scholarly journals Pratylenchus penetrans Parasitizing Potato Crops: Morphometric and Genetic Variability of Portuguese Isolates

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 603
Author(s):  
Diogo Gil ◽  
Joana M.S. Cardoso ◽  
Isabel Abrantes ◽  
Ivânia Esteves
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Phylogenetic Analyses ◽  
Intraspecific Variability ◽  
Its Region ◽  
Genomic Region ◽  
Internal Transcribed Spacers ◽  
Coi Gene ◽  
Pratylenchus Penetrans ◽  
Wide Range

The root lesion Pratylenchus penetrans is an economically important pest affecting a wide range of plants. The morphometry of five P. penetrans isolates, parasitizing potato roots in Portugal, was compared and variability within and between isolates was observed. Of the 15 characters assessed, vulva position (V%) in females and the stylet length in both females/males showed the lowest coefficient of intra and inter-isolate variability. Moreover, DNA sequencing of the internal transcribed spacers (ITS) genomic region and cytochrome c oxidase subunit 1 (COI) gene was performed, in order to evaluate the intraspecific genetic variability of this species. ITS revealed higher isolate genetic diversity than the COI gene, with 15 and 7 different haplotypes from the 15 ITS and 14 COI sequences, respectively. Intra- and inter-isolate genetic diversity was found considering both genomic regions. The differentiation of these isolates was not related with their geographical origin. In spite of the high intraspecific variability, phylogenetic analyses revealed that both ITS region and COI gene separate P. penetrans from other related species. Our findings contribute to increasing the understanding of P. penetrans variability.

Genetic analysis of pathogenic and nonpathogenic Fusarium oxysporum from tomato plants

2002 ◽  
Vol 80 (3) ◽  
pp. 271-279 ◽  
Author(s):  
Jian R Bao ◽  
Deborah R Fravel ◽  
Nichole R O'Neill ◽  
George Lazarovits ◽  
Peter van Berkum
Keyword(s):  
Genetic Diversity ◽  
Fusarium Oxysporum ◽  
Geographic Origin ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Aflp Data ◽  
5.8S Rrna Gene ◽  
Rdna Its ◽  
Wide Range

Forty-three Fusarium oxysporum strains and one Fusarium solani strain were analyzed for genetic diversity. These strains represent a wide range of geographic locations and were collected primarily from tomato (Lycopersicon esculentum) roots. Among all 43 F. oxysporum strains, 21 were not pathogenic to tomato, 20 were pathogenic, including 13 strains of Fusarium oxysporum lycopersici and seven strains of Fusarium oxysporum radicis-lycopersici, and two were other formae speciales of the fungus. Genetic diversity of all 43 strains was assessed by vegetative compatibility group (VCG), sequence analysis of the rDNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene, and amplified fragment length polymorphism (AFLP). Most of the F. o. lycopersici strains were assigned to VCG 0030, while most nonpathogenic ones were incompatible with each other. ITS region analysis grouped the strains into four clusters. The nonpathogenic F. oxysporum strains were in two groups, while the pathogenic strains were placed in two different groups. Pathogenic and nonpathogenic strains were also separated into different clusters based on AFLP data, although some nonpathogenic strains grouped with pathogenic strains. The population of pathogenic strains was less diverse than that of the nonpathogenic strains, suggesting that the pathogenic strains were possibly of monophyletic origin. For both pathogenic and nonpathogenic F. oxysporum strains, no relationship was observed between the genetic profiles and geographic origin; this may indicate that pathogens did not originate independently at each locality.Key words: Fusarium oxysporum, VCG, rDNA (ITS) sequence, AFLP.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

scholarly journals Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 87
Author(s):  
Kumpei Shiragaki ◽  
Shuji Yokoi ◽  
Takahiro Tezuka
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Species ◽  
Morphological Characteristics ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rdna Its ◽  
Rdna Its Region ◽  
Genus Capsicum

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

scholarly journals Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae:Culexspp.) from the Sonoran Desert of North America

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Edward Pfeiler ◽  
Carlos A. Flores-López ◽  
Jesús Gerardo Mada-Vélez ◽  
Juan Escalante-Verdugo ◽  
Therese A. Markow
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Sonoran Desert ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Population Expansion ◽  
The Other ◽  
Coi Gene ◽  
Unidentified Species

The population genetics and phylogenetic relationships ofCulexmosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochromecoxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding toCx. quinquefasciatus, Cx. tarsalis,and two unidentified species,Culexsp. 1 and sp. 2.Culex quinquefasciatuswas found at all localities and was the most abundant species collected.Culex tarsaliswas collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species ofCulexwere most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower inCx. quinquefasciatuscompared with the other three species. Analysis of molecular variance revealed little structure among seven populations ofCx. quinquefasciatus, whereas significant structure was found between the two populations ofCx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found forCx. tarsalis. Possible explanations for the large differences in genetic diversity betweenCx. quinquefasciatusand the other species ofCulexare presented.

scholarly journals Characterization of genetic diversity on tropical Trichoderma germplasm by sequencing of rRNA internal transcribed spacers

