Ancylostoma ceylanicum: The Neglected Zoonotic Parasite of Community Dogs in Thailand and Its Genetic Diversity among Asian Countries

Ancylostoma ceylanicum is a zoonotic helminth that is commonly found in domestic dogs and cats throughout Asia but is largely neglected in many countries. This study aimed to confirm the species of hookworm in dogs and soil environments and investigate the evolutionary analyses of A. ceylanicum among Thai and Asian populations. In a total of 299 dog fecal samples and 212 soil samples from 53 temples, the prevalence rates of hookworm infection by microscopic examination were 26.4% (79/299) and 10.4% (22/212) in dog and soil samples, respectively. A PCR-RFLP targeting the ITS region was then utilized to identify the hookworm species. In dogs, A. ceylanicum was the main hookworm species, and the rates of A. ceylanicum and A. caninum infections were 96.6% and 3.5%, respectively. The genetic characterization and diversity indices of the A. ceylanicumcox1 gene among Thai and Asian populations were evaluated. Nine haplotypes were identified from Thai A. ceylanicum, in which the haplotype diversity and the nucleotide diversity were 0.4436 and 0.0036, respectively. The highest nucleotide diversity of Chinese A. ceylanicum populations suggested that it could be the ancestor of the populations. Pairwise fixation indices indicated that Thai A. ceylanicum was closely related to the Malaysian population, suggesting a gene flow between these populations. The temples with hookworm-positive dogs were associated with the presence of hookworm-contaminated soil, as these levels showed an approximately four-fold increase compared with those in temples with hookworm-negative dogs (OR = 4.38, 95% CI: 1.55–12.37). Interestingly, the genotypes of A. ceylanicum in the contaminating soil and infecting dogs were identical. Therefore, increased awareness and concern from the wider public communities with regard to the responsibility of temples and municipal offices to provide proper deworming programs to community dogs should be strongly endorsed to reduce the risk of the transmission of this zoonotic disease. In addition, parasitic examination and treatment should be strongly implemented before dogs are imported and exported worldwide.

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Gene Genealogies Reveal High Nucleotide Diversity and Admixture Haplotypes Within Three Alternaria Species Associated with Tomato and Potato

Phytopathology ◽

10.1094/phyto-12-19-0487-r ◽

2020 ◽

Vol 110 (8) ◽

pp. 1449-1464

Author(s):

Tika B. Adhikari ◽

Thomas Ingram ◽

Dennis Halterman ◽

Frank J. Louws

Keyword(s):

Nucleotide Diversity ◽

Genetic Relationships ◽

Haplotype Diversity ◽

Population Expansion ◽

Its Region ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Alternaria Species ◽

Neutrality Tests ◽

Species Specific

Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. alternata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson’s theta were higher in A. alternata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. alternata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. alternata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlH1 to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaH1, AsAlH2/AsAlH3, and AsAlH4 and consisted exclusively of A. alternata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp.

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Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

Acrocephalus ◽

10.1515/acro-2019-0004 ◽

2019 ◽

Vol 40 (180-181) ◽

pp. 69-78

Author(s):

Ida Svetličić ◽

Jelena Kralj ◽

Miloš Martinović ◽

Davorin Tome ◽

Tilen Basle ◽

...

Keyword(s):

Genetic Diversity ◽

Control Region ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Mitochondrial Control Region ◽

Diversity Indices ◽

Common Tern ◽

Sterna Hirundo ◽

Mitochondrial Dna Control Region ◽

High Level

Abstract63 Common Tern Sterna hirundo samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.

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Antifungal activity of several isolates of Trichoderma against Cladosporium and Botrytis

Ukrainian Journal of Ecology ◽

10.15421/2018_191 ◽

2018 ◽

Vol 8 (1) ◽

pp. 88-91 ◽

Cited By ~ 1

Author(s):

M. Skaptsov ◽

S. Smirnov ◽

M. Kutsev ◽

O. Uvarova ◽

T. Sinitsyna ◽

...

