Molecular diversity of small balsam populations in relation to site characteristics

2013 ◽  
Vol 8 (10) ◽  
pp. 1048-1061 ◽  
Author(s):  
Eugenija Kupcinskiene ◽  
Lina Zybartaite ◽  
Rasa Janulioniene ◽  
Judita Zukauskiene ◽  
Algimantas Paulauskas
Keyword(s):  
Molecular Diversity ◽  
Genetic Distances ◽  
Randomly Amplified Polymorphic Dna ◽  
Multiple Introductions ◽  
Habitat Features ◽  
Site Characteristics ◽  
Impatiens Parviflora ◽  
Geographical Distances ◽  
Favorable Conditions ◽  
Simple Sequence

AbstractClimatic shifts within recent decades created favorable conditions for invasive species flourishing in more Northern parts of Europe. Our study was aimed at evaluation of genetic variability and habitat features of Impatiens parviflora populations growing in Lithuania. Twenty one populations were selected and analysed using simple sequence repeat (SSR) and randomly amplified polymorphic DNA (RAPD) assays. Evaluated by SSRs, 315 individuals were all monomorphic and homozygous at 4 loci and heterozygous at 1 locus. RAPD analyses revealed that the percentage of polymorphic DNA loci (% P) per population ranged from 7 to 39% and genetic differentiation between populations was ΦPT=0.790 (P<0.01). Genetic distances among populations (0.135–0.426) correlated significantly with geographical distances (r=0.183; P<0.008). Populations in overmoistured soil contained higher % P (28.3) when compared to drier soil (18.7; P<0.05). All recorded populations were close to roads; their % P did not depend on proximity to buildings, light intensity or population size. Our RAPD analyses indicate multiple introductions of this species in Lithuania. Analyses of I. parviflora at SSR and RAPD loci show that the invasion process is reflected in genetic structure.

scholarly journals European Impatiens species differences at RAPD and ISSR loci

Biologija ◽  
2016 ◽  
Vol 62 (1) ◽  
Author(s):  
Edita Ramonienė ◽  
Lina Jocienė ◽  
Algimantas Paulauskas ◽  
Eugenija Kupčinskienė
Keyword(s):  
Genetic Differentiation ◽  
Species Differences ◽  
Geographic Area ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genetic Distances ◽  
Molecular Characteristics ◽  
Randomly Amplified Polymorphic Dna ◽  
Rapd And Issr ◽  
Simple Sequence

Information concerning comparison of three widely spread European species of Impatiens along wider geographical areas is still missing. The present study is aimed at comparing genetic variability at RAPD and ISSR loci of Impatiens noli-tangere, I. parviflora, and I. glandulifera, covering a marked geographic area. Twenty four populations of these Impatiens (eight populations of each species) from two countries (Lithuania and Czech Republic) were examined. Eight randomly amplified polymorphic DNA (RAPD) and 5 inter simple sequence repeat (ISSR) markers were chosen considering the lack of data on the general molecular characteristics of Impatiens. The highest genetic differentiation at RAPD loci (GST = 0.81) was characteristic of I. parviflora, and the highest genetic differentiation at ISSR loci (GST = 0.73) was documented for I. glandulifera. According to Nei’s genetic distances between two species populations, significant correlations were determined for I. noli-tangere and I. parviflora (r = 0.79; p 

scholarly journals The evolution of hard tick-borne relapsing fever borreliae is correlated with vector species rather than geographical distance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ranna Nakao ◽  
Kentaro Kasama ◽  
Bazartseren Boldbaatar ◽  
Yoshitoshi Ogura ◽  
Hiroki Kawabata ◽  
...  
Keyword(s):  
Core Gene ◽  
Genetic Distances ◽  
Hard Tick ◽  
Vector Species ◽  
Relapsing Fever ◽  
Strain Isolation ◽  
Ecological Features ◽  
Geographical Distances ◽  
History Of ◽  
Hokkaido Island

