scholarly journals Genetic Diversity of Grapevine virus A in Washington and California Vineyards

2014 ◽  
Vol 104 (5) ◽  
pp. 548-560 ◽  
Author(s):  
Olufemi J. Alabi ◽  
Maher Al Rwahnih ◽  
Tefera A. Mekuria ◽  
Rayapati A. Naidu
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Management Strategies ◽  
Geographic Origin ◽  
Phylogenetic Network ◽  
Grapevine Virus ◽  
Grapevine Virus A ◽  
Strong Negative Selection ◽  
Epidemiological Characteristics

Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.

scholarly journals Diversity of microcystin-producing genotypes in Brazilian strains of Microcystis (Cyanobacteria)

2011 ◽  
Vol 71 (1) ◽  
pp. 209-216 ◽  
Author(s):  
MC Bittencourt-Oliveira ◽  
MC Oliveira ◽  
E Pinto
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Gene Cluster ◽  
Geographic Origin ◽  
Toxic Blooms ◽  
First Time

Microcystis Kützing ex Lemmermann is among the genera of cyanobacteria often associated to toxic blooms with the release of microcystins. A gene cluster codes for microcystin synthetases, which are involved in the biosynthesis of this toxin. The aim of the present study was to investigate the genetic diversity of the mcyB gene, specifically the B1 module, in Brazilian strains of Microcystis spp. and its microcystin variants. Broad genetic diversity was revealed in this region. From the phylogenetic analysis, three clusters were obtained that were not related to the geographic origin or morphospecies of the strains, nor with the variant of the microcystin produced. A group of strains that did not produce microcystins was found, despite the presence of the mcyB1 fragment. Eight microcystin isoforms were detected: MC-LR, [D-Asp³]-MC-LR, [Asp³]-MC-LR, MC-RR, [Dha7]-MC-LR, MC-LF, MC-LW and [D-Asp³, EtAdda5]-MC-LH, the latter of which is described for the first time in Brazil. Moreover, five other variants were not identified and indicate being new.

Sequence variation in mitochondrial cox1 and nad1 genes of ascaridoid nematodes in cats and dogs from Iran

2014 ◽  
Vol 89 (4) ◽  
pp. 496-501 ◽  
Author(s):  
F. Mikaeili ◽  
H. Mirhendi ◽  
M. Mohebali ◽  
M. Hosseini ◽  
M. Sharbatkhori ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Variation ◽  
Sequence Data ◽  
Pairwise Comparison ◽  
Toxocara Canis ◽  
Mitochondrial Genes ◽  
Toxocara Cati ◽  
Maximum Likelihood Methods ◽  
Toxascaris Leonina

AbstractThe study was conducted to determine the sequence variation in two mitochondrial genes, namely cytochrome c oxidase 1 (pcox1) and NADH dehydrogenase 1 (pnad1) within and among isolates of Toxocara cati, Toxocara canis and Toxascaris leonina. Genomic DNA was extracted from 32 isolates of T. cati, 9 isolates of T. canis and 19 isolates of T. leonina collected from cats and dogs in different geographical areas of Iran. Mitochondrial genes were amplified by polymerase chain reaction (PCR) and sequenced. Sequence data were aligned using the BioEdit software and compared with published sequences in GenBank. Phylogenetic analysis was performed using Bayesian inference and maximum likelihood methods. Based on pairwise comparison, intra-species genetic diversity within Iranian isolates of T. cati, T. canis and T. leonina amounted to 0–2.3%, 0–1.3% and 0–1.0% for pcox1 and 0–2.0%, 0–1.7% and 0–2.6% for pnad1, respectively. Inter-species sequence variation among the three ascaridoid nematodes was significantly higher, being 9.5–16.6% for pcox1 and 11.9–26.7% for pnad1. Sequence and phylogenetic analysis of the pcox1 and pnad1 genes indicated that there is significant genetic diversity within and among isolates of T. cati, T. canis and T. leonina from different areas of Iran, and these genes can be used for studying genetic variation of ascaridoid nematodes.

scholarly journals Global transmission of influenza viruses from humans to swine

2012 ◽  
Vol 93 (10) ◽  
pp. 2195-2203 ◽  
Author(s):  
Martha I. Nelson ◽  
Marie R. Gramer ◽  
Amy L. Vincent ◽  
Edward C. Holmes
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Large Scale ◽  
Sequence Data ◽  
Virus Genome ◽  
Influenza Viruses ◽  
Substantial Contribution ◽  
Human Influenza ◽  
Swine Workers

To determine the extent to which influenza viruses jump between human and swine hosts, we undertook a large-scale phylogenetic analysis of pandemic A/H1N1/09 (H1N1pdm09) influenza virus genome sequence data. From this, we identified at least 49 human-to-swine transmission events that occurred globally during 2009–2011, thereby highlighting the ability of the H1N1pdm09 virus to transmit repeatedly from humans to swine, even following adaptive evolution in humans. Similarly, we identified at least 23 separate introductions of human seasonal (non-pandemic) H1 and H3 influenza viruses into swine globally since 1990. Overall, these results reveal the frequency with which swine are exposed to human influenza viruses, indicate that humans make a substantial contribution to the genetic diversity of influenza viruses in swine, and emphasize the need to improve biosecurity measures at the human–swine interface, including influenza vaccination of swine workers.

scholarly journals Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection Between Pathogenicity and Molecular Diversity

2021 ◽  
Vol 7 (9) ◽  
pp. 713
Author(s):  
Abdelhameed Elameen ◽  
Svein Stueland ◽  
Ralf Kristensen ◽  
Rosa F. Fristad ◽  
Trude Vrålstad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Geographic Origin ◽  
Mantel Test ◽  
Group Method ◽  
Aflp Analysis ◽  
Its Sequencing ◽  
Sequencing Data ◽  
Pair Group

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of Saprolegnia spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 Saprolegnia spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 Saprolegnia sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the Saprolegnia isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of Saprolegnia spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (r2 = 0.8317).

