scholarly journals First molecular characterization of Galba neotropica in Uruguay

2016 ◽  
Vol 15 (1/2) ◽  
pp. 9-13 ◽  
Author(s):  
María Teresita ARMÚA-FERNANDEZ ◽  
Oscar CASTRO ◽  
Oscar CORREA ◽  
Luis CARVALHO ◽  
Atilio MANGOLD ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Fasciola Hepatica ◽  
Phylogenetic Analyses ◽  
First Record ◽  
Northern Region ◽  
Homology Search ◽  
Likelihood Method ◽  
Additional Species ◽  
Larval Stages ◽  
Para Determinar

Until recently, it was believed that only two lymnaeid species (i.e. Galba viatrix and Pseudosuccinea columella) occurred in Uruguay. However, based on a molecular approach, an additional species Galba cubensis, was recently discovered. The aim of this study was to molecularly characterize different lymnaeid populations from the northern region of Uruguay. The lymnaeids collections were carried out in two farms of the departments of Paysandú and Tacuarembó. The collected lymnaeids were divided in two fractions, one fraction was used for conchological analyses and detection of trematode larval stages, while the other fraction was used for molecular studies. Three PCRs targeting the 16S, ITS-2 and COI DNA regions were performed and the amplicons obtained were direct sequenced. The sequences were used for homology search and construction of phylogenetic trees by the maximum-likelihood method. The sequencing results revealed that both isolates corresponded to Galba neotropica. The phylogenetic analyses placed our isolates among the G. neotropica monophyletic group, closely related to other isolates of this species found in several South American countries. To our knowledge, this is the first record of G. neotropica in Uruguay and the confirmation as competent intermediate host of Fasciola hepatica. Further studies are needed to define the distribution and the role of each lymnaeid species in the transmission of F. hepatica in Uruguay.   RESUMEN. Primera caracterización molecular de Galba neotropica en Uruguay. Tradicionalmente se indicaba que existían dos especies de limneidos en Uruguay: Galba viatrix y Pseudosuccinea columella. Sin embargo, en los últimos años se identificó por medio de técnicas moleculares una tercera especie, Galba cubensis. El objetivo de los autores fue muestrear e identificar por medios moleculares poblaciones de limneidos del norte del país. Las colectas fueron realizadas en establecimientos rurales de los departamentos de Tacuarembó y Paysandú. Los caracoles colectados fueron divididos en dos fracciones, una de ellas fue destinada para el estudio morfológico de las conchillas y búsqueda de larvas de trematodos. La otra fracción se usó para la caracterización molecular. Tres genes fueron amplificados (ITS2, COI y 16S) utilizando protocolos de PCRs previamente descriptos. Las secuencias obtenidas se utilizaron para estudios de homología y construcción de árboles filogenéticos por medio del método de máxima verosimilitud. Por medio de la secuenciación se pudo confirmar que los dos aislamientos corresponden a Galba neotropica. Los estudios filogenéticos colocan ambos aislamientos dentro del grupo monofilético de G. neotropica junto a otros encontrados en distintas regiones de Sudamérica. Hasta lo que sabemos, el presente, es el primer registro de G. neotropica en Uruguay, además de comprobarse su capacidad para actuar como hospedero intermediario de Fasciola hepatica en condiciones de campo.  Se sugieren futuros estudios para determinar la distribución y el rol de cada especie de limneido en la transmisión de F. hepatica.

scholarly journals Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

2021 ◽  
Author(s):  
Blessing Amaka Ezeonuegbu ◽  
Dauda Abdullahi Machido ◽  
Clement Z. Whong ◽  
Wisdom S. Japhet ◽  
Clement Ameh Yaro ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Industrial Effluent ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Likelihood Method ◽  
Internal Transcribed Spacer Region ◽  
Fungal Isolates ◽  
Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

PHYLOGENETIC ANALYSES OF FRINGILLIDAE (AVES: PASSERIFORMES) USING MITOCHONDRIAL tRNA GENE SEQUENCES AND SECONDARY STRUCTURE

2006 ◽  
Vol 14 (03) ◽  
pp. 413-424
Author(s):  
BO CUI ◽  
FEI MA ◽  
XIANG WANG ◽  
YI SUN ◽  
LI YU ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Trna Gene ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Likelihood Method ◽  
Trna Genes ◽  
Gene Sequences ◽  
Mitochondrial Trna ◽  
Mitochondrial Trna Genes ◽  
Mitochondrial Trna Gene