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Yara Barros Feitosa ◽  
Valter Cruz-Magalhães ◽  
Ronaldo Costa Argolo-Filho ◽  
Jorge Teodoro de Souza ◽  
Leandro Lopes Loguercio
Keyword(s):  
Genetic Diversity ◽  
Molecular Level ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Plant Diseases ◽  
Rrna Genes ◽  
Physiological Data ◽  
Biotic And Abiotic Stresses ◽  
Beneficial Effects

Abstract Objective Trichoderma species are found in soil and in association with plants. They can act directly or indirectly in the biological control of plant diseases and in the promotion of plant growth, being among the most used fungi in the formulation of bioproducts applied to agricultural systems. The main objective of this study was to characterize at a first-tier level a collection of 67 Trichoderma isolates from various tropical sources, based solely on sequencing of the internal transcribed spacer (ITS) region of the rRNA genes. Our goal was to provide a preliminary idea of the baseline diversity in this collection, to combine this information later with an array of other isolate-specific physiological data. This study provides a required knowledge at molecular level for assessment of this germplasm potential as a source of biotechnological products for beneficial effects in plants. Results Sequencing of the ITS region showed that the 67 Trichoderma isolates belonged in 11 species: T. asperellum, T. atroviride, T. brevicompactum, T. harzianum, T. koningiopsis, T. longibrachiatum, T. pleuroticola, T. reesei, T. spirale, T. stromaticum and T. virens. A total of 40.3% of the isolates were very closely related to each other and similar to T. harzianum. The baseline genetic diversity found indicates that the collection has different genotypes, which can be exploited further as a source of bioproducts, aiming at providing beneficial effects to plants of interest to cope with biotic and abiotic stresses.

Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem

2017 ◽  
Vol 98 (4) ◽  
pp. 777-789
Author(s):  
Katerina Vasileiadou ◽  
Christina Pavloudi ◽  
Federica Camisa ◽  
Irene Tsikopoulou ◽  
Nina Fragopoulou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Factors ◽  
Population Distribution ◽  
Seasonal Pattern ◽  
Local Population ◽  
Management Strategies ◽  
Intraspecific Variability ◽  
Coi Gene ◽  
Dispersal Ability ◽  
Genetic Structuring

Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats.

scholarly journals Distribution, Function, and Evolution of a Gene Essential for Trichothecene Toxin Biosynthesis in Trichoderma

2021 ◽  
Vol 12 ◽  
Author(s):  
Santiago Gutiérrez ◽  
Susan P. McCormick ◽  
Rosa E. Cardoza ◽  
Hye-Seon Kim ◽  
Laura Lindo Yugueros ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Deletion Mutant ◽  
Phylogenetic Analyses ◽  
Parent Compound ◽  
Genomic Region ◽  
The Other ◽  
Terpene Synthase ◽  
Biosynthetic Gene ◽  
Study Analysis ◽  
Wide Range

Trichothecenes are terpenoid toxins produced by species in 10 fungal genera, including species of Trichoderma. The trichothecene biosynthetic gene (tri) cluster typically includes the tri5 gene, which encodes a terpene synthase that catalyzes formation of trichodiene, the parent compound of all trichothecenes. The two Trichoderma species, Trichoderma arundinaceum and T. brevicompactum, that have been examined are unique in that tri5 is located outside the tri cluster in a genomic region that does not include other known tri genes. In the current study, analysis of 35 species representing a wide range of the phylogenetic diversity of Trichoderma revealed that 22 species had tri5, but only 13 species had both tri5 and the tri cluster. tri5 was not located in the cluster in any species. Using complementation analysis of a T. arundinaceum tri5 deletion mutant, we demonstrated that some tri5 homologs from species that lack a tri cluster are functional, but others are not. Phylogenetic analyses suggest that Trichoderma tri5 was under positive selection following its divergence from homologs in other fungi but before Trichoderma species began diverging from one another. We propose two models to explain these diverse observations. One model proposes that the location of tri5 outside the tri cluster resulted from loss of tri5 from the cluster in an ancestral species followed by reacquisition via horizontal transfer. The other model proposes that in species that have a functional tri5 but lack the tri cluster, trichodiene production provides a competitive advantage.

scholarly journals Molecular characterization of COI gene of Ixodes ricinus (Linnaeus, 1758) from Serbia

2014 ◽  
Vol 66 (3) ◽  
pp. 1243-1251
Author(s):  
Sanja Cakic ◽  
Miljana Mojsilovic ◽  
Darko Mihaljica ◽  
Marija Milutinovic ◽  
Andjeljko Petrovic ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ixodes Ricinus ◽  
Intraspecific Variability ◽  
Balkan Peninsula ◽  
Coi Gene ◽  
Gene Sequences ◽  
Ricinus Tick ◽  
Pathogenic Agents ◽  
Font Color

