scholarly journals A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

2010 ◽  
Vol 76 (18) ◽  
pp. 6085-6100 ◽  
Author(s):  
Henk C. den Bakker ◽  
Brittany N. Bundrant ◽  
Esther D. Fortes ◽  
Renato H. Orsi ◽  
Martin Wiedmann
Keyword(s):  
Gene Cluster ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Virulence Gene ◽  
Selective Advantage ◽  
Opportunistic Pathogens ◽  
Evolution Of Virulence ◽  
Average Sequence Divergence ◽  
Phylogeny And Evolution ◽  
Environmental Pathogens

ABSTRACT The genus Listeria includes (i) the opportunistic pathogens L. monocytogenes and L. ivanovii, (ii) the saprotrophs L. innocua, L. marthii, and L. welshimeri, and (iii) L. seeligeri, an apparent saprotroph that nevertheless typically contains the prfA virulence gene cluster. A novel 10-loci multilocus sequence typing scheme was developed and used to characterize 67 isolates representing six Listeria spp. (excluding L. grayi) in order to (i) provide an improved understanding of the phylogeny and evolution of the genus Listeria and (ii) use Listeria as a model to study the evolution of pathogenicity in opportunistic environmental pathogens. Phylogenetic analyses identified six well-supported Listeria species that group into two main subdivisions, with each subdivision containing strains with and without the prfA virulence gene cluster. Stochastic character mapping and phylogenetic analysis of hly, a gene in the prfA cluster, suggest that the common ancestor of the genus Listeria contained the prfA virulence gene cluster and that this cluster was lost at least five times during the evolution of Listeria, yielding multiple distinct saprotrophic clades. L. welshimeri, which appears to represent the most ancient clade that arose from an ancestor with a prfA cluster deletion, shows a considerably lower average sequence divergence than other Listeria species, suggesting a population bottleneck and a putatively different ecology than other saprotrophic Listeria species. Overall, our data suggest that, for some pathogens, loss of virulence genes may represent a selective advantage, possibly by facilitating adaptation to a specific ecological niche.

scholarly journals Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

2017 ◽  
Author(s):  
Milan Malinsky ◽  
Hannes Svardal ◽  
Alexandra M. Tyers ◽  
Eric A. Miska ◽  
Martin J. Genner ◽  
...  
Keyword(s):  
Gene Flow ◽  
Fish Species ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Sequence Divergence ◽  
Single Species ◽  
Lake Malawi ◽  
Genomic Diversity ◽  
Average Sequence Divergence ◽  
Deep Water Species

AbstractThe hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalistAstatotilapia-likeancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.

scholarly journals Intraspecific Phylogeny and Lineage Group Identification Based on the prfA Virulence Gene Cluster of Listeria monocytogenes†

2004 ◽  
Vol 186 (15) ◽  
pp. 4994-5002 ◽  
Author(s):  
Todd J. Ward ◽  
Lisa Gorski ◽  
Monica K. Borucki ◽  
Robert E. Mandrell ◽  
Jan Hutchins ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Gene Cluster ◽  
Phylogenetic Analyses ◽  
Group Identification ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Virulence Gene ◽  
Distinct Species ◽  
Production Environment ◽  
Serotype 4B

ABSTRACT Listeria monocytogenes is a serious food-borne pathogen that can cause invasive disease in humans and other animals and has been the leading cause of food recalls due to microbiological concerns in recent years. In order to test hypotheses regarding L. monocytogenes lineage composition, evolution, ecology, and taxonomy, a robust intraspecific phylogeny was developed based on prfA virulence gene cluster sequences from 113 L. monocytogenes isolates. The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. In addition, a PCR-based test for lineage identification was developed and used in a survey of food products demonstrating that the low frequency of association between lineage 3 isolates and human listeriosis cases likely reflects rarity of exposure and not reduced virulence for humans as has been previously suggested. However, prevalence data do suggest lineage 3 isolates may be better adapted to the animal production environment than the food-processing environment. Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept.

scholarly journals Analysis of the Type 1 Pilin Gene Clusterfim in Salmonella: Its Distinct Evolutionary Histories in the 5′ and 3′ Regions

1999 ◽  
Vol 181 (4) ◽  
pp. 1301-1308 ◽  
Author(s):  
E. Fidelma Boyd ◽  
Daniel L. Hartl
Keyword(s):  
Gene Cluster ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Horizontal Transmission ◽  
Size Variation ◽  
Sequence Divergence ◽  
Intergenic Regions ◽  
Natural Isolates ◽  
Pilin Gene

