Search Results - "Phylogenetics"

Analysis of a chitinase from EpapGV, a fast killing betabaculovirus by Salvador, Ricardo, Ferrelli, Maria Leticia, Sciocco, Alicia Ines, Romanowski, Victor

“…Amino acid sequence analysis indicated that the C-terminal KDEL present in most alphabaculovirus chitinases is absent in EpapGV V-CHIA, as well as in the rest of the betabaculoviruses. Phylogenetic analysis was performed with bacterial, lepidopteran, and baculoviral chitinase sequences available in databases. …”
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Distinct strains of the re-emergent Cassava common mosaic virus (genus: Potexvirus) infecting cassava in Argentina by Zanini, Andrea Alejandra, Cuellar, Wilmer J., Celli, Marcos Giovani, Luque, Andres Vicente, Medina, Ricardo Daniel, Conci, Vilma Cecilia, Di Feo, Liliana Del Valle

“…Interestingly, a separate phylogenetic cluster was formed by isolates from the NEA region that only shared 77.1% to 80.3% nucleotide identity with the other clusters. …”
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Molecular and antigenic characterization of bovine Coronavirus circulating in Argentinean cattle during 1994–2010 by Bok, Marina, Miño, Samuel, Rodriguez, Daniela, Badaracco, Alejandra, Nuñes, I., Souza, Sibele P., Bilbao, G., Louge Uriarte, Enrique Leopoldo, Galarza, Roxana Ivon, Vega, Celina Guadalupe, Odeon, Anselmo Carlos, Saif, LInda J., Parreño, Gladys Viviana

“…The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. …”
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Detection and first molecular characterization of bovine papular stomatitis virus in dairy calves in Argentina by Micheloud, Juan Francisco, Aguirre, Laura S., Sandoval, Gabriela V., Avellaneda Cáceres, Agustín, Diodati, Julian Angel, Peralta, Andrea Veronica

“…The sequence analysis revealed 99%, 85%, and 84% similarity with BPSV, Pseudocowpox virus, and Orf virus, respectively. A phylogenetic tree constructed using the B2L sequence showed that the virus clustered with BPSV isolates. …”
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Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens by Agudelo Romero, Patricia, Margarida Fortes, Ana, Suárez, Trinidad, Lascano, Hernan Ramiro, Saavedra, Laura

“…In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. …”
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Description of a new soft tick species (Acari: Argasidae: Ornithodoros) parasite of Octodon degus (Rodentia: Octodontidae) in northern Chile by Muñoz-Leal, Sebastian, Venzal, José Manuel, Nava, Santiago, Marcili, Arlei, González-Acuña, Daniel, Martins, Thiago F., Labruna, Marcelo B.

“…While nymphal stages of O. octodontus lack cheeks and possess a micromammillated dorsal integument, adults have cheeks and exhibit markedly irregular mammillae along their dorsal surface. Phylogenetic analyses of neotropical Argasidae based on mitochondrial 16S rDNA sequences point that O. octodontus forms a monophyletic group with O. xerophylus and an unidentified Ornithodoros sp. from Bolivia, all of them associated with burrow-dweller rodents. …”
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A novel specific duplex real-time RT-PCR method for absolute quantitation of Grapevine Pinot gris virus in plant material and single mites by Morán, Félix, Olmos, Antonio, Lotos, Leonidas, Katis, Nikolaos, Glasa, Miroslav, Predajna, Lukas, Ruiz-García, Ana B.

“…In addition, in the current study a new polymorphism in the GPGV genome responsible for a shorter movement protein has been found. A phylogenetic study based on this genomic region has shown a high variability among Spanish isolates and points to a different evolutionary origin of this new polymorphism. …”
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Performance of diagnostic tests for the detection and identification of Pseudomonas syringae pv. actinidiae (Psa) from woody samples by Loreti, Stefania, Cunty, Amandine, Pucci, Nicoletta, Chabirand, Aude, Stefani, Emilio, Abelleira, Adela, Balestra, Giorgio M., Cornish, Deirdre A., Gaffuri, Francesca, Giovanardi, Davide, Gottsberger, Richard A., Holeva, Maria C., Karahan, Aynur, Karafla, Charikleia D., Mazzaglia, Angelo, Taylor, Robert, Cruz, Leonor, López, María M., Vanneste, Joel L., Poliakoff, Francoise

“…In order to provide complete validation data, both for detection and identification, this TPS was supplemented by a further study of identification from pure culture of phylogenetically closely related Pseudomonas spp., Psa, and bacterial strains associated with kiwifruit. …”
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Performance of outbreak management plans for emerging plant diseases: the case of almond leaf scorch caused by Xylella fastidiosa in mainland Spain by Cendoya, Martina, Lázaro, Elena, Navarro-Quiles, Ana, López-Quílez, Antonio, Conesa, David, Vicent, Antonio

