Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences

In this study, genetic diversity of Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey was evaluated based on gene sequence analysis of mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) locus. Six polymorphic sites and seven haplotypes were detected in 47 samples collected from four populations viz., Adiyaman, Birecik, Bismil and Batman. The mean haplotype diversity (h) and nucleotide diversity (π) were calculated as h = 0,6420 and π = 0,00138 respectively. Pairwise FST statistics of different populations were found to be negative, low and were insignificant, indicating gene flow. AMOVA analysis showed Fst = 0.09865 and p = 0.00489, indicating that the populations were isolated. The results of Neutrality tests showed an increase in Adiyaman, Birecik and Bismil populations and a decline in Batman population, all values being statistically insignificant (p>0.05). Three haplotypes determined for mtDNA COI locus in the present study form important data set for genetic diversity of this species.

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Genetic diversity in Brazilian tall coconut populations by microsatellite markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332013000400006 ◽

2013 ◽

Vol 13 (4) ◽

pp. 356-362 ◽

Cited By ~ 4

Author(s):

Francisco Elias Ribeiro ◽

Luc Baudouin ◽

Patricia Lebrun ◽

Lázaro José Chaves ◽

Claudio Brondani ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Cape Verde ◽

Coconut Palm ◽

Different Populations ◽

The Mean ◽

High Level ◽

Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

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Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Genetics Research ◽

10.1017/s0016672307008695 ◽

2007 ◽

Vol 89 (2) ◽

pp. 93-106 ◽

Cited By ~ 37

Author(s):

NOELLE A. BARKLEY ◽

ROB E. DEAN ◽

ROY N. PITTMAN ◽

MING L. WANG ◽

CORLEY C. HOLBROOK ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Data Set ◽

Mini Core Collection ◽

Genomic Ssr ◽

Cultivated Peanut ◽

The Mean ◽

Wild Accessions ◽

Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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Molecular Evaluation of Three Populations of Farafra Sheep in Comparison to Ossimi and Rahmani Sheep Breeds

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun202068060929 ◽

2020 ◽

Vol 68 (6) ◽

pp. 929-936

Author(s):

Talaat Bashandy ◽

Ahmed Hussein ◽

Mohamed Solma ◽

Ayman Kassab ◽

Hatem Hamdon

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Rapd Markers ◽

Rapd Marker ◽

Sheep Breeds ◽

Main Cluster ◽

Ideal Approach ◽

Different Populations ◽

The Mean ◽

Molecular Evaluation

Molecular markers are the most ideal approach to study genetic diversity. Consequently, we utilized both ISSR and RAPD markers to assess genetic diversity and relationships among three different populations of Farafra, Ossimi and Rahmani Egyptian sheep breeds. Both ISSR and RAPD gave moderate polymorphism 41.3% and 48.51%, respectively. Besides, this value was consistent with the moderate value of the mean of polymorphism information content (0.16 and 0.20, respectively). Farafra-F and Farafra-D populations had the highest similarity which was 0.92 for ISSR and 0.90 for the RAPD marker. Furthermore, ISSR and RAPD constructed dendrogram separated all the studied sheep into two main clusters. All the three populations of Farafra breed combined into one main cluster, while the second cluster contained both Rahmani and Ossimi breeds. The used molecular markers were able to discriminate among evaluated sheep and displayed that Farafra breed more closely related to Ossimi than Rahmani breed.

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Genetic Diversity of Tamarixia radiata Populations and Their Associated Endosymbiont Wolbachia Species from China

Agronomy ◽

10.3390/agronomy11102018 ◽

2021 ◽

Vol 11 (10) ◽

pp. 2018

Author(s):

Hafiza Javaria Ashraf ◽

Komivi Senyo Akutse ◽

Irum Mukhtar ◽

Luis Carlos Ramos Aguila ◽

Muhammad Qasim ◽

...

