (3) ◽  
pp. 640-644 ◽  
Author(s):  
Anuwat Wiratsudakul ◽  
Ladawan Sariya ◽  
Phirom Prompiram ◽  
Siriporn Tantawet ◽  
Duangkhamol Suraruangchai ◽  
...  
Keyword(s):  
Wild Boar ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Genotype 3 ◽  
Virus Genotype ◽  
Phylogenetic Characterization

Sequencing and phylogenetic characterization of a novel RNA virus in Arma chinensis

2021 ◽  
Vol 65 (03) ◽  
pp. 320-323
Author(s):  
Yonghao Dong ◽  
Pengjun Xu ◽  
Guangwei Ren ◽  
Changchun Feng ◽  
Dongyang Liu ◽  
...  
Keyword(s):  
Rna Virus ◽  
Phylogenetic Characterization

scholarly journals Las degradation in a fluidized bed reactor and phylogenetic characterization of the biofilm

2013 ◽  
Vol 30 (3) ◽  
pp. 521-529 ◽  
Author(s):  
L. L. Oliveira ◽  
R. B. Costa ◽  
I. K. Sakamoto ◽  
I. C. S. Duarte ◽  
E. L. Silva ◽  
...  
Keyword(s):  
Fluidized Bed ◽  
Fluidized Bed Reactor ◽  
Phylogenetic Characterization

scholarly journals Molecular epidemiology of blaCTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Mehrdad Halaji ◽  
Shahrzad Shahidi ◽  
Behrooz Ataei ◽  
Abdolamir Atapour ◽  
Awat Feizi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Kidney Transplant ◽  
Phylogenetic Group ◽  
Control Group ◽  
M Gene ◽  
Mlst Analysis ◽  
Phylogenetic Characterization ◽  
Transplant Patients ◽  
Kidney Transplant Patients

Abstract Background This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing blaCTX-M gene. Methods To this end, we determined virulence marker and the phylogenetic characterization of UPEC in non-KTPs (n = 65) and KTPs (n = 46). The non-KTPs were considered the control group of the study. Also, according to the Achtman scheme, we performed multilocus sequence typing to assess the relationship between twenty-nine of ESBL-producing isolates containing blaCTX-M gene. Results According to the results of PCR assay, the prevalence of virulence factor genes ranged from 0% (cnf and papG III) to 93.7% (fimH). Also, KTP isolates significantly differed from non-KTP isolates only in terms of the prevalence of pap GI elements. Moreover, the most frequent UPEC isolates were in phylogenetic group B2, followed by group D (18.9%), and group A (13.5%). Furthermore, except for phylogenetic group C, there was no significant correlation between phylogenetic distribution in KTPs and non-KTPs. Additionally, MLST analysis of blaCTX-M carrying isolates identified 18 unique sequence types (ST) the most common of which was ST131 (24.1%), followed by ST1193 (10.3%), while fourteen STs were detected only once. Conclusions The results further revealed significant differences between the UPEC isolates from KTPs and non-KTPs regarding the phylogroups C and PAI gene. Based on MLST analysis, we also observed a relatively high diversity in UPEC isolates obtained from KTPs and non-KTPs. Moreover, clonal complex (CC) 131 and ST131 were found to be the most prevalent clones and ST types, respectively. Besides, for the first time, ST8503 were reported in KTPs. These results suggested regular studies on characterization of UPEC isolates among KTPs.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

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