“…The emergence of this outbreak was dated based on phylogenetic studies, and official surveys were used to delimit the current extent of the disease. …”
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Masked genotype 6 of bovine leukemia virus is found in colombian cattle by Corredor Figueroa, Adriana Patricia, Olaya Galán, Nury Nathalia, Salas, Sandra Patricia, Quintero, Juan Sebastián, Fajardo, Álvaro, Soñora, Martín, Moreno, Pilar, Cristina, Juan, Sánchez, Alfredo, Tobón, Julio, Ortiz, Diego, Gutierrez, María Fernanda

“…The obtained amplicons were sequenced and then subjected to phylogenetic analyses. Results A total of 62% of the cows present at 92% of the farms were BLV-positive. …”
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Genome of the African cassava whitefly Bemisia tabaci and distribution and genetic diversity of cassava-colonizing whiteflies in Africa by Chen, W., Wosula, Everlyne N., Hasegawa, D.K., Casinga, C., Shirima, R.R., Fiaboe, K.K.M., Hanna, R., Fosto, A., Goergen, Georg E., Tamò, Manuele, Mahuku, George S., Murithi, H.M., Tripathi, L., Mware, B., Kumar, P. Lava, Ntawuruhunga, Pheneas, Moyo, C., Yomeni, M., Boahen, S., Edet, M., Awoyale, W., Wintermantel, William M., Ling, K.S., Legg, James P., Fei, Z.

“…The SSA-ECA genome assembled from Illumina short reads has a total size of 513.7 Mb and a scaffold N50 length of 497 kb, and contains 15,084 predicted protein-coding genes. Phylogenetic analysis suggests that SSA-ECA diverged from MEAM1 around 5.26 million years ago. …”
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Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds by Chen Wang, Yao-sheng Chen, Han Jianlin, De-lin Mo, Xiu-jin Li, Xiao-hong Liu

“…We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs. Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant. …”
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Genomic characterization of multidrug-resistant Salmonella serovars Derby and Rissen from the pig value chain in Vietnam by González Santamarina, B., García-Soto, S., Sinh Dang-Xuan, Abdel-Glil, M.Y., Meemken, D., Fries, R., Tomaso, H.

“…Plasmid replicons were found in almost all strains [95.6% (22/23)], and the phylogenetic analysis detected nine clusters (S. Derby, n = 5; S. …”
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Molecular survey of cattle ticks in Burundi: First report on the presence of the invasive Rhipicephalus microplus tick by Nyabongo, Lionel, Odongo, David O., Milton, G., Machuka, Eunice M., Vudriko, P., Pelle, Roger, Kanduma, E.G.

“…Chi-square test was used to test for association between agroecological zones and the prevalence of tick species. Phylogenetic relationships were inferred using bayesian and maximum likelihood algorithms. …”
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Haplotype analysis of the mitochondrial DNA d- loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democra... by Simon, P.B., Junga, J.O., Mekuriaw, Getinet, Machuka, Eunice M., Tiambo, Christian K., Kabange, D., Dieudinné, K.M.M., Kizungu, R.V., Ochieng, J.W., Pelle, Roger

“…A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. …”
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A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids by Guyot, V., Rajeswaran, R., Chu, H.C., Karthikeyan, C., Laboureau, N., Galzi, S., Mukwa, L., Krupovic, M., Kumar, P. Lava, Iskra-Caruana, M.L., Pooggin, M.

“…Illumina sequencing analysis of banana aphids and leaf samples from Africa revealed an alphasatellite that should be classified in a new genus, phylogenetically related to alphasatellites of nanoviruses infecting dicots. …”
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Metagenomic investigation of ticks from Kenyan wildlife reveals diverse microbial pathogens and new country pathogen records by Ergunay, K., Mutinda, M., Bourke, B., Justi, S.A., Caicedo-Quiroga, L., Kamau, J., Mutura, S., Akunda, I.K., Cook, Elizabeth A.J., Gakuya, F., Omondi, P., Murray, S., Zimmerman, D., Linton, Y.-M.

“…This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. …”
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Regional drivers of diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus by Liu, S., Liu, Y., Jelen, E., Alibadian, M., Yao, C.-T., Li, X., Kayvanfar, N., Wang, Y., Vahidi, F.S.M., Han Jianlin, Sundev, G., Zhang, Z., Schweizer, M.

“…We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree and inferred demographic history within and migration between lineages. …”
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Genome-wide Analysis of MYB Gene Family in Potato Provides Insights into Tissue-specific Regulation of Anthocyanin Biosynthesis by Li, Y., Liang, J., Zeng, X., Guo, H., Luo, Y., Kear, P., Zhang, S., Zhu, G.

“…Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization, further supporting the results of phylogenetic analysis. Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB, as the anthocyanins could be accumulated in different tissues, showing colorful phenotypes. …”
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Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping by Bhattacharjee, Ranjana, Luseni, M.M., Ametefe, K., Agre, P.A., Kumar, P.L., Grenville-Briggs, L.J.

“…The genetic diversity among different accessions was assessed using three complementary clustering methods including the model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. A network analysis was further carried out to understand the genetic relationships among cacao accessions from Sierra Leone and Togo. …”
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