ABSTRACT The type 1 pilin encoded by fim is present in bothEscherichia coli and Salmonella natural isolates, but several lines of evidence indicate that similarities at the fim locus may be an example of independent acquisition rather than common ancestry. For example, the fim gene cluster is found at different chromosomal locations and with distinct gene orders in these closely related species. In this work we examined the fim gene cluster of Salmonella, the genes of which show high nucleotide sequence divergence from their E. coli counterparts, as well as a different G+C content and codon usage. DNA hybridization analysis revealed that, among the salmonellae, the fim gene cluster is present in all isolates of S. enterica but is absent from S. bongori. Molecular phylogenetic analyses of the fimA and fimIgenes yield an estimate of phylogeny that is in satisfactory congruence with housekeeping and other virulence genes examined in this species. In contrast, phylogenetic analyses of the fimZ,fimY, and fimW genes indicate that horizontal transfer of this region has occurred more than once. There is also size variation in the fimZ, fimY, andfimW intergenic regions in the 3′ region, and these genes are absent in isolate S2983 of subspecies IIIa. Interestingly, the G+C contents of the fimZ, fimY, andfimW genes are less than 46%, which is considerably lower than those of the other six genes of the fim cluster. This study demonstrates that horizontal transmission of all or part of the same gene cluster can occur repeatedly, with the result that different regions of a single gene cluster may have different evolutionary histories.

Three evolutionarily significant units for conservation in the iguanid genus Brachylophus

2006 ◽  
Vol 12 (1) ◽  
pp. 64
Author(s):  
Emma L. Burns ◽  
Brian H. Costello ◽  
Bronwyn A. Houlden
Keyword(s):  
Pacific Islands ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Conservation Priorities ◽  
Separate Species ◽  
Island Populations ◽  
Evolutionarily Significant Units ◽  
Average Sequence Divergence ◽  
History Of ◽  
South Pacific Islands

We examined phylogenetic relationships within the genus Brachylophus, which comprises two endangered iguana species endemic to the South Pacific islands of Fiji and Tonga. Genetic variation among Fijian Crested Iguanas B. vitiensis and Fijian and Tongan Banded Iguanas B. fasciatus was analysed using mitochondrial DNA (mtDNA) cytochrome b (cyt b) characterized from 35 individuals from island populations. Three distinct clades of Brachylophus were identified. The most divergent clade comprised B. fasciatus from Tonga, which supports the recognition of Tongan iguanas as a separate species. Molecular clock estimates suggested that the average sequence divergence (6.4%) between Tongan and Fijian B. fasciatus clades equated to 7 - 15.8 MY of separation, confirming that extant Brachylophus species have a long history of evolution in situ in the Fijian and Tongan archipelago. Phylogenetic analyses also revealed that Fijian B. fasciatus and B. vitiensis iguana populations were not reciprocally monophyletic. One clade comprised two mtDNA haplotypes from the Fijian islands of Monu, Monuriki, Devuilau, Waya and Yadua Taba. The other clade comprised B. fasciatus haplotypes from Kadavu and Gau, which was divergent from both the aforementioned Fijian clade (dA = 3.5%), and the Tongan clade (dA = 6.4%). In addition to mtDNA data, variation was assessed at microsatellite loci, and significant differentiation between iguana populations was detected. Based on both mtDNA and microsatellite analysis, the conservation priorities for these endangered lizards must be reassessed to protect iguanas as three distinct evolutionarily significant units.

scholarly journals Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

2018 ◽  
Vol 19 (8) ◽  
pp. 2383 ◽  
Author(s):  
Qixiang Lu ◽  
Wenqing Ye ◽  
Ruisen Lu ◽  
Wuqin Xu ◽  
Yingxiong Qiu
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Disjunct Distribution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

2009 ◽  
Vol 57 (4) ◽  
pp. 167 ◽  
Author(s):  
Gavin Huttley
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Protein Coding ◽  
Substitution Models ◽  
True Tree ◽  
Molecular Phylogenetic ◽  
Tree Topologies ◽  
Mammal Evolution ◽  
Genome Projects

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

Survey of Postharvest-Processed Oysters in the United States for Levels of Vibrio vulnificus and Vibrio parahaemolyticus

2009 ◽  
Vol 72 (10) ◽  
pp. 2110-2113 ◽  
Author(s):  
ANGELO DePAOLA ◽  
JESSICA L. JONES ◽  
KATHY E. NOE ◽  
ROBIN H. BYARS ◽  
JOHN C. BOWERS
Keyword(s):  
Vibrio Vulnificus ◽  
Gulf Coast ◽  
Virulence Gene ◽  
Selective Advantage ◽  
The United States ◽  
Most Probable Number ◽  
Probable Number ◽  
Mild Heat ◽  
Thermostable Direct Hemolysin ◽  
The Mean