The Ixodes ricinus tick is common in the central part of the Balkan Peninsula. It is a vector of pathogenic agents causing diseases in humans and animals. Little is known about the genetic structure of I. ricinus in this region. We have investigated intraspecific variability of the COI gene among I. ricinus ticks collected from different regions of Serbia, and the correlation between the various types of habitat and genetic variability of ticks. The obtained COI gene sequences are the first barcoding sequences of I. ricinus ticks collected at localities in Serbia. Intraspecific variability of these COI gene sequences was very low, and there was no correlation between the various types of habitat and genetic variability of ticks. Samples from isolated localities (canyon/gorge) showed no genetic differentiations from the majority of samples from open areas. [Projekat Ministarstva nauke Republike Srbije, br. ON 173006] <br><br><font color="red"><b> This article has been retracted. Link to the retraction <u><a href='http://dx.doi.org/10.2298/ABS1404689U'>10.2298/ABS1404689U</a><u></b></font>

scholarly journals Multilocus Phylogeography of the Tuber mesentericum Complex Unearths Three Highly Divergent Cryptic Species

2021 ◽  
Vol 7 (12) ◽  
pp. 1090
Author(s):  
Marco Leonardi ◽  
Daniele Salvi ◽  
Mirco Iotti ◽  
Gian Luigi Rana ◽  
Aurelia Paz-Conde ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Central Italy ◽  
Elongation Factor ◽  
Its Region ◽  
Wide Range ◽  
Volatile Organic ◽  
Phylogenetic Lineages ◽  
High Degree ◽  
Tuber Mesentericum ◽  
Elongation Factor 1

Tuber mesentericum is an edible European black truffle, apparently easy to recognize, but showing a high degree of genetic variability. In this study, we performed an integrative taxonomic assessment of the T. mesentericum complex, combining a multilocus phylogeographic approach with morphological analyses, and including authentic specimens of Vittadini, and Berkeley and Broome. We performed maximum likelihood phylogenetic analyses, based on single and concatenated gene datasets (ITS rDNA, β-tubulin, elongation factor 1-α), and including all available sequences from previous studies. Phylogenetic analyses consistently recovered three reciprocally monophyletic and well-supported clades: clade I, with a wide range across Europe; clade II, specimens collected mainly in the Iberian, Italian, and Balkan peninsulas; and clade III, specimens collected almost exclusively in central Italy. Genetic distance between clades ranged from 10.4% to 13.1% at the ITS region. We also designed new primer pairs specific for each phylogenetic lineage. Morphology of spores, asci, and peridium were investigated on specimens representing the three lineages. Macro- and micromorphological analyses of ascomata revealed only a few, but not diagnostic, differences between the three phylogenetic lineages, thus, confirming that they are morphologically cryptic. By studying authentic specimens of Vittadini, and Berkeley and Broome, it was possible to identify the three clades as T. mesentericum, Tuber bituminatum, and Tuber suave sp. nov., and to designate an epitype for T. mesentericum s.s. and a lectotype for T. bituminatum. Future investigations on volatile organic compound (VOC) composition are needed to define the aroma repertoires in this species complex.

scholarly journals ​Estimation of Genetic Variability and Genetic Divergence in Dolichos Bean [Lablab purpureus (L.) Sweet.] Genotypes

2021 ◽  
Author(s):  
Udit Kumar ◽  
Pramila . ◽  
K. Prasad ◽  
R.K. Tiwari ◽  
Saipayan Ghosh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Coefficient Of Variation ◽  
Genetic Divergence ◽  
Mean Value ◽  
Yellow Mosaic Virus ◽  
Lablab Purpureus ◽  
Wide Range ◽  
Cluster Distance ◽  
Maturity Period

Background: Dolichos bean is an important leguminous vegetable having a wide range of variation in different quantitative characters. Assessing genetic diversity among dolichos bean accessions can ensure development of suitable high-yielding and adapted varieties with suitable maturity period. Methods: Fifteen genotypes were evaluated for different characters in Dolichos bean at two locations of Dr. Rajendra Prasad Central Agricultural University viz. Vegetable Research Farm, Pusa and Krishi Vigyan Kendra, Birauli, Samastipur, Bihar during the year 2018-19 and pooled data was analyzed. The genotypes were evaluated for genetic variability and genetic divergence for 14 characters. For the assessment of genetic diversity among the fifteen genotypes of dolichos bean, Mahalanobis (D2) statistic (Mahalanobis, 1936) was used, following the procedure given by Rao, 1952. Grouping of genotypes into clusters was done using Tocher’s method as described by Rao, 1952. Result: Phenotypic Coefficient of Variation (PCV) was slightly higher than Genotypic Coefficient of Variation (GCV) for all the characters indicated that the characters were less influenced by environment. The characters having high heritability and high genetic advance include harvesting duration, number of pods per plant, pod length, pod diameter, individual pod weight, weight of seeds per pod, 100 fresh green seed weight, pod yield and percent incidence of yellow mosaic virus. Therefore, selection for above characters is highly effective. Genetic diversity analysis evaluated that all genotypes could be placed into 6 clusters. Genotypes grouped in Cluster III and I have highest mean value for all characters as well as highest inter-cluster distance.

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