Keyword(s):

Antifungal Activity ◽

Trichoderma Harzianum ◽

Its Region ◽

Botanical Garden ◽

Antagonistic Activity ◽

Antagonistic Effect ◽

Soil Samples ◽

Morphological Observation ◽

The South

Trichoderma isolates (SSBGT07, SSBGT08, SSBGT09, SSBGT10) were isolated from the soil samples of the South-Siberian Botanical Garden and identified using morphological observation and ITS region analysis as Trichoderma harzianum, T. asperellum, T. ghanense, and T. longibranchiatum. Antagonistic activity against Cladosporium sp. and Botrytis sp. was evaluated in vitro. All isolates showed antagonistic effect by competition against Cladosporium sp. T. asperellum and T. longibranchiatum showed antagonism against Botrytis sp. All isolates showed hyper sporulation on the sclerotia of Botrytis sp. (except the T. ghanense) and colonies of the Cladosporium sp. Our study provides new isolates that affect the Cladosporium sp. and Botrytis sp.

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Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221020 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

ABDUL BASITH ◽

Abinawanto Abinawanto ◽

ENI KUSRINI ◽

YASMAN YASMAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Phylogenetic Reconstruction ◽

Partial Sequence ◽

Diversity Analysis ◽

Epinephelus Coioides ◽

Substitution Model ◽

Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

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Fungal diversity in high Andean ecuadorian forest soil

10.22541/au.161546623.36028736/v1 ◽

2021 ◽

Author(s):

Adrian Valdez ◽

Sergio Covarrubias

Keyword(s):

Fungal Diversity ◽

High Performance ◽

Its Region ◽

Taxonomic Composition ◽

Soil Samples ◽

Fungal Communities ◽

Gallery Forest ◽

Volcanic Soils ◽

Altitudinal Gradients ◽

The Andes

The Andes range in Ecuador presents high biodiversity and characteristic altitudinal gradients, which are frequently threatened by deforestation and farming. In particular, forest have developed in the high inter-Andean alley on volcanic soils forming a unique ecoregion. Little is known on the fungal biodiversity of soil in such high Andean gallery forest submitted to strong degradation pressures. Therefore, in this study we evaluated wether the soil mycobiome was associated with altitudinal gradients during the dry season. Three representative locations were selected based on altitude: A (3,309 meters above the sea level, masl), B (3,809 masl) and C (4,409 masl). High performance sequencing (NGS) of the ITS region of ribosomal DNA genes with Illumina technology was used to explore the fungal taxonomic composition in the soil samples. Our results showed changes in the structure of fungal communities in the different locations, related to the relative abundance of Amplicon Sequence Variants (ASV). Higher fungal diversity was related with the altitudinal gradient with average taxa ranging from 675, 626 and 556 ASVs, respectively from location A to C. The results highlight the complexity and diversity of fungal communities in high Andean forest and the need to protect these unique mycobiomes. The findings in this ecosystem of Ecuador will improve our understanding of distribution, diversity, ecology, and biological perspectives for the restoration of terrestrial microbiomes.

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Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000100013 ◽

2000 ◽

Vol 23 (1) ◽

pp. 71-78 ◽

Cited By ~ 13

Author(s):

Vera Margarete Scarpassa ◽

Silvia Geurgas ◽

Ana Maria L. Azeredo-Espin ◽

Wanderli Pedro Tadei

Keyword(s):

Mitochondrial Dna ◽

Genetic Divergence ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Sequence Divergence ◽

Brazilian Amazon ◽

Restriction Endonucleases ◽

Separate Species ◽

Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

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Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Genome ◽

10.1139/gen-2014-0039 ◽

2014 ◽

Vol 57 (4) ◽

pp. 239-244 ◽

Cited By ~ 1

Author(s):

Xifeng Ren ◽

Yonggang Wang ◽

Songxian Yan ◽

Dongfa Sun ◽

Genlou Sun

Keyword(s):

