scholarly journals Allelic Diversity and Population Structure in Vibrio cholerae O139 Bengal Based on Nucleotide Sequence Analysis

2002 ◽  
Vol 184 (5) ◽  
pp. 1304-1313 ◽  
Author(s):  
M. Farfán ◽  
D. Miñana-Galbis ◽  
M. C. Fusté ◽  
J. G. Lorén
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Vibrio Cholerae ◽  
Allelic Diversity ◽  
Nucleotide Sequence Analysis ◽  
Intragenic Recombination ◽  
Enzyme Electrophoresis ◽  
Epidemic Period ◽  
The Matrix ◽  
Clonal Population Structure

ABSTRACT Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

scholarly journals Clonal Population Structure of Pseudomonas stutzeri, a Species with Exceptional Genetic Diversity

2001 ◽  
Vol 183 (2) ◽  
pp. 736-744 ◽  
Author(s):  
Núria Rius ◽  
M. Carme Fusté ◽  
Caterina Guasp ◽  
Jorge Lalucat ◽  
José G. Lorén
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Bacterial Species ◽  
Pseudomonas Stutzeri ◽  
Null Alleles ◽  
Enzyme Electrophoresis ◽  
Single Strain ◽  
Multilocus Enzyme Electrophoresis ◽  
Clonal Population Structure

ABSTRACT Genetic diversity and genetic relationships among 42Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, thisP. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (IA ) for the P. stutzeri strains analyzed was 1.10. The IA values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.

scholarly journals Genetic diversity and antibiotic resistance of clinical and environmental Vibrio cholerae suggests that many serogroups are reservoirs of resistance

2004 ◽  
Vol 132 (5) ◽  
pp. 985-992 ◽  
Author(s):  
L. C. CAMPOS ◽  
V. ZAHNER ◽  
K. E. S. AVELAR ◽  
R. M. ALVES ◽  
D. S. G. PEREIRA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Pcr Analysis ◽  
Enzyme Electrophoresis ◽  
South American ◽  
Antibiotic Resistance Profile ◽  
Class 1 ◽  
Pandemic Strains ◽  
Close Genetic Relationship

Vibrio cholerae is an important human pathogen and the cause of cholera. Since genetic variation and antibiotic resistance of strains have implications for effective treatment of the disease, we examined the genetic diversity and antibiotic resistance profile in 92 clinical strains (serogroup O1) and 56 environmental strains (O1 antigen, 42 strains; non-O1 antigen, 14 strains) isolated in Brazil between 1991 and 1999. Clinical and environmental O1 strains showed greater drug resistance compared to environmental non-O1 strains. Nearly all clinical O1 strains were resistant to one or more antibiotics while half of the environmental O1 and non-O1 strains were resistant to one or more antibiotics. No plasmids or class 1 integrons were detected in the strains by PCR analysis. Multilocus enzyme electrophoresis analysis (MLEE) suggests most of the O1 strains belong to a single (South American) clone that is related but different to seventh-pandemic strains isolated from other parts of the world. Our results show that there is a close genetic relationship between clinical and environmental O1 strains and that many serogroups and the environment can be a reservoir for antibiotic resistance.

scholarly journals GENETIC DIFFERENTIATION OF THE KAMPAR RIVER'S GIANT FEATHERBACK (Chitala lopis BLEEKER 1851) BASE ON MITOCHONDRIAL DNA ANALYSIS

2017 ◽  
Vol 16 (2) ◽  
pp. 49 ◽  
Author(s):  
Arif Wibowo ◽  
Ridwan Affandi ◽  
Kadarwan Soewardi ◽  
Sudarto Sudarto
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Dna Analysis ◽  
Nucleotide Sequence Analysis ◽  
Mitochondrial Dna Control Region ◽  
Mitochondrial Dna Analysis ◽  
Important Fish

Although the giant featherback Chitala lopis is an important fish in Kampar River, the population structure has not been investigated. In this study, genetic diversity and population structure of giant featherback were examined using nucleotide sequence analysis of mitochondrial DNA control region for 54 fish collected from Kampar River.

scholarly journals Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 68 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Gyu-Taek Cho ◽  
Do Yoon Hyun
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Research Effort ◽  
Molecular Genetic ◽  
Allelic Diversity ◽  
Perennial Herb ◽  
Molecular Evidence ◽  
Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

scholarly journals Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

2004 ◽  
Vol 70 (12) ◽  
pp. 7210-7219 ◽  
Author(s):  
Blanca de las Rivas ◽  
Ángela Marcobal ◽  
Rosario Muñoz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
The United States ◽  
Oenococcus Oeni ◽  
23S Rrna ◽  
Rrna Gene ◽  
Single Strain

ABSTRACT Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.

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