scholarly journals Housekeeping Genes for Phylogenetic Analysis of Eutherian Relationships

2006 ◽  
Vol 23 (8) ◽  
pp. 1493-1503 ◽  
Author(s):  
Morgan Kullberg ◽  
Maria A. Nilsson ◽  
Ulfur Arnason ◽  
Eric H. Harley ◽  
Axel Janke
Keyword(s):  
Phylogenetic Analysis ◽  
Housekeeping Genes

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

2000 ◽  
Vol 44 (8) ◽  
pp. 2207-2210 ◽  
Author(s):  
Nadia Maggi Solcà ◽  
Marco Valerio Bernasconi ◽  
Jean-Claude Piffaretti
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Resistant Strain ◽  
Point Mutations ◽  
Housekeeping Genes ◽  
Amino Acid Substitutions ◽  
Metronidazole Resistance ◽  
Nucleotide Mutation ◽  
Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

scholarly journals Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes

2004 ◽  
Vol 54 (5) ◽  
pp. 1511-1519 ◽  
Author(s):  
L. Soler ◽  
M. A. Yáñez ◽  
M. R. Chacon ◽  
M. G. Aguilera-Arreola ◽  
V. Catalán ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Housekeeping Genes ◽  
Nucleotide Sequences ◽  
Aeromonas Salmonicida ◽  
Species Level ◽  
Substitution Rates ◽  
Aeromonas Veronii ◽  
Taxonomic Organization ◽  
Phylogenetic Divergence

The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the σ 70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.

scholarly journals Multilocus Sequence-Typing of Anthrax Microbe Strains Isolated in Russia and Neighboring Countries

2021 ◽  
pp. 95-102
Author(s):  
Yu. O. Goncharova ◽  
I. V. Bakhteeva ◽  
R. I. Mironova ◽  
A. G. Bogun ◽  
K. V. Khlopova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Multilocus Sequence Typing ◽  
Software Package ◽  
Housekeeping Genes ◽  
Common Mutation ◽  
Whole Genome ◽  
New Generation Sequencing ◽  
New Generation ◽  
Sequence Types ◽  
Generation Sequencing

Objective – genotyping by multilocus sequence-typing (MLST) and phylogenetic analysis of 40 Bacillus anthracis strains isolated in Russia and neighboring countries.Materials and methods. In this study, the sequences of seven housekeeping genes of B. anthracis strains were assembled based on the data of a whole genome new generation sequencing, after which the identified mutations and their coordinates were described. The obtained sequences were used for genotyping of the investigated sample using the MLST method. The results are compared with the data presented in PubMLST database. A phylogenetic analysis was performed for the in silico fused sequences of the seven loci of the identified sequence types. The MEGA 7.0 software package was used to build the dendrograms.Results and discussion. Two sequence types (ST) have been found in the examined sample: 35 strains belong to ST-1, and five strains that differed by one common mutation at the glpF locus – to ST-3 (according to PubMLST coding), which emphasizes the genetic separation of this group of strains. One strain has a unique mutation in the gmk gene located outside the region used for MLST. 

scholarly journals Phylogenetic analysis of Helicobacter pylori strains circulating in Yakutia by three housekeeping genes atpA, mutY, ppa

2020 ◽  
pp. 105-106
Author(s):  
Т.В. Борисова ◽  
Н.Н. Готовцев ◽  
Н.А. Барашков ◽  
М.В. Пак ◽  
М.П. Алексеева ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Housekeeping Genes

В работе представлен филогенетический анализ штаммов Helicobacter pylori, циркулирующих в Якутии, по данным трех генов домашнего хозяйства atpA, mutY, ppa. The work presents a phylogenetic analysis of Helicobacter pylori strains circulating in Yakutia, according to three housekeeping genes of the atpA, mutY, ppa.

scholarly journals Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus

2019 ◽  
Vol 69 (4) ◽  
pp. 1060-1069 ◽  
Author(s):  
Pedro Raposo ◽  
Tomeu Viver ◽  
Luciana Albuquerque ◽  
Hugo Froufe ◽  
Cristina Barroso ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
As Species ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene ◽  
Core Genes

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermus with validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus . The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov.

scholarly journals Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae

2008 ◽  
Vol 190 (10) ◽  
pp. 3494-3504 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Jennifer C. Ast ◽  
Allison J. Kaeding ◽  
James D. Oliver ◽  
Paul V. Dunlap
Keyword(s):  
Phylogenetic Analysis ◽  
Horizontal Transfer ◽  
Vibrio Vulnificus ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Vibrio Splendidus ◽  
Photobacterium Leiognathi ◽  
Photobacterium Damselae ◽  
Phylogenetic Divergence ◽  
Distinctive Phenotype

ABSTRACT Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib 2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib 2 operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa.

scholarly journals Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries

2007 ◽  
Vol 56 (11) ◽  
pp. 1460-1466 ◽  
Author(s):  
Seon Young Choi ◽  
Yoon-Seong Jeon ◽  
Je Hee Lee ◽  
Boram Choi ◽  
Sun Hwa Moon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
Shigella Flexneri ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Asian Countries ◽  
Allelic Variants ◽  
Sequence Types

The multilocus sequence typing scheme used previously for phylogenetic analysis of Escherichia coli was applied to 107 clinical isolates of Shigella flexneri. DNA sequencing of 3423 bp throughout seven housekeeping genes identified eight new allele types and ten new sequence types among the isolates. S. flexneri serotypes 1–5, X and Y were clustered together in a group containing many allelic variants while serotype 6 formed a distinct group, as previously established.

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