Search Results - "Phylogenetics"

Genetic characterization and pathogenicity of Rhizoctonia solani associated with common bean web blight in the main bean growing area of Argentina by Spedaletti, Yamila Andrea, Aparicio Gonzalez, Monica Alicia, Mercado Cardenas, Guadalupe Eugenia, Rodriguero, Marcela Silvina, Taboada, Gisel María, Aban, Carla Luciana, Sühring, Silvia Susana, Vizgarra, Oscar Nicéforo, Galvan, Marta Zulema

“…All the isolates were identified as R. solani AG 2‐2WB, and they exhibited considerable intragroup variation. The phylogenetic tree generated with the ITS sequences confirmed the isolates identification. …”
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MLST reveals a separate and novel clonal group for Acidovorax avenae strains causing red stripe in sugarcane from Argentina by Fontana, Paola Daniela, Tomasini, Nicolás, Fontana, Cecilia Alejandra, Di Pauli, Valentina, Cocconcelli, Pier Sandro, Vignolo, Graciela Margarita, Salazar, Sergio Miguel

“…This study included 15 local strains isolated from four different sugarcane planting regions and selected after RAPD analysis and reference strains of A. citrulli, A. avenae, and A. oryzae to investigate their phylogenetic relationships. MLST analysis resulted in five sequence types (STs) among the sugarcane A. avenae strains which constitute a clonal complex, meaning a common and close origin. …”
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Exploring the ancestral mechanisms of regulation of horizontally acquired nitrogenases by Pascuan, Cecilia Gabriela, Fox, Ana Romina, Soto, Gabriela Cinthia, Ayub, Nicolás Daniel

“…Here, we integrated evolutionary and functional approaches to elucidate this unusual phenotype. Phylogenetic analysis showed that polyhydroxybutyrate (PHB) biosynthesis genes from natural nitrogen-fixing Pseudomonas strains have been acquired by horizontal transfer. …”
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The first caprine rotavirus detected in Argentina displays genomic features resembling virus strains infecting members of the Bovidae and Camelidae by Louge Uriarte, Enrique Leopoldo, Badaracco, Alejandra, Matthijnssens, Jelle, Zeller, Mark, Heylen, Elizabeth, Manazza, Jorge Alberto, Miño, Samuel, Ranst, Marc Van, Odeon, Anselmo Carlos, Parreño, Gladys Viviana

“…The RVA strain RVA/Goat-wt/ARG/0040/2011/G8P[1] displayed the following genomic constellation: G8-P[1]-I2-R5-C2-M2-A3-N2-T6-E12-H3, reminiscent to guanaco and other bovine-like RVA strains detected in Argentina. Phylogenetic analyses revealed that most of the genome segments had a rather close relatedness with RVA strains typically obtained from cattle, sheep, South American camelids and goats. …”
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Identification and expression analysis of NAC transcription factors potentially involved in leaf and petal senescence in Petunia hybrida by Trupkin, Santiago Ariel, Astigueta, Francisco H., Baigorria, Amilcar Hernan, Garcia, Martin Nahuel, Delfosse, Veronica Cecilia, González, Sergio A., Perez De La Torre, Mariana, Moschen, Sebastian, Lia, Veronica Viviana, Fernandez, Paula Del Carmen, Heinz, Ruth Amelia

“…Expression data and phylogenetic analysis were used to generate a list of 10–15 candidate genes; 7 of these were considered key regulatory candidates in senescence because of their consistent upregulation in the three senescence processes examined. …”
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Biological and molecular characterization of Rachiplusia nu single nucleopolyhedrovirus, a promising biocontrol agent against the South American soybean pest Rachiplusia nu by Jakubowicz, Violeta, Taibo, Catalina Beatriz, Sciocco, Alicia Ines, Arneodo Larochette, Joel Demian

“…Histopathology of infected late-instar larvae revealed broad tissue tropism, where fat bodies and epidermis were the most affected organs. Phylogenetic analysis of concatenated polh, lef-8 and lef-9 partial sequences classified RanuNPV as a new species that clusters with other group II alphabaculoviruses infecting larvae of Plusiinae. …”
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A new species of Ornithodoros (Acari: Argasidae) from desert areas of northern Chile by Muñoz-Leal, Sebastian, Venzal, José Manuel, González-Acuña, Daniel, Nava, Santiago, Lopes, Marcos G., Martins, Thiago F., Figueroa, Cecilia, Fernández, Nicolás, Labruna, Marcelo B.

“…The larval diagnostic characters for this species are a combination of a large pyriform dorsal plate with a length of approximately 300 μm, 17 pairs of dorsal setae with five central pairs, hypostome with apex pointed and dental formula 2/2 in most rows, 3/3 apically, and capsule of the Haller’s organ oval in shape without reticulations. Phylogenetic analyses inferred from the mitochondrial 16S rRNA gene and a Principal Component Analysis based on morphometric characters provide additional support to the description of O. atacamensis as an independent lineage within the genus clustering within the O. talaje species group.…”
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Phytoplasmas diversity and identification of new aster yellows subgroup (16SrI) associated with weed species in Argentina by Fernandez, Franco Daniel, Galdeano, Ernestina, Conci, Luis Rogelio

“…To confirm the association of phytoplasma infection with symptomatic plants, PCR, RFLP and phylogenetic analyses based on 16S rRNA-encoding sequences were performed. …”
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Identification and Characterization of Diaporthe spp. Associated with Twig Cankers and Shoot Blight of Almonds in Spain by León, Maela, Berbegal, Mónica, Rodríguez-Reina, José M., Elena, Georgina, Abad-Campos, Paloma, Ramón-Albalat, Antonio, Olmo, Diego, Vicent, Antonio, Luque, Jordi, Miarnau, Xavier, Agustí-Brisach, Carlos, Trapero, Antonio, Capote, Nieves, Arroyo, Francisco T., Avilés, Manuel, Gramaje, David, Andrés-Sodupe, Marcos, Armengol, Josep

