Search Results - "Phylogenetics"

Borrelia infection in Ixodes pararicinus ticks (Acari: Ixodidae) from northwestern Argentina by Nava, Santiago, Barbieri, Amália Regina Mar, Maya, Leticia, Colina, Rodney, Mangold, Atilio Jose, Labruna, Marcelo B., Venzal, José Manuel

“…One male and one female of I. pararicinus collected in Jujuy were found to be positive to Borrelia infection with the three molecular markers tested. Phylogenetically, the Borrelia found in I. pararicinus from Jujuy belongs to the B. burgdorferi s.l complex, and it was similar to one of the genospecies detected in I. aragaoi from Uruguay. …”
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Identification and molecular characterization of a novel circular single-stranded DNA virus associated with yerba mate in Argentina by Bejerman, Nicolas Esteban, De Breuil, Soledad, Nome Docampo, Claudia

“…Its unique genome organization and phylogenetic relationships indicates that YMaCV represents a distinct evolutionary lineage within the ssDNA viruses and therefore this virus should be classified as a member of a new species within an unassigned genus or family.…”
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Identification and molecular characterization of a phytoplasma associated with sunflower in Argentina by Guzmán, Fabiana, Giolitti, Fabian, Fernandez, Franco Daniel, Nome Docampo, Claudia, Lenardon, Sergio Luis, Conci, Luis Rogelio

“…The 16S rDNA sequence from SunPhy showed the highest identity (99 %) with 16SrIII members and the phylogenetic tree confirmed a closer relationship to subgroup J of the 16SIII ribosomal group. …”
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Geographical distribution, genetic studies and vector transmission of alfalfa enamovirus-1 infecting alfalfa crop in Argentina by Trucco, Veronica Milagros, Cabrera Mederos, Dariel, Lenardon, Sergio Luis, Giolitti, Fabian

“…The CP sequence identity among 16 AEV-1 isolates from Argentina was from 98 to 100% and from 98.9 to 100% at nucleotide and amino acid levels, respectively, indicating a low level of sequence variation among these isolates. The phylogenetic analysis based on the complete nucleotide sequence of the CP gene indicated that AEV-1 isolates are closely related and clustered in a monophyletic group. …”
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Sobre la mancha púrpura de la semilla de la soja: naturaleza de su etiología y diversidad by Guillin, Eduardo Alejandro

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Genetic characterization of canine respiratory coronavirus by Larsson, Simon

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Reproduction of contagious caprine pleuropneumonia reveals the ability of convalescent sera to reduce hydrogen peroxide production in vitro by Liljander, Anne M., Sacchini, F., Stoffel, M.H., Schieck, Elise G., Stokar-Regenscheit, N., Labroussaa, F., Heller, M., Salt, Jeremy, Frey, J., Falquet, L., Goovaerts, D., Jores, Joerg

“…Reannotation of the genome sequence of ILRI181 and F38T revealed the existence of genes encoding the complete glycerol uptake and metabolic pathways involved in hydrogen peroxide (H2O2) production in the phylogenetically related pathogen M. mycoides subsp. mycoides. …”
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Status and epidemiology of maize lethal necrotic disease in northern Tanzania by Kiruwa, F.H., Mutiga, Samuel K., Njuguna, Joyce N., Machuka, Eunice M., Senay, S., Feyissa, T., Ndakidemi, P.A., Stomeo, Francesca

“…In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. …”
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Detection and diversity of maize yellow mosaic virus infecting maize in Nigeria by Yahaya, A., Dangora, D.B., Alabi, O.J., Zongoma, A.M., Kumar, P. Lava

“…In pairwise comparisons, the MaYMV sequences derived in this study shared 97–99% nucleotide identity with sequences of other MaYMV isolates available in the NCBI GenBank. Phylogenetic analysis revealed the segregation of global MaYMV sequences into three host-independent clusters with pattern of geographic structuring.…”
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The genome of Caenorhabditis bovis by Stevens, L., Rooke, S., Falzon, Laura C., Machuka, Eunice M., Momanyi, Kelvin N., Murungi, Maurice K., Njoroge, Samuel M., Odinga, Christian O., Ogendo, A., Ogola, J., Fèvre, Eric M., Blaxter, M.