Keyword(s):

Genetic Diversity ◽

Management Strategies ◽

Haplotype Diversity ◽

Single Species ◽

Economic Loss ◽

Parasitism Rate ◽

Candidatus Liberibacter ◽

Citrus Huanglongbing ◽

Coi Sequences ◽

Wsp Gene

Tamarixia radiata is one of the established biocontrol pests against the major Asian citrus psyllid, Diaphorina citri, a vector of Candidatus Liberibacter that is a causal agent of citrus Huanglongbing (HLB) disease. Updated information and regional exploration on biocontrol pests are important elements for effective disease management strategies. In this study, the diversity and parasitism rate of T. radiata populations were evaluated. Due to the importance of the host–parasitoid relationship, the presence of Wolbachia as an endosymbiont was also investigated. The parasitism rate of various T. radiata populations from Ecuador and China ranged between 57.27% and 66.32%, respectively, with a non-significant emergence rate and a statistically similar sex ratio. Sequence analysis of ITS and COI from T. radiata populations was consistent with the morphological hypothesis that the collections represent a single species, whereas phylogeny of the wsp gene confirmed the presence of Wolbachia pipientis as an endosymbiont within T. radiata populations. Based on partial COI sequences, the maximum genetic diversity such as total haplotype diversity (Hd = 0.788), nucleotide, diversity (π = 0.2439), and average nucleotide difference (k = 171.844) was also estimated for different T. radiata populations. Furthermore, neutrality tests based on COI sequences indicated an overall contraction in T. radiata populations, whereas an expansion trend was observed in associated W. pipientis strains. This study clearly demonstrated the presence of genetically diverse T. radiata populations that were able to parasitize D. citri effectively, and these can be further explored as promising biocontrol candidates in integrated pest management strategies to solve citriculture economic loss caused by D. citri.

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Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral Echinopora lamellosa to Bleaching

Journal of Tropical Biodiversity and Biotechnology ◽

10.22146/jtbb.66161 ◽

2021 ◽

Vol 6 (2) ◽

pp. 66161

Author(s):

Imam Bachtiar ◽

Muhammad Irsyad Abiyusfi Ghafari ◽

Ibadur Rahman ◽

Baiq Hilda Astriana

Keyword(s):

Genetic Diversity ◽

Haplotype Diversity ◽

Its Region ◽

Haplotype Network ◽

Restricted Gene Flow ◽

Long Distance ◽

Reproduction Mode ◽

Algal Symbiont ◽

Different Populations ◽

The Stability

Genetic diversity has an important role in the stability of coral populations in coping with disturbances. In the last three bleaching events, the coral Echinopora lamellosa survived better in the eastern- than the western- Lombok waters that are not related to algal symbiont diversity. The present study aimed to assess the genetic diversity of E. lamellosa from the two locations in the Lombok waters. The ITS1-5.8S-ITS2 (whole ITS region) marker was used to identify and to determine the genetic structure, genetic variation, and demographic pattern of E. lamellosa. The results showed that E. lamellosa of the two locations are two different populations. The haplotype diversity was very high indicating a predominance of sexual reproduction mode for both eastern and western populations. The phylogenetic topology suggests there is possible connectivity between populations, whereas the haplotype network exhibits a restricted gene flow between the two populations. The results suggest that the present E. lamellosa populations were from both surviving colonies and new recruitment of long-distance larvae. Both population likely shares the same larvae supply brought from source-reefs in the Flores Sea or Makassar Strait by the Indonesian Throughflow. The present and previous studies revealed that genetic diversity alone yet to explain the resistance of E. lamellosa in eastern and western Lombok waters.

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Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

ZooKeys ◽

10.3897/zookeys.911.39222 ◽

2020 ◽

Vol 911 ◽

pp. 139-160 ◽

Cited By ~ 1

Author(s):

Shyama Sundari Devi Chanthran ◽

Phaik-Eem Lim ◽

Yuan Li ◽

Te-Yu Liao ◽

Sze-Wan Poong ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Genetic ◽

Haplotype Diversity ◽

Dispersal Ability ◽

Human Consumption ◽

Stock Management ◽

Genetic Structuring ◽

Migration Ability ◽

Mtdna Coi

A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

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Genetic structure of populations of several endangered and endemic Dianthus species revealed by microsatellite markers