Are they different species or vicariant elevational races of the same species? The case of an Iberian endemic plant, Ranunculus bupleuroides (Ranunculaceae)

Phytotaxa ◽  
2015 ◽  
Vol 239 (3) ◽  
pp. 242 ◽  
Author(s):  
José Antonio Fernández Prieto ◽  
Joaquín Molero Mesa ◽  
Marta Pérez Suárez ◽  
Mauro Sanna ◽  
José Miguel Muñoz Díaz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Iberian Peninsula ◽  
Sierra Nevada ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
High Mountain ◽  
Endemic Plant ◽  
Systematic Treatment ◽  
Mountain Plants

The infrageneric taxonomy and evolution of Ranunculus are still not well understood. In this regard, we investigated the origin and genetic diversity of the Iberian endemic plant Ranunculus bupleuroides s.l. by analysis of nuclear internal transcribed spacers (ITS) and plastid (rpl32-trnL, rps16-trnQ, trnK-matK, ycf6-psbM) sequence data. Phylogenetic analysis reveals two geographically well supported subclades: one formed by high mountain plants and another by more typical samples of Ranunculus bupleuroides from the lowlands of the western Iberian Peninsula. The subclade of montane plants includes both plants originating in Gredos and Béjar (Ranunculus cherubicus subsp. cherubicus) and those from Sierra Nevada (R. cherubicus subsp. girelai). In the light of the new molecular results obtained, combined with an assessment of morphological, geographical and ecological characters, a new systematic treatment is proposed.

Species-specific probes for the identification of the African tsetse-transmitted trypanosomes

Parasitology ◽  
2009 ◽  
Vol 136 (12) ◽  
pp. 1501-1507 ◽  
Author(s):  
W. GIBSON
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Quantitative Information ◽  
Morphological Identification ◽  
Trypanosome Species ◽  
Accurate Identification ◽  
Identification Methods ◽  
Detection And Identification ◽  
Species Specific

SUMMARYThe first step in studying the epidemiology of a disease is the accurate identification of the pathogen. Traditional reliance on morphological identification has given way to the use of molecular methods for the detection and identification of pathogens, greatly improving our understanding of epidemiology. For the African tsetse-transmitted trypanosomes, the growth of PCR methods for identification of trypanosomes has led to increased appreciation of trypanosome genetic diversity and discovery of hitherto unknown trypanosome species, as well as greater knowledge about the number and type of trypanosome infections circulating in mammalian hosts and vectors. Sequence data and phylogenetic analysis have provided quantitative information on the relatedness of different trypanosome species and allowed the new trypanosome genotypes discovered through the use of species identification methods in the field to be accurately placed in the phylogenetic tree.

scholarly journals Genetic variability among Fusarium oxysporum isolates from melon (Cucumis melo) in Qazvin province, Iran

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Mohammadreza Mahdikhani
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Oxysporum ◽  
Cucumis Melo ◽  
Sequence Data ◽  
Geographic Origin ◽  
Neighbor Joining ◽  
Factors Affecting ◽  
Future Studies ◽  
In The Beginning ◽  
Almost All

<p><em>Fusarium</em> wilt, caused by <em>Fusarium oxysporum</em> f. sp. <em>melonis</em> (Fom), the soil-borne fungus that can due to more losses in yield of melon plants. Fusarium is a variable fungi in terms of morphology, symptom production, pathogenicity and wide host range. From 2013 to 2015, 120 isolates of <em>F. oxysporum,</em> <em>F. acuminatum, F. graminearum, </em> <em>F. proliferatum</em> and <em>F. solani</em> from melon, were collected from disease suspected plants from the field and defined for pathogenicity in our melon plants. Then, a sort of those were elected for phylogenetic analysis. In the beginning, the <em>Fusarium</em> isolates were classified based on morphology and identifications were authenticated based on sequence data from, EF1α and DNA, and then were used to determine whether <em>Fusarium</em> variability is relevant to geographic origin and pathogenicity. Neighbor-joining analyses datasets indicated some clades based on geographic origin but there is not even a single clades including solely of pathogens. Because of the factors affecting in pathogenicity are variable, we should be considered them in future studies. Due to the presence of FOM and some nonpathogenic isolates in almost all clades, it is obvious that <em>Fusarium oxysporum</em> f. sp. <em>melonis</em> is not monophyletic.</p>

scholarly journals Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data

2016 ◽  
Vol 106 (6) ◽  
pp. 636-644 ◽  
Author(s):  
Marie-Claude Gagnon ◽  
Theo A. J. van der Lee ◽  
Peter J. M. Bonants ◽  
Donna S. Smith ◽  
Xiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Geographic Origin ◽  
Whole Genome Sequence ◽  
Specific Detection ◽  
Potato Wart ◽  
Intraspecific Genetic Diversity ◽  
Polymorphic Microsatellite ◽  
Genetic Clustering ◽  
Species Specific

Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.

scholarly journals Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

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