From June through October 2004, the U.S. Food and Drug Administration collected oysters (61 samples) that had been subjected to postharvest processing (PHP) methods, including mild heat treatment, freezing, and high hydrostatic pressure, from processors and retail markets in various states to determine Vibrio vulnificus and V. parahaemolyticus levels. Presence in a 25-g sample and most probable number (MPN) using standard enrichment and selective isolation procedures were utilized. Suspect colonies were isolated and identified using DNA probe colony hybridization. Neither species of vibrio was detected in 25-g portions of most samples regardless of the PHP. The lowest frequency of isolation of either pathogen (<10%) was observed with the mild heat process. Few (12 to 13%) frozen samples collected at the processor but not at retail contained >30 MPN/g of either pathogen. The mean levels of either organism in PHP oysters observed in the present study were 5 to 6 log less than in unprocessed raw Gulf Coast oysters. Of the 70 V. vulnificus isolates examined, only 5 possessed the putative virulence marker, type B 16S rRNA. Neither the thermostable direct hemolysin (tdh) nor the tdh-related hemolysin (trh) virulence gene was detected in any of the 40 V. parahaemolyticus isolates examined in the present study. These data suggest that if there is any selective advantage to pathogenic strains of V. vulnificus and V. parahaemolyticus, these differences are minimal. These results indicate that all PHP treatments greatly reduce exposure of V. vulnificus and V. parahaemolyticus to raw-oyster consumers. Consequently, these PHP oysters pose a much lower risk of illness to consumers due to these pathogens.

scholarly journals Mutational and Phylogenetic Analyses of the Mycobacterial mbt Gene Cluster

2011 ◽  
Vol 193 (21) ◽  
pp. 5905-5913 ◽  
Author(s):  
S. S. Chavadi ◽  
K. L. Stirrett ◽  
U. R. Edupuganti ◽  
O. Vergnolle ◽  
G. Sadhanandan ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Phylogenetic Analyses

scholarly journals Characterization of the Nodularin Synthetase Gene Cluster and Proposed Theory of the Evolution of Cyanobacterial Hepatotoxins

2004 ◽  
Vol 70 (11) ◽  
pp. 6353-6362 ◽  
Author(s):  
Michelle C. Moffitt ◽  
Brett A. Neilan
Keyword(s):  
Gene Cluster ◽  
Rational Design ◽  
Polyketide Synthase ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Cyanobacterial Bloom ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Microcystin Synthetase

ABSTRACT Nodularia spumigena is a bloom-forming cyanobacterium which produces the hepatotoxin nodularin. The complete gene cluster encoding the enzymatic machinery required for the biosynthesis of nodularin in N. spumigena strain NSOR10 was sequenced and characterized. The 48-kb gene cluster consists of nine open reading frames (ORFs), ndaA to ndaI, which are transcribed from a bidirectional regulatory promoter region and encode nonribosomal peptide synthetase modules, polyketide synthase modules, and tailoring enzymes. The ORFs flanking the nda gene cluster in the genome of N. spumigena strain NSOR10 were identified, and one of them was found to encode a protein with homology to previously characterized transposases. Putative transposases are also associated with the structurally related microcystin synthetase (mcy) gene clusters derived from three cyanobacterial strains, indicating a possible mechanism for the distribution of these biosynthetic gene clusters between various cyanobacterial genera. We propose an alternative hypothesis for hepatotoxin evolution in cyanobacteria based on the results of comparative and phylogenetic analyses of the nda and mcy gene clusters. These analyses suggested that nodularin synthetase evolved from a microcystin synthetase progenitor. The identification of the nodularin biosynthetic gene cluster and evolution of hepatotoxicity in cyanobacteria reported in this study may be valuable for future studies on toxic cyanobacterial bloom formation. In addition, an appreciation of the natural evolution of nonribosomal biosynthetic pathways will be vital for future combinatorial engineering and rational design of novel metabolites and pharmaceuticals.

scholarly journals Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant Escherichia coli Strains from Chicken and Pig Farms in Spain

2010 ◽  
Vol 76 (9) ◽  
pp. 2799-2805 ◽  
Author(s):  
Pilar Cortés ◽  
Vanessa Blanc ◽  
Azucena Mora ◽  
Ghizlane Dahbi ◽  
Jesús E. Blanco ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Phylogenetic Analyses ◽  
Virulence Gene ◽  
E Coli ◽  
Isolation And Characterization ◽  
Zoonotic Risk ◽  
Poultry Farms ◽  
Pig Farms ◽  
Genes Encoding

ABSTRACT To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing Escherichia coli isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms. E. coli isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic E. coli (ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a-ST648-D, producing CTX-M-32. The virulence genes and PFGE profiles of these two groups were very similar to those of clinical human isolates. While further studies are required to determine the true zoonotic potential of these clonal groups, our results emphasize the zoonotic risk posed especially by poultry farms, but also by pig farms, as reservoirs of ESBL- and CMY-2-encoding E. coli.

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