Acta Botanica Croatica ◽

10.2478/botcro-2018-0022 ◽

2018 ◽

Vol 77 (2) ◽

pp. 181-188 ◽

Cited By ~ 1

Author(s):

Anca Butiuc-Keul ◽

Cornelia Crăciunaș ◽

Irina Goia ◽

Anca Farkas ◽

Liliana Jarda ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Genetic Structure Of Populations ◽

Ssr Loci ◽

Different Populations ◽

The Mean ◽

Simple Sequence

Abstract In order to develop a proper conservation programme for several endangered, rare or endemic species of Dianhtus from Romania, molecular characterization by simple sequence repeat (SSR) markers has been accomplished. Amplification of SSR loci in individuals belonging to different populations of D. callizonus, D. glacialis ssp. gelidus, D. henteri, D. nardiformis and D. tenuifolius revealed 23 polymorphic alleles. D. callizonus and D. tenuifolius showed particular sets of SSR alleles. D. glacialis ssp. gelidus, D. henteri and D. nardiformis proved to share almost the same alleles in most of the loci. The highest genetic diversity was observed in D. glacialis ssp. gelidus and D. tenuifolius in locus MS-DINMADSBOX. Allelic patterns across Dianthus species indicate that the mean number of different alleles was highest in D. glacialis ssp. gelidus, while the number of effective alleles was highest in D. tenuifolius. There are no particular differences in individuals belonging to the same species. Genetic diversity is generally low, ranging from 0.18 (D. callizonus) to 0.44 (D. henteri). Regarding the genetic diversity within populations of the same species, no differences were revealed by the use of the SSR markers tested in the present study.

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Genetic Diversity Analysis of Surface-Related Antigen (SRA) in Plasmodium falciparum Imported From Africa to China

Frontiers in Genetics ◽

10.3389/fgene.2021.688606 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bo Yang ◽

Hong Liu ◽

Qin-Wen Xu ◽

Yi-Fan Sun ◽

Sui Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Amino Acid ◽

Migrant Workers ◽

Vaccine Development ◽

Vaccine Candidate ◽

Haplotype Diversity ◽

Low Genetic Diversity ◽

Neutrality Tests ◽

Unique Amino Acid

Plasmodium falciparum surface-related antigen (SRA) is located on the surfaces of gametocyte and merozoite and has the structural and functional characteristics of potential targets for multistage vaccine development. However, little information is available regarding the genetic polymorphism of pfsra. To determine the extent of genetic variation about P. falciparum by characterizing the sra sequence, 74 P. falciparum samples were collected from migrant workers who returned to China from 12 countries of Africa between 2015 and 2019. The full length of the sra gene was amplified and sequenced. The average pairwise nucleotide diversities (π) of P. falciparum sra gene was 0.00132, and the haplotype diversity (Hd) was 0.770. The average number of nucleotide differences (k) for pfsra was 3.049. The ratio of non-synonymous (dN) to synonymous (dS) substitutions across sites (dN/dS) was 1.365. Amino acid substitutions of P. falciparum SRA could be categorized into 35 unique amino acid variants. Neutrality tests showed that the polymorphism of PfSRA was maintained by positive diversifying selection, which indicated its role as a potential target of protective immune responses and a vaccine candidate. Overall, the ability of the N-terminal of PfSRA antibodies to evoke inhibition of merozoite invasion of erythrocytes and conserved amino acid at low genetic diversity suggest that the N-terminal of PfSRA could be evaluated as a vaccine candidate against P. falciparum infection.

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Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

Diversity ◽

10.3390/d13120654 ◽

2021 ◽

Vol 13 (12) ◽

pp. 654

Author(s):

Jian-Feng Huang ◽

Clive T. Darwell ◽

Yan-Qiong Peng

Keyword(s):

Genetic Diversity ◽

Human Activity ◽

Spatial Genetic Structure ◽

Haplotype Diversity ◽

Habitat Destruction ◽

Phylogeographic Structure ◽

Data Set ◽

Chloroplast Haplotype ◽

Nuclear Microsatellite ◽

Extinction Events

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.

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