scholarly journals Molecular Phylogeny of the Salmonellae: Relationships among Salmonella Species and Subspecies Determined from Four Housekeeping Genes and Evidence of Lateral Gene Transfer Events

2008 ◽  
Vol 190 (21) ◽  
pp. 7060-7067 ◽  
Author(s):  
J. R. McQuiston ◽  
S. Herrera-Leon ◽  
B. C. Wertheim ◽  
J. Doyle ◽  
P. I. Fields ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Salmonella Enterica ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Diverse Group ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Common Serotypes

ABSTRACT The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1760-1777 ◽  
Author(s):  
LAURA M. McDONAGH ◽  
JAMIE R. STEVENS
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Nuclear Gene ◽  
Evolutionary Status ◽  
28S Rrna ◽  
Gene Trees ◽  
Data Set ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

scholarly journals CALLIPHORIDAE (REVIEW)

2021 ◽  
pp. 80-84
Author(s):  
Barashkova ◽  
Budishcheva
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Sequence Data ◽  
28S Rrna ◽  
Cytochrome Oxidase Subunit ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Gene Coi ◽  
Host Tissues

The Calliphoridae family attracts many researchers in the phylogeny of myiasis in this family. Nevertheless, even after more than 50 years of research of the phylogenetic relationships among Calliphoridae subfamilies, the origin of myiasis remains unclear. By studying the peculiarities of the ecology of blue-green meat flies, and their adaptation to various habitats, it was found that the transition to facultative parasitism at the larval stage could occur in several ways, and was accompanied by the formation of viviparity. The larval parasitism of Calliphoridae on birds developed as a tendency of evolution. Larvae of the genus Protocalliphora, began feeding on blood of birds, and larvae of the species of the genus Trypocalliphora feed on the host tissues causing myiasis and the death of chicks. In order to elucidate the problem, we constructed three phylogenetic trees using nucleotide sequence data from cytochrome oxidase subunit one gene (COI), representing a mitochondrial conservative gene, and nuclear 28S subunit of ribosomal RNA gene (28S rRNA) in order to interpret the evolutionary profile of myiasis in the family Calliphoridae. Comparative analysis of the phylogenetic trees shows that the habit of obligatory myiasis originated independently more than five times among different calliphorid taxa in the course of evolutionary history. The inclusion of other myiasis-causing families (Oestridae, Gastrophilidae, and Sarcophagidae) along with fundamental life-history studies that deal with biology, physiology, feeding behavior and host specificity in addition to phylogenetic analysis could provide a more accurate answer to the origin of myiasis

scholarly journals Variation of the Ribosomal Operon 16S-23S Gene Spacer Region in Representatives of Salmonella enterica Subspecies

1998 ◽  
Vol 180 (8) ◽  
pp. 2144-2151 ◽  
Author(s):  
Sara Pérez Luz ◽  
Francisco Rodríguez-Valera ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Salmonella Enterica ◽  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
The Other ◽  
Nucleotide Substitutions ◽  
E Coli ◽  
The Family ◽  
Ribosomal Operon ◽  
Ribosomal Operons ◽  
K 12

ABSTRACT The 16S-23S spacer regions of two ribosomal operons (rrnA and rrnE) have been sequenced in seven representatives of the Salmonella entericasubspecies. Isolated nucleotide substitutions were found at the same sites as in Escherichia coli but the number of polymorphic sites was much larger, as could be expected for a more heterogeneous species. Still, as in E. coli, most of the variation found was due to insertions and/or deletions affecting blocks of nucleotides generally located at equivalent regions of the putative secondary structure for both species. Isolated polymorphic sites generated phylogenetic trees generally consistent with the subspecies structure and the accepted relationships among the subspecies. However, the sequences of rrnE put subspecies I closer to E. coli K-12 than to the other S. enterica subspecies. The distribution of polymorphisms affecting blocks of nucleotides was much more random, and the presence of equivalent sequences in distantly related subspecies, and even in E. coli, could reflect relatively frequent horizontal transfer. The smallest 16S-23S spacers in other genera of the family Enterobacteriaceaewere also sequenced. As expected, the level of variation was much larger. Still, the phylogenetic tree inferred is consistent with those of 16S rRNA or housekeeping genes.

scholarly journals Confusion surrounding Didymosphaeria—phylogenetic and morphological evidence suggest Didymosphaeriaceae is not a distinct family

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 102 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
ERIO CAMPORESI ◽  
KASUN M. THAMBUGALA ◽  
AUSANA MAPOOK ◽  
JI-CHUAN KANG ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Morphological Evidence ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Family Based ◽  
Phylogenetic Lineages ◽  
A New Species

Didymosphaeriaceae is a ubiquitous fungal family that is reported to include saprobic, endophytic and pathogenic species associated with a wide variety of substrates. The family is characterized by 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci. In recent treatments Appendispora, Didymosphaeria, Roussoella, Phaeodothis and Verruculina were placed in the family. The aim of the present study is to delineate phylogenetic lineages within Didymosphaeriaceae and allied genera. A new species, Didymosphaeria rubi-ulmifolii, was isolated and identified based on morphological characters and phylogenetic analyses of partial 18S nrDNA and 28S nrDNA nucleotide sequence data. Didymosphaeria rubi-ulmifolii clustered with Montagnulaceae as a separate genus, while two putative strains (HKUCC 5834 and CMW 22186) of D. futilis from GenBank clustered with Cucurbitariaceae and Didymellaceae, respectively. The new species is characterized by immersed to slightly erumpent ascomata immersed under a clypeus, a peridium with compressed cells of textura intricata, long trabeculate pseudoparaphyses, anastomosing mostly above the asci and brown, 1-septate ascospores with granulate ornamentation. Phylogenetic analysis in combination with morphology and a review of literature show that Appendispora, Phaeodothis, Roussoella and Verruculina should be excluded from the family. Phaeodothis belongs in Montagnulaceae, Verruculina in Testudinaceae, while Appendispora and Roussoella belong in Roussoellaceae. The position of Didymosphaeriaceae as a distinct family, based on 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci is doubtful. Fresh collections of more Didymosphaeria strains are needed for epitypification and to obtain sequence data to establish if this family can be maintained.

scholarly journals Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael J. Ormsby ◽  
Robert L. Davies
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Atlantic Salmon ◽  
Sequence Variation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Yersinia Ruckeri ◽  
Amino Acid Sequence Variation

AbstractYersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.

scholarly journals Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function

Open Biology ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 170144 ◽  
Author(s):  
Christopher J. Stubenrauch ◽  
Gordon Dougan ◽  
Trevor Lithgow ◽  
Eva Heinz
Keyword(s):  
Escherichia Coli ◽  
Time Delay ◽  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Drug Resistant ◽  
Protein Diversity ◽  
E Coli ◽  
Wide Range ◽  
The Family ◽  
And Function

Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli , and further focus on a so far undescribed chaperone–usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter . We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.

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