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Additions to the knowledge of Manota Williston (Diptera: Mycetophilidae) from the Neotropical region, with description of four new species

Zootaxa ◽  
2021 ◽  
Vol 4938 (1) ◽  
pp. 85-100
Author(s):  
OLAVI KURINA ◽  
HEIKKI HIPPA
Keyword(s):  
New Species ◽  
Dominican Republic ◽  
French Guiana ◽  
New Records ◽  
First Record ◽  
Neotropical Region ◽  
Caribbean Island ◽  
Additional Species ◽  
Neotropical Species ◽  
Southern Caribbean

The Neotropical species of the genus Manota Williston are studied, based on material of 146 specimens from French Guiana, Ecuador, Nicaragua, Dominica and the Dominican Republic. Four new species are described, viz. M. corniculata sp. n. (French Guiana), M. pseudocavata sp. n. (French Guiana), M. truuverki sp. n. (French Guiana) and M. vladi sp. n. (Dominican Republic). Manota defecta Williston, 1896, the type species of the genus, is listed from Dominica, representing the first record since its description more than a century ago from a Southern Caribbean Island, St. Vincent. New records of 13 additional species are provided: M. acutistylus Jaschhof & Hippa, 2005 (Dominica), M. aligera Hippa, Kurina & Sääksjärvi, 2017 (French Guiana), M. digitata Hippa, Kurina & Sääksjärvi, 2017 (French Guiana), M. iota Hippa & Kurina, 2013 (French Guiana), M. micula Hippa & Kurina, 2013 (French Guiana), M. nordestina Kurina, Hippa & Amorim, 2018 (French Guiana), M. parva Jaschhof & Hippa, 2005 (Nicaragua), M. pauloides Hippa, Kurina & Sääksjärvi, 2017 (Ecuador), M. perplexa Kurina, Hippa & Amorim, 2017 (Nicaragua), M. rotundistylus Jaschhof & Hippa, 2005 (Ecuador), M. serrulata Hippa, Kurina & Sääksjärvi, 2017 (French Guiana), M. spinosa Jaschhof & Hippa, 2005 (French Guiana), M. subaristata Kurina, Hippa & Amorim, 2017 (Ecuador). The number of Neotropical Manota species has risen to 96. 

Prevalence and genetic diversity of viruses associated with rugose wood complex in Greek vineyards

Plant Disease ◽  
2021 ◽  
Author(s):  
Chrysoula Orfanidou ◽  
Kalliopi Moraki ◽  
Polina Panailidou ◽  
Leonidas Lotos ◽  
Asimina T Katsiani ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
First Record ◽  
Grapevine Virus ◽  
Multiple Introductions ◽  
Worldwide Distribution ◽  
Grapevine Virus A ◽  
Transmission Modes ◽  
Virus Incidence ◽  
Grapevine Virus B ◽  
Rupestris Stem Pitting

Rugose wood is one of the most important disease syndromes of grapevine and it has been associated with at least three viruses: grapevine rupestris stem pitting associated virus (GRSPaV), grapevine virus A (GVA) and grapevine virus B (GVB). All three viruses show a worldwide distribution pattern, and their genetic composition has been the focus of extensive research over the past years. Despite their first record in Greece almost 20 years ago, there is a lack of knowledge on the distribution and genetic variability of their populations in Greek vineyards. In this context, we investigated the distribution of GRSPaV, GVA and GVB in rootstocks, self-rooted and grafted grapevine cultivars, originating from different geographic regions that are representing important viticultural areas of Greece. Three new RT-PCR assays were developed for the reliable detection of GRSPaV, GVA and GVB. Our results indicated that GVA is the most prevalent in Greek vineyards, followed by GRSPaV and GVB. However, virus incidence differed among self-rooted and grafted grapevine cultivars or rootstocks tested. Selected isolates from each virus were further molecularly characterized to determine their phylogenetic relationships. All three viruses exhibited high nucleotide diversity, which was depicted in the constructed phylogenetic trees. Isolates from Greece were placed in various phylogroups, reinforcing the scenario of multiple introductions of GVA, GVB and GRSPaV in Greece and highlighting the effect of different transmission modes in the evolutionary course of the three viruses.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240953
Author(s):  
Christian Schulz ◽  
Eivind Almaas
Keyword(s):  
Phylogenetic Trees ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Significant Heterogeneity ◽  
Metabolic Reaction ◽  
High Quality ◽  
Conserved Genes ◽  
Genome Scale

Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.

scholarly journals Characterization of Coolia spp. (Gonyaucales, Dinophyceae) from Southern Tunisia: first record of Coolia malayensis in the Mediterranean Sea

ALGAE ◽  
2021 ◽  
Vol 36 (3) ◽  
pp. 175-193
Author(s):  
Moufida Abdennadher ◽  
Amel Bellaaj Zouari ◽  
Walid Medhioub ◽  
Antonella Penna ◽  
Asma Hamza
Keyword(s):  
Electron Microscopy ◽  
Mediterranean Sea ◽  
Phylogenetic Trees ◽  
Eastern Mediterranean ◽  
First Record ◽  
Morphological Characterization ◽  
Mucus Production ◽  
Rdna Sequences ◽  
The Mediterranean ◽  
Morphological Differences

This study provides the first report of the presence of Coolia malayensis in the Mediterranean Sea, co-occurring with C. monotis. Isolated strains from the Gulf of Gabès, Tunisia (South-eastern Mediterranean) were identified by morphological characterization and phylogenetic analysis. Examination by light and scanning electron microscopy revealed no significant morphological differences between the Tunisian isolates and other geographically distant strains of C. monotis and C. malayensis. Phylogenetic trees based on ITS1-5.8S-ITS2 and D1‒D3/28S rDNA sequences showed that C. monotis strains clustered with others from the Mediterranean and Atlantic whereas the C. malayensis isolate branched with isolates from the Pacific and the Atlantic, therefore revealing no geographical trend among C. monotis and C. malayensis populations. Ultrastructural analyses by transmission electron microscopy revealed the presence of numerous vesicles containing spirally coiled fibers in both C. malayensis and C. monotis cells, which we speculate to be involved in mucus production.

scholarly journals Phylogenetic analysis of canine parvoviruses from Turkey

2020 ◽  
Vol 76 (01) ◽  
pp. 6334-2020
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B.
Keyword(s):  
High Mortality ◽  
Phylogenetic Trees ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Canine Parvovirus ◽  
Mortality And Morbidity ◽  
Identity Match ◽  
Genomic Characterization

Canine parvovirus (CPV) type 2 is the causative agent of acute hemorrhagic enteritis and high mortality in the affected dogs. Numerous studies have been done to understand the origin of the virus and to exhibit new variants and circulating strains. This report describes the detection and genomic characterization of CPV strains from indoor and outdoor dogs in Ankara, Turkey. Samples were sent to our laboratory due to clinical symptoms in puppies. We tested blood and swab samples to determine the presence of canine parvovirus (CPV) in three puppies and two adult dogs by reverse transcription-polymerase chain reaction (RT-PCR) using VP2 (capsid protein) region primers of canine parvoviruses. Following that, to provide molecular characterization data Maximum Likelihood (ML) method was used for phylogenetic analyses. Constructed phylogenetic trees from the aligned nucleotide sequences revealed that our CPV strains demonstrated high genetic similarities, with 100% identity match on nucleotide alignments with each other and classified in CPV-2b genotypes.They have placed on a monophyletic clade as a sister branch with CPV VAC S quantum with 98.9% nucleotide homology. Our findings suggest that CPV-2b is actual and frequently seen variant in Turkey and shows high similarities with other CPV variants and a bit less with FPVs in Turkey and around the world. CPV causes high mortality and morbidity in dogs and to develop effective vaccines for protection of dogs in Turkey where there are few numbers of studies that have been done, field strains should be isolated and characterised.

scholarly journals First Record of a Novel Mitochondrial DNA Haplotype of a Marble Trout Lineage of Salmo Trutta in Turkey

10.4194/ga452 ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Fevzi Bardakci ◽  
Nazan Acar ◽  
Tulin Arslan ◽  
Riadh Badraoui
Keyword(s):  
Mitochondrial Dna ◽  
Salmo Trutta ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Aegean Sea ◽  
First Record ◽  
Unique Haplotype ◽  
Marble Trout ◽  
Mitochondrial Dna Control Region ◽  
Mitochondrial Dna Haplotype

