Search Results - "Phylogenetics"

Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi by Wilson, C.N., Musicha, P., Beale, M.A., Diness, Y., Kanjerwa, O., Salifu, C., Katuah, Z., Duncan, P., Nyangu, J., Mungu, A., Deleza, M., Banda, L., Makhaza, L., Elviss, N., Jewell, C.P., Pinchbeck, G., Feasey, N.A., Fèvre, Eric M., Thomson, N.R.

“…Using whole genome sequencing and fine-resolution bioinformatic and phylogenetic analyses we found evidence of sharing of <i>Salmonella</i> species and strains between humans, animals and the environment, both within and between households. …”
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Genetic diversity and population structure of alpacas (Vicugna pacos) in Peru: A microsatellite analysis by Peralta, Wilber, Nestares Palomino, Agustin, Gamarra Reyes, Julyssa del Pilar, Rojas, Miler, Sullca, Juan, Estrada Cañari, Richard

“…Analyses of molecular variance (AMOVA), principal coordinate analysis (PCoA), Bayesian clustering, and phylogenetic reconstruction indicated moderate genetic differentiation between Suitucancha and Huayre, likely influenced by the use of selected males under controlled mating in Suitucancha versus natural, unregulated group mating in Huayre, which facilitates broader gene flow. …”
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Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome by Debat, Humberto Julio

“…The proposed aplysia californica nido-like virus (AcNV), with a genome sequence of ca.35,906 nt, represents the longest ever recorded RNA virus yet. Phylogenetic insights indicate that AcNV clusters in a major phylloclade of unclassified invertebrate nidoviruses, Roniviridae, and Mesoniviridae. …”
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Characterization of a new Helicoverpa armigera nucleopolyhedrovirus variant causing epizootic on a previously unreported host, Helicoverpa gelotopoeon (Lepidoptera: Noctuidae) by Ferrelli, Maria Leticia, Taibo, Catalina Beatriz, Fichetti, Patricia, Sciocco, Alicia Ines, Arneodo Larochette, Joel Demian

“…Nucleocapsids were singly enveloped. Phylogenetic analysis of lef-8, lef-9, polh, orf5/5b and hr3-orf62 viral sequences identified this new NPV isolate (hereafter HegeSNPV) as a variant of Helicoverpa armigera nucleopolyhedrovirus (HearNPV). …”
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HoBi-like pestivirus in 2 cases of fatal respiratory disease of feedlot cattle in Argentina by Margineda, Carlos Augusto, Ferreyra, Franco Matías, Masnyj, Franco Ezequiel, Audrito, Maximiliano, Favaro, Paula Melisa, Dus Santos, Maria Jose, Pecora, Andrea

“…HoBiPeV was detected by RT-PCR in lungs of both animals and by immunohistochemistry in case 2. Phylogenetic analysis showed that both strains clustered within the “Brazilian-Italian” clade. …”
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Molecular genotyping of Theileria spp. detected in horses from Corrientes City, Argentina by Benitez Ibalo, Alicia P., Debárbora, Valeria Natalia, Mangold, Atilio Jose, Nava, Santiago, Sebastian, Patrick

“…Four nearly complete 18 S rDNA gene sequences were obtained and phylogenetic analyses were carried out. The maximum likelihood tree constructed in this study revealed that two different 18 S rDNA genotypes - namely Genotype A (T. equi sensu stricto) and Genotype C (T. equi sensu lato/Theileria haneyi) - are circulating in the same horse population. …”
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Molecular genotyping of Theileria spp. detected in horses from Corrientes City, Argentina by Benitez Ibalo, Alicia P., Debárbora, Valeria Natalia, Mangold, Atilio Jose, Nava, Santiago, Sebastian, Patrick

“…Four nearly complete 18 S rDNA gene sequences were obtained and phylogenetic analyses were carried out. The maximum likelihood tree constructed in this study revealed that two different 18 S rDNA genotypes - namely Genotype A (T. equi sensu stricto) and Genotype C (T. equi sensu lato/Theileria haneyi) - are circulating in the same horse population. …”
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Genetic Diversity in Phytoplasmas from X-Disease Group Based in Analysis of idpA and imp Genes by Alessio, Florencia Ivette, Bongiorno, Vanina Aylén, Marcone, Carmine, Conci, Luis Rogelio, Fernandez, Franco Daniel

“…In contrast, idpA exhibited strong negative selection, indicating functional conservation. Phylogenetic analyses revealed that imp and idpA provide higher resolution than the 16S rRNA gene, enabling finer differentiation within subgroups. …”
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Molecular evidence of Babesia species in Procyon cancrivorus (Carnivora, Procyonidae) in Uruguay by Thompson, Carolina Soledad, Mangold, Atilio Jose, Félix, María L., Carvalho, Luis A., Armúa-Fernández, María Teresita, Venzal, José Manuel

“…Subsequently, the obtained amplicons were sequenced and full-length sequences was assembled. A phylogenetic tree was constructed and revealed that the Babesia sp. found in this work clustered with other 18sRNA sequences of Babesia spp. obtained from P. lotor from Japan and USA, along with Babesia spp. of maned wolf and I. ovatus. …”
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Complete genome sequence of maize yellow striate virus, a new cytorhabdovirus infecting maize and wheat crops in Argentina by Maurino, Maria Fernanda, Dumon, Analia Delina, Llauger, Gabriela, Alemandri, Vanina Maria, De Haro, Luis Alejandro, Mattio, Maria Fernanda, Del Vas, Mariana, Laguna, Irma Graciela, Gimenez Pecci, Maria De La Paz