Abstract Background Relapsing fever (RF) borreliae are arthropod-borne spirochetes and some of them cause human diseases, which are characterized by relapsing or recurring episodes of fever. Recently, it has been classified into two groups: soft tick-borne RF (STRF) borreliae and hard tick-borne RF (HTRF) borreliae. STRF borreliae include classical RF agents and HTRF borreliae, the latter of which include B. miyamotoi, a human pathogen recently identified in Eurasia and North America. Results In this study, we determined the genome sequences of 16 HTRF borreliae strains: 15 B. miyamotoi strains (9 from Hokkaido Island, Japan, 3 from Honshu Island, Japan, and 3 from Mongolia) and a Borrelia sp. tHM16w. Chromosomal gene synteny was highly conserved among the HTRF strains sequenced in this study, even though they were isolated from different geographic regions and different tick species. Phylogenetic analysis based on core gene sequences revealed that HTRF and STRF borreliae are clearly distinguishable, with each forming a monophyletic group in the RF borreliae lineage. Moreover, the evolutionary relationships of RF borreliae are consistent with the biological and ecological features of each RF borreliae sublineage and can explain the unique characteristics of Borrelia anserina. In addition, the pairwise genetic distances between HTRF borreliae strains were well correlated with those of vector species rather than with the geographical distances between strain isolation sites. This result suggests that the genetic diversification of HTRF borreliae is attributed to the speciation of vector ticks and that this relationship might be required for efficient transmission of HTRF borreliae within vector ticks. Conclusions The results of the present study, together with those from previous investigations, support the hypothesis that the common ancestor of borreliae was transmitted by hard-bodied ticks and that only STRF borreliae switched to using soft-bodied ticks as a vector, which was followed by the emergence of Borrelia recurrentis, lice-borne RF borreliae. Our study clarifies the phylogenetic relationships between RF borreliae, and the data obtained will contribute to a better understanding of the evolutionary history of RF borreliae.

Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 757-763 ◽  
Author(s):  
Shanmukhaswami S. Salimath ◽  
Antonio C. de Oliveira ◽  
Jeffrey L. Bennetzen ◽  
Ian D. Godwin
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Finger Millet ◽  
Dna Marker ◽  
Fragment Length Polymorphism ◽  
Eleusine Coracana ◽  
Randomly Amplified Polymorphic Dna ◽  
Simple Sequence ◽  
Restriction Fragment Length

Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe – 3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.Key words: Eleusine coracana, finger millet, genome analysis, microsatellites, randomly amplified polymorphic DNA, restriction fragment length polymorphism, simple sequence repeats.

scholarly journals Genetic structure and gene flow of Eugenia dysenterica natural populations

2005 ◽  
Vol 40 (10) ◽  
pp. 975-980 ◽  
Author(s):  
Maria Imaculada Zucchi ◽  
José Baldin Pinheiro ◽  
Lázaro José Chaves ◽  
Alexandre Siqueira Guedes Coelho ◽  
Mansuêmia Alves Couto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Variability ◽  
Pearson Correlation ◽  
Natural Populations ◽  
Similarity Index ◽  
Genetic Distances ◽  
Strong Positive Correlation ◽  
Randomly Amplified Polymorphic Dna ◽  
Jaccard Similarity ◽  
Eugenia Dysenterica

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

scholarly journals Biogeography and Independent Diversification in the Protist Symbiont Community of Heterotermes tenuis

2021 ◽  
Vol 9 ◽  
Author(s):  
Francesca De Martini ◽  
Nicole L. Coots ◽  
Daniel E. Jasso-Selles ◽  
Jordyn Shevat ◽  
Alison Ravenscraft ◽  
...  
Keyword(s):  
Regional Differences ◽  
Amplicon Sequencing ◽  
Genetic Distances ◽  
Species Level ◽  
Mantel Tests ◽  
Geographical Distances ◽  
Host Phylogeny ◽  
Single Cell Isolation ◽  
Host Genetic ◽  
Protist Species

