Haplotype Diversity and Reconstruction of Ancestral Haplotype Associated with the c.35delG Mutation in the GJB2 (Cx26) Gene among the Volgo-Ural Populations of Russia

Acta Naturae ◽  
2011 ◽  
Vol 3 (3) ◽  
pp. 52-63 ◽  
Author(s):  
L U Dzhemileva ◽  
O L Posukh ◽  
N A Barashkov ◽  
S A Fedorova ◽  
F M Teryutin ◽  
...  
Keyword(s):  
Haplotype Diversity ◽  
Ancestral Haplotype ◽  
35Delg Mutation

scholarly journals Study on Genetic Diversity of Phellodendron amurense based on cpDNA

2021 ◽  
Vol 271 ◽  
pp. 03059
Author(s):  
Hongsheng Yang ◽  
Donghong Yang ◽  
Xuewen Yang ◽  
Qingbo Zhou ◽  
Haitao Cheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Northeast China ◽  
Mismatch Distribution ◽  
Nucleotide Diversity ◽  
North China ◽  
Haplotype Diversity ◽  
Common Origin ◽  
Ancestral Haplotype ◽  
Phellodendron Amurense ◽  
Tajima’S D

In this study, 3 haplotypes were found in populations of Phellodendron amurense based on two combined cpDNA regions (psbA-trnH and trnT-trnL). Nucleotide diversity and haplotype diversity were 0.43×10-3 and 0.41, respectively at the level of species. The AMOVA revealed that only 8.53% of the variation was explained by differences among geographical groups, whereas inter-population and intrapopulation differences explained 18.32% and 71.35% of the variation, respectively. Phylogeographical relationships showed that all haplotypes were clustered into two lineages. Haplotype H1 and H2 cluster together, and Haplotype H3 composed a group. TCS network of haplotypes showed that haplotype H1 located in the center of the lineage, and it appears to be an ancestral haplotype. So we hypothesized that Northeast China populations and North China populations had a common origin. The mismatch distribution of this species suggested that all populations and populations in North China had not undergone recent expansion, but populations in Northeast China had undergone recent expansion. The results were consistent with the results of Tajima’s D and Fu’s and Li’s D test.

scholarly journals Sequence analysis of Plasmodium vivax Duffy binding proteins reveals the presence of unique haplotypes and diversifying selection in Ethiopian isolates

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Lemu Golassa ◽  
Alebachew Messele ◽  
Eniyou Cheryll Oriero ◽  
Alfred Amambua-Ngwa
Keyword(s):  
Vaccine Development ◽  
Haplotype Diversity ◽  
Sri Lankan ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
South Korean ◽  
Blood Stage Infection ◽  
Vaccine Approach ◽  
Papua New Guinean ◽  
Reference Haplotype

Abstract Background Red blood cell invasion by the Plasmodium vivax merozoite requires interaction between the Duffy antigen receptor for chemokines (DARC) and the P. vivax Duffy-binding protein II (PvDBPII). Given that the disruption of this interaction prevents P. vivax blood-stage infection, a PvDBP-based vaccine development has been well recognized. However, the polymorphic nature of PvDBPII prevents a strain transcending immune response and complicates attempts to design a vaccine. Methods Twenty-three P. vivax clinical isolates collected from three areas of Ethiopia were sequenced at the pvdbpII locus. A total of 392 global pvdbpII sequences from seven P. vivax endemic countries were also retrieved from the NCBI archive for comparative analysis of genetic diversity, departure from neutrality, linkage disequilibrium, genetic differentiation, PvDBP polymorphisms, recombination and population structure of the parasite population. To establish a haplotype relationship a network was constructed using the median joining algorithm. Results A total of 110 variable sites were found, of which 44 were parsimony informative. For Ethiopian isolates there were 12 variable sites of which 10 were parsimony informative. These parsimony informative variants resulted in 10 nonsynonymous mutations. The overall haplotype diversity for global isolates was 0.9596; however, the haplotype diversity was 0.874 for Ethiopia. Fst values for genetic revealed Ethiopian isolates were closest to Indian isolates as well as to Sri Lankan and Sudanese isolates but further away from Mexican, Papua New Guinean and South Korean isolates. There was a total of 136 haplotypes from the 415 global isolates included for this study. Haplotype prevalence ranged from 36.76% to 0.7%, from this 74.2% were represented by single parasite isolates. None of the Ethiopian isolates grouped with the Sal I reference haplotype. From the total observed nonsynonymous mutations 13 mapped to experimentally verified epitope sequences. Including 10 non-synonymous mutations from Ethiopia. However, all the polymorphic regions in Ethiopian isolates were located away from DARC, responsible for junction formation. Conclusion The results of this study are concurrent with the multivalent vaccine approach to design an effective treatment. However, the presence of novel haplotypes in Ethiopian isolates that were not shared by other global sequences warrant further investigation.

