scholarly journals Genetic Diversity ofEchinococcus granulosusin Southwest China Determined by the Mitochondrial NADH Dehydrogenase Subunit 2 Gene

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Jiahai Wang ◽  
Ning Wang ◽  
Dandan Hu ◽  
Xiuqin Zhong ◽  
Shuxian Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nadh Dehydrogenase ◽  
Southwest China ◽  
Genetic Relationships ◽  
Sensu Stricto ◽  
Control Measures ◽  
Nadh Dehydrogenase Subunit ◽  
High Genetic Diversity ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Genetic Diversity And Structure

We evaluated genetic diversity and structure ofEchinococcus granulosusby analyzing the complete mitochondrial NADH dehydrogenase subunit 2 (ND2) gene in 51 isolates ofE. granulosus sensu strictometacestodes collected at three locations in this region. We detected 19 haplotypes, which formed a distinct clade with the standard sheep strain (G1). Hence, all 51 isolates were identified asE. granulosus sensu stricto(G1–G3). Genetic relationships among haplotypes were not associated with geographical divisions, and fixation indices (Fst) among sampling localities were low. Hence, regional populations ofE. granulosusin the southwest China are not differentiated, as gene flow among them remains high. This information is important for formulating unified region-wide prevention and control measures. We found large negative Fu’s Fs and Tajima’sDvalues and a unimodal mismatch distribution, indicating that the population has undergone a demographic expansion. We observed high genetic diversity among theE. granulosus s. s.isolates, indicating that the parasite population in this important bioregion is genetically robust and likely to survive and spread. The data from this study will prove valuable for future studies focusing on improving diagnosis and prevention methods and developing robust control strategies.

scholarly journals Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates

2020 ◽  
Author(s):  
Musab M Ali. Albsheer ◽  
Eyoab Iyasu Gebremeskel ◽  
Daniel Kepple ◽  
Eugenia Lo ◽  
Virginie Rougeron ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Plasmodium Vivax ◽  
Genetic Relationships ◽  
Regional Scale ◽  
Principal Component ◽  
Control Measures ◽  
Effective Control ◽  
High Genetic Diversity ◽  
Geographical Isolates

AbstractPlasmodium vivax malaria is a neglected tropical disease in Africa due to low occurrence rates and lack of accurate diagnosis. Recently, there has been a dramatic increase in P. vivax cases in East Africa and reportedly spreading to western countries. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan by 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two districts, New Halfa and Khartoum in Sudan. In addition, data from 841 geographical samples retrieved from the database for global genetic analysis were included in the analysis to further the genetic relationships among the P. vivax isolates at regional and worldwide scales. On a regional scale, we observed 91 unique and 8 shared haplotypes amongst the Sudan samples. Such a high genetic diversity compared to other geographical isolates lends support to hypothesis that P. vivax was originated from Africa. On a global scale, as already demonstrated, we observed distinct genetic clustering of P. vivax isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) with limited admixture in all three clusters. The principal component analysis and phylogenetic tree showed similar clustering patterns and highlighted the contribution of the African isolates to the genetic variation observed globally. The East African P. vivax showed similarity with some of the Asian isolates suggesting potential recent introductions. Our results show extensive genetic diversity co-occurring with significant multi-locus linkage disequilibrium, demonstrating the effectiveness of using microsatellite markers to implement effective control measures.

Departure from Neutrality at the Mitochondrial NADH Dehydrogenase Subunit 2 Gene in Humans, but Not in Chimpanzees

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 409-421 ◽  
Author(s):  
Cheryl A Wise ◽  
Michaela Sraml ◽  
Simon Easteal
Keyword(s):  
Nadh Dehydrogenase ◽  
Statistical Tests ◽  
Low Frequency ◽  
Nadh Dehydrogenase Subunit ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Tests Of Neutrality ◽  
Slightly Deleterious Mutations ◽  
Neutral Marker ◽  
Transmembrane Regions ◽  
Interspecific Comparisons

Abstract To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as Tajima's D test, and the D and F tests proposed by Fu and Li, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a “neutral” marker in evolutionary and population genetic studies.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

scholarly journals Genetic Diversity and Structure of Latvian Tilia cordata Populations