“…The highest amino acid sequence identity of the MYSV and BYSMV proteins was 80% between the L proteins, and the lowest was 37% between the proteins 4. Phylogenetic analysis suggested that the MYSV isolates are new members of the genus Cytorhabdovirus, family Rhabdoviridae. …”
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Papaya ringspot virus W infecting Luffa aegyptiaca in Cuba by Cabrera Mederos, Dariel, Giolitti, Fabian, Nome Docampo, Claudia, Bejerman, Nicolas Esteban, Portal, Orelvis

“…Sequence analysis of the RT-PCR product obtained from the capsid protein gene showed highest identity with other PRSV isolates from United States of America, Australia, Venezuela, Brazil, India and Cuba, ranging between 93.2–96.5% and 93.4–98.1% for nucleotide and amino acid sequences, respectively. Phylogenetic analysis showed two main clusters. Cluster I included isolates from the Americas-Australia group and India, including sponge gourd isolate, while the cluster II included isolates from China, Thailand and Taiwan. …”
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Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviru... by Bejerman, Nicolas Esteban, Giolitti, Fabian, De Breuil, Soledad, Trucco, Veronica Milagros, Nome Docampo, Claudia, Lenardon, Sergio Luis, Dietzgen, Ralf Georg

“…The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. …”
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Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in pseudomonas backgrounds as a microevolutionary process by Stritzler, Margarita, Berini, Carolina Andrea, Jozefkowicz, Cintia, Soto, Gabriela Cinthia, Ayub, Nicolás Daniel

“…Although there are increasing evidence that phylogenetically related proteins play different functions in different subcellular compartments, the number of evolutionary steps required for the emergence of a novel protein with a novel subcellular localization remains unclear. …”
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Borrelia burgdorferi sensu lato in Ixodes cf. neuquenensis and Ixodes sigelos ticks from the Patagonian region Argentina by Saracho Bottero, María Noelia, Lareschi, Marcela, Venzal, José Manuel, Carvalho, Luis A., Nava, Santiago, Sebastian, Patrick Stephan, Mackenstedt, Ute

“…The samples of I. sigelos were also positive for the IGS-PCR. Phylogenetically, the haplotypes found in the positive ticks belong to the B. burgdorferi s.l. complex, and they were closely related to Borrelia chilensis, a genospecies isolated from Ixodes stilesi in Chile. …”
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Anthracnose on alfalfa caused by Colletotrichum americae-borealis in Córdoba province, Argentina by Bernanrdi Lima, Nelson, Conforto, Erica Cinthia, Serri, Dannae Lilia, Campilongo Mancilla, Ernesto Javier, Stenglein, Sebastian, Vargas Gil, Silvina

“…Based on the morphology and multilocus phylogenetic analysis, combined sequences of the partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3) and actin (ACT) genes, the three isolates were identified as Colletotrichum americae-borealis. …”
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First Detection and Molecular Characterization of Apple Stem Grooving Virus, Apple Chlorotic Leaf Spot Virus, and Apple Hammerhead Viroid in Loquat in Spain by Canales, Celia, Morán, Félix, Olmos, Antonio, Ruiz-García, Ana B.

“…Studies on all the full-length sequences available in the databases were performed in order to establish the phylogenetic relationships of the Spanish isolates of these two viral species. …”
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High-Throughput Sequencing Discloses the Cucumber Mosaic Virus (CMV) Diversity in Slovakia and Reveals New Hosts of CMV from the Papaveraceae Family by Mrkvová, Michaela, Hancinsky, Richard, Predajna, Lukas, Alaxin, Peter, Achs, Adam, Tomasechová, Jana, Soltys, Katarína, Mihálik, Daniel, Olmos, Antonio, Ruiz-García, Ana B., Glasa, Miroslav

“…Based on a BLAST search and phylogenetic analysis, the Slovak CMV isolates can be divided into two genetically different Groups, Ia and II, respectively. …”
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Isolation and Molecular Identification of Rhizospheric Fungi Associated with Opuntia cochenillifera from Semiarid in Alagoas, Brazil by João Manoel, da Silva, Araujo Dalbon, Viviane, la Rosa Massahud, Regla Toujaguez, Molina Acevedo, Juan Pablo, Machado de Medeiros Ferro, Mayra, Carvalho dos Santos, Tania Marta, Simões do Amaral Alves, Elizabeth, Andrade Lima, Gaus Silvestre

“…The sequences were analyzed with Staden Package and MEGA softwares, followed by the BLASTn search in GenBank. Through the phylogenetic analysis of the rDNA ITS, the species belonging to Coprinellus, Paecilomyces, Aspergillus, Penicillium, and Neurospora were identified. …”
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First report of the fall armyworm, Spodoptera frugiperda (J E Smith) (Lepidoptera: Noctuidae), an alien invasive pest on maize in India by Sharanabasappa, S.D., Kalleshwara Swamy, C.M., Asokan, R., Swamy, H.M.M., Maruthi, M.S., Pavithra, H.B., Hegbe, K., Navi, S., Prabhu, S.T., Goergen, Georg E.

“…Identification of FAW has been carried out employing morphological and DNA barcoding. Phylogenetic analysis has revealed that FAW clustered with Florida (rice strain), Ghana, Nigeria, Uganda on maize. …”
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Discordances between morphological systematics and molecular taxonomy in the stem line of equids: A review of the case of taxonomy of genus Equus by Kefena, E., Mekasha, Yoseph, Han, J.L., Rosenbom, S., Haile, Aynalem, Dessie, Tadelle, Beja-Pereira, A.

“…We also compare and contrast evolutionary histories and phylogenetic relationships of equids inferred from paleontological as well as varieties of molecular data and their implications. …”
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