scholarly journals Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes

2014 ◽  
Vol 81 (3) ◽  
pp. 966-975 ◽  
Author(s):  
Kun Cheng ◽  
Xiaoying Rong ◽  
Adrián A. Pinto-Tomás ◽  
Marcela Fernández-Villalobos ◽  
Catalina Murillo-Cruz ◽  
...  
Keyword(s):  
Population Structure ◽  
Homologous Recombination ◽  
Population Genetic ◽  
Microbial Evolution ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Streptomyces Albidoflavus ◽  
Phylogenetic Discordance ◽  
Great Sense ◽  
Ecological Difference

ABSTRACTExamining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains ofStreptomyces albidoflavusderived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected inS. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination withinStreptomycesspecies. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred forS. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.

scholarly journals First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India

2018 ◽  
Vol 6 (22) ◽  
Author(s):  
Ritesh Mishra ◽  
Basavaprabhu L. Patil
Keyword(s):  
Nucleotide Sequence Identity ◽  
Population Genetic ◽  
Virus Isolate ◽  
Ringspot Virus ◽  
Papaya Ringspot Virus ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Northeastern Region ◽  
Sequence Identity ◽  
French Isolate

ABSTRACT This is the first report of a Papaya ringspot virus (PRSV) isolate from the northeastern region of India. The nucleotide sequence identity of PRSV-Meghalaya was in the range of 72.6 to 82.5% with other Indian PRSV isolates, and the highest identity of 84.4% was with a French isolate. Population genetic analysis indicated positive selection.

scholarly journals Population structure in the Neisseria , and the biological significance of fuzzy species

2011 ◽  
Vol 9 (71) ◽  
pp. 1208-1215 ◽  
Author(s):  
Jukka Corander ◽  
Thomas R. Connor ◽  
Clíona A. O'Dwyer ◽  
J. Simon Kroll ◽  
William P. Hanage
Keyword(s):  
Population Structure ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Vaccine Development ◽  
Sequence Data ◽  
Genetic Material ◽  
Biological Significance ◽  
Population Genetic Analysis ◽  
Uniform Manner ◽  
Complex Forms

Phenotypic and genetic variation in bacteria can take bewilderingly complex forms even within a single genus. One of the most intriguing examples of this is the genus Neisseria , which comprises both pathogens and commensals colonizing a variety of body sites and host species, and causing a range of disease. Complex relatedness among both named species and previously identified lineages of Neisseria makes it challenging to study their evolution. Using the largest publicly available collection of bacterial sequence data in combination with a population genetic analysis and experiment, we probe the contribution of inter-species recombination to neisserial population structure, and specifically whether it is more common in some strains than others. We identify hybrid groups of strains containing sequences typical of more than one species. These groups of strains, typical of a fuzzy species, appear to have experienced elevated rates of inter-species recombination estimated by population genetic analysis and further supported by transformation experiments. In particular, strains of the pathogen Neisseria meningitidis in the fuzzy species boundary appear to follow a different lifestyle, which may have considerable biological implications concerning distribution of novel resistance elements and meningococcal vaccine development. Despite the strong evidence for negligible geographical barriers to gene flow within the population, exchange of genetic material still shows directionality among named species in a non-uniform manner.

scholarly journals Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Rob J. L. Willems ◽  
Janetta Top ◽  
Willem van Schaik ◽  
Helen Leavis ◽  
Marc Bonten ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Enterococcus Faecium ◽  
Population Genetic ◽  
Effective Control ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Sequence Types ◽  
Insight Into

ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. IMPORTANCE Multiresistant Enterococcus faecium has become one of the most important nosocomial pathogens, causing increasing numbers of nosocomial infections worldwide. Here, we used Bayesian population genetic analysis to identify groups of related E. faecium strains and show a significant association of hospital and farm animal isolates to different genetic groups. We also found that hospital isolates could be divided into three lineages originating from sequence types (STs) 17, 18, and 78. We propose that, driven by the selective pressure in hospitals, the three hospital lineages have arisen through horizontal gene transfer, but once adapted to the distinct pathogenic niche, this population has become isolated and recombination with other populations declines. Elucidation of the population structure is a prerequisite for effective control of multiresistant E. faecium since it provides insight into the processes that have led to the progressive change of E. faecium from an innocent commensal to a multiresistant hospital-adapted pathogen.

scholarly journals mSphere of Influence: the Wild Genetic Diversity of Our Closest Yeast Companions

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Douda Bensasson
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Natural Variation ◽  
Field Survey ◽  
Population Genomics ◽  
Yeast Species ◽  
Natural Environments ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Wild Yeast

ABSTRACT Douda Bensasson uses the population genomics of model yeast species to understand how wild yeast colonize new environments, such as humans or their food. In this mSphere of Influence article, she reflects on how the discovery of “Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity” (Q.-M. Wang, W.-Q. Liu, G. Liti, S.-A. Wang, and F.-Y. Bai, Mol Ecol 21:5404–5417, 2012, https://doi.org/10.1111/j.1365-294X.2012.05732.x) showed that a field survey and population genetic analysis of old growth forests could “unveil the hidden part of the iceberg” of natural variation in S. cerevisiae that went unnoticed for over a hundred years of yeast research.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

Multilocus sequence typing and clonal population genetic structure ofCyclospora cayetanensisin humans

Parasitology ◽  
2017 ◽  
Vol 144 (14) ◽  
pp. 1890-1897 ◽  
Author(s):  
JUNQIANG LI ◽  
YANKAI CHANG ◽  
KE SHI ◽  
RONGJUN WANG ◽  
KANDA FU ◽  
...  
Keyword(s):  
Population Structure ◽  
Urban Areas ◽  
Population Genetic ◽  
Age Groups ◽  
Small Subunit ◽  
Central China ◽  
Population Genetic Analysis ◽  
Clonal Population ◽  
Population Structure Analysis ◽  
Clonal Population Structure

SUMMARYTo investigate the prevalence ofCyclospora cayetanensisin a longitudinal study and to conduct a population genetic analysis, fecal specimens from 6579 patients were collected during the cyclosporiasis – prevalent seasons in two urban areas of central China in 2011–2015. The overall incidence ofC. cayetanensisinfection was 1·2% (76/6579): 1·6% (50/3173) in Zhengzhou and 0·8% (26/3406) in Kaifeng (P< 0·05), with infections in all age groups (P> 0·05). All the isolates clustered in theC. cayetanensisclade based on the small subunit ribosomal RNA gene sequence phylogenetic analysis. There were 45 specimens positive for all the fiveC. cayetanensismicrosatellite loci, and formed 29 multilocus genotypes (MLGs). The phylogenetic relationships of 54 distinct MLGs (including 25 known reference MLGs), based on the concatenated multilocus sequences, formed three main clusters. A population structure analysis showed that the 79 isolates (including 34 known reference isolates) ofC. cayetanensisproduced three distinct subpopulations based on allelic profile data. In conclusion, we determined the frequency ofC. cayetanensisinfection in humans in Henan Province. The clonal population structure of the humanC. cayetanensis isolates showed linkage disequilibrium and three distinct subpopulations.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

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