A new record of a marble trout mtDNA haplotype known to be restricted to Adriatic basin (called marmoratus lineage within Salmo trutta complex) has been reported from Eşen Stream in the Aegean Sea basin of southeastern Turkey, based on sequence data of the mitochondrial DNA control region. The results of this study showed a single unique haplotype from this population, called MATR1. Phylogenetic analyses of this haplotype along with other haplotypes belonging to different mitochondrial DNA lineages of the S. trutta complex confirmed the existence of the marmoratus lineage in Turkey, suggesting a possible river capture between the Adriatic and Aegean Sea basins until the last (Würmian) marine regression.

scholarly journals First Report of Fusarium pernambucanum Causing Fruit Rot of Muskmelon in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Xianping Zhang ◽  
Jiwen Xia ◽  
Jiakui Liu ◽  
Dan Zhao ◽  
Lingguang Kong ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Apical Cell ◽  
Morphological Characteristics ◽  
Fruit Rot ◽  
Likelihood Method ◽  
Correct Identification ◽  
Pathogenicity Test ◽  
First Report ◽  
The Core ◽  
Representative Isolate

Muskmelon (Cucumis melo L.) is one of the most widely cultivated and economically important fruit crops in the world. However, many pathogens can cause decay of muskmelons; among them, Fusarium spp. is the most important pathogen, affecting fruit yield and quality (Wang et al. 2011). In May 2017, fruit rot symptoms were observed on ripening muskmelons (cv. Jipin Zaoxue) in several fields in Liaocheng of Shandong Province, China. Symptoms appeared as brown, water-soaked lesions, irregularly circular in shape, with the lesion size ranging from a small spot (1 to 2 cm) to the decay of the entire fruit. The core and the surface of the infected fruit were covered with white to rose-reddish mycelium. Two infected muskmelons were collected from each of two fields, 10 km apart. Tissues from the inside of the infected fruit were surface disinfected with 75% ethanol for 30 s, and cultured on potato dextrose agar (PDA) at 25 °C in the dark for 5 days. Four purified cultures were obtained using the single spore method. On carnation leaf agar (CLA), macroconidia had a pronounced dorsiventral curvature, falcate, 3 to 5 septa, with tapered apical cell, and foot-shaped basal cell, measuring 19 to 36 × 4 to 6 μm. Chlamydospores were abundant, 5.5–7.5 μm wide, and 5.5–10.5 μm long, ellipsoidal or subglobose. No microconidia were observed. These morphological characteristics were consistent with the descriptions of F. pernambucanum (Santos et al. 2019). Because these isolates had similar morphology, one representative isolate was selected for multilocus phylogenetic analyses. DNA was extracted from the representative isolate using the CTAB method. The nucleotide sequences of the internal transcribed spacers (ITS) (White et al. 1990), translation elongation factor 1-α gene (TEF1), RNA polymerase II second largest subunit gene (RPB2), calmodulin (CAM) (Xia et al. 2019) were amplified using specific primers, sequenced, and deposited in GenBank (MN822926, MN856619, MN856620, and MN865126). Based on the combined dataset of ITS, TEF1, RPB2, CAM, alignments were made using MAFFT v. 7, and phylogenetic analyses were processed in MEGA v. 7.0 using the maximum likelihood method. The studied isolate (XP1) clustered together with F. pernambucanum reference strain URM 7559 (99% bootstrap). To perform pathogenicity test, 10 μl of spore suspensions (1 × 106 conidia/ml) were injected into each muskmelon fruit using a syringe, and the control fruit was inoculated with 10 μl of sterile distilled water. There were ten replicated fruits for each treatment. The test was repeated three times. After 7 days at 25 °C, the interior of the inoculated muskmelons begun to rot, and the rot lesion was expanded from the core towards the surface of the fruit, then white mycelium produced on the surface. The same fungus was re-isolated from the infected tissues and confirmed to fulfill the Koch’s postulates. No symptoms were observed on the control muskmelons. To our knowledge, this is the first report of F. pernambucanum causing of fruit rot of muskmelon in China. Considering the economic value of the muskmelon crop, correct identification can help farmers select appropriate field management measures for control of this disease.

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