“…We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. …”
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Association of LEI0258 marker alleles and susceptibility to virulent Newcastle Disease Virus infection in Kuroiler, Sasso, and Local Tanzanian Chicken Embryos by Mpenda, Fulgence N., Tiambo, Christian K., Kyallo, Martina M., Juma, John, Pelle, Roger, Lyantagaye, Sylvester L., Buza, Joram

“…A total of 75 DNA sequences comprised of 29 Kuroiler, 29 local Tanzanian chickens, and 17 Sasso were analyzed. Neighbor-joining phylogenetic trees were constructed to depict the clustering of LEI0258 marker alleles and relationship with susceptibility. …”
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Antimicrobial resistant and extended-spectrum ß-lactamase (ESBL) producing Escherichia coli isolated from fecal samples of African dromedary camels by Nüesch-Inderbinen, M., Kindle, P., Baschera, M., Liljander, Anne M., Jores, Joerg, Corman, V.M., Stephan, R.

“…PCR and amplicon sequencing showed that the ESBL producer belonged to E. coli phylogenetic group A, sequence type (ST) 48, and harbored blaCTX-M-15. …”
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Detection of circulating hepatitis B virus immune escape and polymerase mutants among HBV-positive patients attending Institut Pasteur de Bangui, Central African Republic by Koyaweda, G.W., Ongus, J.R., Machuka, Eunice M., Juma, John, Macharia, R., Komas, N.P., Pelle, Roger

“…HBV sequences were genotyped/subgenotyped by phylogenetic analysis and serotyped based on predicted amino acid residues at positions s122, s127, s140, s159, and s160. …”
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Toward unifying global hotspots of wild and domesticated biodiversity by Pironon, Samuel, Borrell, James S., Ondo, Ian, Douglas, Ruben, Phillips, Charlotte, Khoury, Colin K., Kantar, Michael B., Fumia, Nathan, Soto Gomez, Marybel, Viruel, Juan, Govaerts, Rafael, Forest, Félix, Antonelli, Alexandre

“…Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. …”
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Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats by Mekuriaw, Getinet, Khayatzadeh, N., Liu, B., Osama, S., Haile, Aynalem, Rischkowsky, Barbara A., Zhang, W., Tesfaye, K., Dessie, Tadelle, Okeyo Mwai, Ally, Djikeng, Appolinaire, Mwacharo, Joram M.

“…Although runs of homozygosity (ROH) were ubiquitous genome‐wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. …”
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Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic by Ling, J., Hickman, R.A., Li, J., Lu, X., Lindahl, Johanna F., Lundkvist, Å., Järhult, J.D.

“…Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. …”
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Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers by Zhong, T., Han, J.L., Guo, J., Zhao, Q.J., Fu, B.L., He, X.H., Jeon, J.T., Guan, Wei-Jun, Ma, Y.H.

“…To determine the genetic diversity and phylogenetic relationships among Chinese sheep, 10 indigenous breeds and one introduced breed were genotyped for 19 microsatellite loci. …”
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Genome Wide Identification of the MLO Gene Family Associated with Powdery Mildew Resistance in Rubber Trees (Hevea brasiliensis) by Liyanage, K.K., Khan, S., Herath, V., Brooks, S., Mortimer, P.E., Nadir, S., Hyde, Kevin D., Xu, J.C.

“…Sequence analysis identified non-synonymous variations (NSVs) in 12 HbMLO proteins. Phylogenetic analysis of the HBMLO genes revealed seven different clades. …”
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Occurrence of a novel strain of Moroccan watermelon mosaic virus infecting pumpkins in Kenya by Mumo, N., Ateka, E.M., Mamati, E., Rimberia, F.K., Asudi, G.O., Machuka, Eunice M., Juguna, J.N., Stomeo, Francesca, Pelle, Roger

“…The isolates shared 83.4 to 83.7% nucleotide (nt) and 92.3 to 95.1% amino acid (aa) sequence identities in the coat protein and 79.5 to 79.9% nt and 89.2 to 89.7% aa identities in the polyprotein with papaya isolates of MWMV. Phylogenetic analysis using complete polyprotein nt sequences revealed the clustering of both pumpkin isolates of MWMV with corresponding sequences of cucurbit isolates of the virus from other parts of Africa and the Mediterranean regions, distinct from a clade formed by papaya isolates. …”
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Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations by Nguluma, A., Kyallo, Martina M., Mekuriaw, Getinet, Loina, R., Nziku, Z., Chenyambuga, S., Pelle, Roger

“…We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D‐loop. …”
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