“…Moreover, a novel phylogenetic species, D. mediterranea, was described. …”
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Olive Leaf Mottling Virus: A New Member of the Genus Olivavirus by Ruiz-García, Ana B., Candresse, Thierry, Malagón, José, Ruiz-Torres, Manuel, Paz, Sergio, Pérez-Sierra, Ana, Olmos, Antonio

“…The genomic organization contained 10 open reading frames (ORFs) from 5′ to 3′ : ORF1a, ORF1b (RdRp), ORF2 (p22), ORF3 (p7), ORF4 (HSP70h), ORF5 (HSP90h), ORF6 (CP), ORF7 (p19), ORF8 (p12), ORF9 (p23) and ORF10 (p9). Phylogenetic analyses clustered this virus in the genus Olivavirus, family Closteroviridae, with the closest species being Olivavirus flaviolae, commonly named olive leaf yellowing-associated virus (OLYaV). …”
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Identification of potential vectors and alternative plant hosts for the phytoplasma associated with Napier grass stunt disease in Ethiopia by Arocha, Y., Zerfy, T., Abebe, G., Proud, J., Hanson, Jean, Wilson, M., Jones, Peter G., Lucas, J.

“…Restriction fragment length polymorphism (RFLP), sequencing of PCR products and phylogenetic analysis were conducted for a finer identification and characterization of the phytoplasma associated with NGS. …”
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The development of a multiplex PCR assay for the detection of Fusarium oxysporum f. sp. cubense lineage VI strains in East and Central Africa by Ndayihanzamaso, Privat, Karangwa, Patrick, Mostert, Diane, Mahuku, George S., Blomme, Guy, Beed, Fenton D., Swennen, Rony L., Viljoen, Altus

“…Banana Fusarium wilt is managed by excluding the pathogen from disease-free areas and by planting disease-resistant varieties in infested fields. Six phylogenetically closely-related vegetative compatibility groups (VCGs) of Foc, VCGs 0124, 0125, 0128, 01212, 01220 and 01222 are present in ECA, which all group together in Foc Lineage VI. …”
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DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms by Ketema, S., Tesfaye, B., Keneni, G., Amsalu, B., Assefa, E., Greliche, N., Machuka, Eunice M., Yao, Nasser

“…Model-based ancestry analysis, the phylogenetic tree, discriminant analysis of principal components and principal coordinate analysis classified the 357 genotypes into three well-differentiated genetic populations. …”
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Genomic diversity, population structure, and signature of selection in five Chinese native sheep breeds adapted to extreme environments by Abied, A., Bagadi, A., Bordbar, F., Pu, Y., Augustino, S.M.A., Xue, X., Xing, F., Gebreselassie, G., Han Jianlin, Mwacharo, Joram M., Ma, Y., Zhao, Q.

“…PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. …”
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Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya by Avedi, E.K., Adediji, A.O., Kilalo, D.C., Olubayo, F.M., Macharia, I., Ateka, E.M., Machuka, Eunice M., Mutuku, Josiah M.

“…Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. …”
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Methicillin-resistant and methicillin-susceptible Staphylococcus from vervet monkeys (Chlorocebus sabaeus) in Saint Kitts by Hoefer, A., Boyen, F., Beierschmitt, A., Moodley, Arshnee, Roberts, M.C., Butaye, P.

“…Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. …”
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Genetic Identity, Diversity, and Population Structure of the International Potato Center's Sweetpotato (I. batatas) Germplasm Collection by Anglin, Noelle L., Robles, R., Rossel, G., Alagon, R., Panta, A., Jarret, Robert L., Manrique, N., Ellis, David

“…Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. …”
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Diversity of water yam (Dioscorea alata L.) accessions from Cote d'Ivoire based on SNP markers and agronomic traits by Bakayoko, L., Pokou, D.N., Kouassi, A.B., Agre, A.P., Kouakou, A.M., Dibi, K.E.B., Nzue, B., Mondo, J., Adebola, P.O., Akintayo, O.T., Asfaw, A., N'guetta, A.S.

“…This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. …”
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Diversity of Tartary Buckwheat (Fagopyrum tataricum) landraces from Liangshan, Southwest China: Evidence from morphology and SSR markers by Song, Yingjie, Cheng, Zhuo, Dong, Yumei, Liu, Dongmei, Bai, Keyu, Jarvis, Devra I., Feng, Jinchao, Long, Chunlin

“…All accessions were divided into three categories according to phylogenetic dendrogram analysis, which was consistent with folk nomenclature and taxonomy. …”
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Outbreaks of foot-and-mouth disease in Burundi, East Africa, in 2016, caused by different serotypes by Estevez Garcia, A.I., Lefebvre, D.J., Nyabongo, Lionel, Haegeman, A., Nkundwanayo, C., Vleeschauwer, A. de, Ntakirutimana, D., Leeuw, I. de, Nsanganiyumwami, D., Niyokwizera, P., Berg, T. van den, Niyokwishimira, A., Clercq, K.D.

“…In Bururi and Cankuzo provinces, the serological profile suggested a recent incursion with serotype SAT2, while in Bubanza province, the serological profile suggested past incursions with serotype O and possibly serotype SAT1. The phylogenetic assessments showed the presence of topotypes A/Africa/G-I and SAT2/IV, similarly to previously characterized virus strains from other countries in the region, suggesting a transboundary origin and necessitating a regional approach for vaccination and control of FMD.…”
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