2021 ◽  
Vol 75 (4) ◽  
pp. 261-267
Author(s):  
Dainis Edgars Ruņģis ◽  
Baiba Krivmane
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Vegetative Reproduction ◽  
Growth Conditions ◽  
Climatic Conditions ◽  
Tilia Cordata ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Broadleaf Tree ◽  
Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

scholarly journals Molecular Characterization of Echinococcus granulosus sensu lato from Humans in Slovenia

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 562
Author(s):  
Barbara Šoba ◽  
Špela Gašperšič ◽  
Darja Keše ◽  
Tadeja Kotar
Keyword(s):  
Molecular Characterization ◽  
Echinococcus Granulosus ◽  
Nadh Dehydrogenase ◽  
Sensu Stricto ◽  
Intermediate Hosts ◽  
Western Balkans ◽  
Nadh Dehydrogenase Subunit ◽  
Important Intermediate ◽  
Echinococcus Granulosus Sensu Lato

The larval form of tapeworms of the Echinococcus granulosus sensu lato species cluster cause an important zoonotic infection, cystic echinococcosis (CE). Molecular characterization of the cluster’s isolates from different hosts greatly contributes to a better understanding of its transmission dynamics. To date, no genetic information is available on CE in Slovenia. In this work, we characterized isolates from human CE cases. Parasite samples from 18 patients were collected, together with the patients’ demographic and clinical data. Genomic DNA was analyzed by conventional PCR and sequencing at four mitochondrial loci (cytochrome c oxidase subunit 1, cox1; NADH dehydrogenase subunit 1, nad1; NADH dehydrogenase subunit 5, nad5; and small ribosomal RNA, rrnS). Thirteen isolates were successfully amplified and sequenced. Seven (58.8%) patients were infected with E. granulosus sensu stricto (s.s.) G1, five (38.5%) with E. canadensis G7 and one (7.7%) with E. granulosus s.s. G3. Echinococcus canadensis G7, the pig genotype, was identified exclusively in autochthonous Slovenes, while the patients originating from the Western Balkans were all infected with E. granulosus s.s. Our findings suggest that pigs are important intermediate hosts for human CE in Slovenia.

scholarly journals Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Evânia Galvão Mendonça ◽  
Anderson Marcos de Souza ◽  
Fábio de Almeida Vieira ◽  
Regiane Abjaud Estopa ◽  
Cristiane Aparecida Fioravante Reis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Rio Grande ◽  
Shannon Index ◽  
High Genetic Diversity ◽  
Family Structures ◽  
Genetic Diversity And Structure ◽  
Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

scholarly journals The pine wood nematode, Bursaphelenchus xylophilus, in Portugal: possible introductions and spread routes of a serious biological invasion revealed by molecular methods

Nematology ◽  
2012 ◽  
Vol 14 (8) ◽  
pp. 899-911 ◽  
Author(s):  
Vera Valadas ◽  
Marta Laranjo ◽  
Pedro Barbosa ◽  
Margarida Espada ◽  
Manuel Mota ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Bursaphelenchus Xylophilus ◽  
Rrna Gene ◽  
Natural Ecosystem ◽  
Pine Wood Nematode ◽  
Northern Spain ◽  
High Genetic Diversity ◽  
Geographic Locations ◽  
Pine Wood

The pine wood nematode (PWN), Bursaphelenchus xylophilus, the causal agent of pine wilt disease (PWD), is a major world-wide pathogen and pest of pine, with impacts on forest health, natural ecosystem stability and international trade. In Portugal, PWN was first diagnosed in 1999, the first occurrence also for Europe. The disease was recently detected on the island of Madeira and in northern Spain. In an attempt to search for more reliable and robust molecular markers that enable the study of intraspecific variability of B. xylophilus from different geographic locations, the intergenic spacer (IGS) region of the 5S rRNA gene and inter-simple sequence repeats (ISSR) analysis were used to determine the genetic relationships among 43 B. xylophilus isolates from Portugal, China, Japan, South Korea and USA. IGS sequence analysis showed that this region can only be used to establish interspecific relationships, since no differences were detected among Portuguese isolates from different geographic locations. Fingerprints obtained with ISSR show high genetic variability among Portuguese isolates, except for the ones obtained prior to 2008. The ISSR dendrogram suggests the spread of the disease inside continental Portugal and to Madeira. Until 2008, B. xylophilus populations found in continental Portugal showed low genetic diversity, pointing to a single introduction, probably from Asia, whereas recent populations from continental Portugal (2009-2010) and Madeira show high genetic diversity, suggesting multiple introductions from different origins.

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