Population Genetics ◽

Phylogenetic Analysis ◽

Genetic Variation ◽

Hordeum Vulgare ◽

Nucleotide Diversity ◽

Wild Barley ◽

Haplotype Diversity ◽

Lateral Spikelet ◽

Cultivated Barley ◽

Barley Population

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

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A minimalist macroparasite diversity in the round goby of the Upper Rhine reduced to an exotic acanthocephalan lineage

Parasitology ◽

10.1017/s0031182017002177 ◽

2017 ◽

Vol 145 (8) ◽

pp. 1020-1026 ◽

Cited By ~ 9

Author(s):

Gwendoline M. David ◽

Cybill Staentzel ◽

Olivier Schlumberger ◽

Marie-Jeanne Perrot-Minnot ◽

Jean-Nicolas Beisel ◽

...

Keyword(s):

Western Europe ◽

Nucleotide Diversity ◽

Round Goby ◽

Haplotype Diversity ◽

Neogobius Melanostomus ◽

Molecular Barcoding ◽

Wide Range ◽

Using Data ◽

Upper Rhine ◽

Invasion Corridor

AbstractThe round goby, Neogobius melanostomus, is a Ponto-Caspian fish considered as an invasive species in a wide range of aquatic ecosystems. To understand the role that parasites may play in its successful invasion across Western Europe, we investigated the parasitic diversity of the round goby along its invasion corridor, from the Danube to the Upper Rhine rivers, using data from literature and a molecular barcoding approach, respectively. Among 1666 parasites extracted from 179 gobies of the Upper Rhine, all of the 248 parasites barcoded on the c oxidase subunit I gene were identified as Pomphorhynchus laevis. This lack of macroparasite diversity was interpreted as a loss of parasites along its invasion corridor without spillback compensation. The genetic diversity of P. laevis was represented by 33 haplotypes corresponding to a haplotype diversity of 0·65 ± 0·032, but a weak nucleotide diversity of 0·0018 ± 0·00015. Eight of these haplotypes were found in 88·4% of the 248 parasites. These haplotypes belong to a single lineage so far restricted to the Danube, Vistula and Volga rivers (Eastern Europe). This result underlines the exotic status of this Ponto-Caspian lineage in the Upper Rhine, putatively disseminated by the round goby along its invasion corridor.

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Population genetics and phylogeography of the blue rockfish (Sebastes mystinus) from Washington to California

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f04-008 ◽

2004 ◽

Vol 61 (3) ◽

pp. 332-342 ◽

Cited By ~ 41

Author(s):

Jason M Cope

Keyword(s):

Nucleotide Diversity ◽

Haplotype Diversity ◽

The United States ◽

Genetic Distances ◽

Mitochondrial Dna Control Region ◽

Full Sequence ◽

Biogeographic Barrier ◽

To Come ◽

Sebastes Mystinus ◽

North And South

Blue rockfish (Sebastes mystinus) are a major component of nearshore ecology and fisheries on the west coast of the United States, but the extent of spatial structuring between localized populations is unknown. I sampled 245 blue rockfish at eight locations from Washington to California and sequenced a 498 base pair portion of the mitochondrial DNA control region to describe genetic diversity, population structure, and phylogeography. Haplotype diversity was high, but nucleotide diversity was low, indicating historically unstable population dynamics. Significantly high levels of population differentiation were detected among sample sites (maximum pairwise FST: full sequence = 0.25, reduced sequence = 0.74, P < 0.001), with a distinct break (ΦCT: full sequence = 0.12; reduced sequence = 0.36, P < 0.05) north and south of Cape Mendocino and no overall trend between geographic and genetic distances. Cape Mendocino may prove an important biogeographic barrier to other marine organisms, but it has not been extensively explored as such. The northern subpopulation derived from the southern subpopulation, but little contact has been made between the populations for potentially thousands of years. Therefore, repopulation of a depleted southern subpopulation is unlikely to come from the less-fished northern subpopulation.

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