scholarly journals Haplotype diversity in the mitochondrial genome of the Egyptian river buffalo (Bubalus bubalis)

2021 ◽  
Vol 6 (1) ◽  
pp. 145-147
Author(s):  
Nouran Adel Youssef ◽  
Manon Curaudeau ◽  
Soheir Mohamed El Nahas ◽  
Amal Ahmed Mohamed Hassan ◽  
Alexandre Hassanin
Keyword(s):  
Mitochondrial Genome ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
River Buffalo

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

scholarly journals perfectphyloR: An R package for reconstructing perfect phylogenies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Charith B. Karunarathna ◽  
Jinko Graham
Keyword(s):  
Binary Tree ◽  
Sequence Data ◽  
R Package ◽  
Binary Sequences ◽  
Ancestral Haplotype ◽  
Perfect Phylogeny ◽  
Nested Partitions ◽  
Genetic Sequence ◽  
Insight Into ◽  
Rooted Binary Tree

Abstract Background A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype. Results We present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package. Conclusion The package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

scholarly journals The myositis clinical phenotype associated with anti-Zo autoantibodies: a case series of nine UK patients

Rheumatology ◽  
2019 ◽  
Vol 59 (7) ◽  
pp. 1626-1631 ◽  
Author(s):  
Sarah L Tansley ◽  
Zoe Betteridge ◽  
Hui Lu ◽  
Emma Davies ◽  
Simon Rothwell ◽  
...  
Keyword(s):  
Interstitial Lung Disease ◽  
Lung Disease ◽  
Interstitial Pneumonia ◽  
Clinical Phenotype ◽  
Disease Onset ◽  
Usual Interstitial Pneumonia ◽  
Trna Synthetase ◽  
Muscle Disease ◽  
Ancestral Haplotype ◽  
Common Finding

Abstract Objectives It has been over 10 years since the first report of autoantibodies directed against phenylalanyl tRNA synthetase (anti-Zo) in a patient with features of the anti-synthetase syndrome. In that time no further cases have been published. Here we aim to characterize more fully the clinical phenotype of anti-Zo–associated myositis by describing the clinical features of nine patients. Methods Anti-Zo was identified by protein-immunoprecipitation in patients referred for extended spectrum myositis autoantibody testing at our laboratory. Results were confirmed by immunodepletion using a reference serum. Medical records were retrospectively reviewed to provide detailed information of the associated clinical phenotype for all identified patients. Where possible, HLA genotype was imputed using Illumina protocols. Results Nine patients with anti-Zo were identified. The median age at disease onset was 51 years, and six patients were female. Seven patients had evidence of inflammatory muscle disease, seven of interstitial lung disease and six of arthritis. The reported pattern of interstitial lung disease varied with usual interstitial pneumonia, non-specific interstitial pneumonia and organizing pneumonia all described. Other features of the anti-synthetase syndrome such as RP and mechanics hands were common. HLA data was available for three patients, all of whom had at least one copy of the HLA 8.1 ancestral haplotype. Conclusion Patients with anti-Zo presenting with features of the anti-synthetase syndrome and interstitial lung disease is a common finding. Like other myositis autoantibodies, there is likely to be a genetic association with the HLA 8.1 ancestral haplotype.

scholarly journals High Intraspecific Genetic Diversity ofNocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Usingsodandhsp65Genes

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
D. Kosova-Maali ◽  
E. Bergeron ◽  
Y. Maali ◽  
T. Durand ◽  
J. Gonzalez ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Characterization ◽  
Haplotype Diversity ◽  
Species Level ◽  
Genotype 1 ◽  
Tropical Regions ◽  
High Bootstrap ◽  
Almost All ◽  
A New Species ◽  
Immunocompetent Patients

This study aims at genetic characterization and phylogenetic relationships ofNocardia brasiliensisfocusing by using housekeepingrrs,hsp65,andsodAgenes.N. brasiliensisis the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases ofN. brasiliensisthat happened in France. Phylogenetic analysis targetingrrsgene showed no robustness at phylogenetic nodes level. However, the use of a concatenation ofhsp65andsodAgenes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) ofhsp65(0.927) andsodA(0.885) genes was higher than that ofrrs(0.824). For this gene, we obtained 16 polymorphic sites whereas, forhsp65andsodAgenes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability ofN. brasiliensisand they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

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