The eukaryotic microbiome of “lower” termites is highly stable and host-specific. This is due to the mutually obligate nature of the symbiosis and the direct inheritance of protists by proctodeal trophallaxis. However, vertical transmission is occasionally imperfect, resulting in daughter colonies that lack one or more of the expected protist species. This phenomenon could conceivably lead to regional differences in protist community composition within a host species. Here, we have characterized the protist symbiont community of Heterotermes tenuis (Hagen) (Blattodea: Rhinotermitidae) from samples spanning South and Central America. Using light microscopy, single cell isolation, and amplicon sequencing, we report eight species-level protist phylotypes belonging to four genera in the phylum Parabasalia. The diversity and distribution of each phylotype’s 18S rRNA amplicon sequence variants (ASVs) mostly did not correlate with geographical or host genetic distances according to Mantel tests, consistent with the lack of correlation we observed between host genetic and geographical distances. However, the ASV distances of Holomastigotoides Ht3 were significantly correlated with geography while those of Holomastigotoides Ht1 were significantly correlated with host phylogeny. These results suggest mechanisms by which termite-associated protist species may diversify independently of each other and of their hosts, shedding light on the coevolutionary dynamics of this important symbiosis.

The use of random amplified microsatellite polymorphic DNA and coefficients of parentage to determine genetic relationships in barley

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 477-486 ◽  
Author(s):  
J A Dávila ◽  
M P Sánchez de la Hoz ◽  
Y Loarce ◽  
E Ferrer
Keyword(s):  
Hordeum Vulgare ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Spring Barley ◽  
Genetic Distances ◽  
Mantel Test ◽  
Winter Barley ◽  
Mean Values ◽  
Simple Sequence ◽  
Hordeum Vulgare Ssp

Seventy European barley lines (Hordeum vulgare ssp. vulgare) and 29 Hordeum vulgare ssp. spontaneum accessions were evaluated for random amplified microsatellite polymorphism (RAMP). PCR was performed with 5'-anchored primers complementary to microsatellites in combination with random primers. Of 20 primers assayed in barley, only 9 produced well-resolved fragment patterns in H. vulgare ssp. spontaneum. On the basis of 56 polymorphic fragments, genetic distances between the two subspecies were calculated. Barley samples were subdivided according to growth habit and spike morphology. The smallest genetic distance was found between winter cultivars and accessions of H. vulgare ssp. spontaneum. The 20 primers assayed in the barley lines produced 140 polymorphic fragments that were used to calculate genetic similarity between lines. Mean genetic similarity within groups of lines ranged from 0.693 for 6-rowed winter barley to 0.657 for 6-rowed spring barley. Within these groups, mean values were significantly higher than mean genetic similarity between groups. Principal-coordinate analysis clearly separated the 2-rowed spring and 6-rowed winter types. Cluster analysis of spring and winter types showed subclustering consistent with the available pedigrees. Coefficients of parentage (COPs) were calculated for 29 spring and 20 winter lines. Mean values of 0.0741 for spring barley and 0.0458 for winter barley were obtained. RAMP-based genetic similarity matrices were compared with the corresponding COP-based matrices by the Mantel test. The correlation between them was poor (r = 0.21, P < 0.05), indicating little relationship between these two estimators of genetic similarity. The relative influence of factors involved in the calculation of these two estimators is discussed.Key words: genetic diversity, microsatellites, simple sequence repeats, fingerprinting, barley.

scholarly journals Ampelographic and molecular diversity among grapevine (Vitis spp.) cultivars

2009 ◽  
Vol 45 (No. 4) ◽  
pp. 160-168 ◽  
Author(s):  
A. Sabir ◽  
S. Tangolar ◽  
S. Buyukalaca ◽  
S. Kafkas
Keyword(s):  
Molecular Characterization ◽  
Molecular Diversity ◽  
Genetic Distances ◽  
Mean Values ◽  
Issr Analysis ◽  
Geographic Origins ◽  
The Mean ◽  
Vitis Spp

This study presents the ampelographic and molecular characterization of 44 grapevine cultivars. Ampelographic data were obtained during two vegetation periods using the latest version of the descriptors. Based on the mean values transformed by the method indicated in IBPGR publications, a dendrogram was constructed. ISSR analysis was also employed to characterize the genotypes at the DNA level. Twenty primers, selected on the basis of their discriminating potential, generated a total of 157 bands, of which 140 were polymorphic. The dendrograms constructed by the two approaches were largely similar in both the clustering position and divergence of varietal groups. The least distance was observed between Yuvarlak Cekirdeksiz and Superior Seedless. The clustering position of cultivars throughout the dendrograms was basically related to the genetic distances and main uses, as well as to geographic origins.

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

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