Resultados de búsqueda - "Phylogenetics"

Characteristics of Staphylococcus aureus isolated from patients in Busia County Referral Hospital, Kenya por Obanda, B.A., Cook, Elizabeth A.J., Fèvre, Eric M., Bebora, L., Ogara, W., Wang, S.-H., Gebreyes, W., Ngetich, R., Wandede, D., Muyodi, J., Blane, B., Coll, F., Harrison, E.M., Peacock, S.J., Gitao, G.C.

“…Virulence genes, Panton-Valentine leukocidin (pvl), toxic shock syndrome toxin-1 (tsst-1), and sasX gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. …”
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Food biodiversity: Quantifying the unquantifiable in human diets por Hanley-Cook, Giles T., Daly, Aisling J., Remans, Roseline, Jones, Andrew D., Murray, Kris A., Huybrechts, Inge, Baets, Bernard de, Lachat, Carl

“…To illustrate: (i) dietary species richness fails to account for the distribution of foods across the diet or their functional traits; (ii) evenness indices, such as the Gini-Simpson index, require widely accepted relative abundance units (e.g., kcal, g, cups) and evidence-based moderation weighting factors; and (iii) functional dissimilarity indices are constructed based on an arbitrary selection of distance measures, cutoff criteria, and number of phylogenetic, nutritional, and morphological traits. …”
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Analysis of population structure and genetic diversity in a Southern African soybean collection based on single nucleotide polymorphism markers por Tsindi, A., Eleblu, J.S.Y., Gasura, E., Mushoriwa, H., Tongoona, P., Danquah, E., Mwadzingeni, L., Zikhali, M., Ziramba, E., Mabuyaye, G., Derera, J.

“…Inference based on three tools, such as the Evanno method, silhouette plots and UPMGA phylogenetic tree showed the existence of three sub-populations. …”
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Studies on genetic polymorphism of improved cowpea varieties using Simple Sequence Repeats (SSR) marker por Olasan, O.J., Omoigui, L., Oluma, H.A., Aguoru, C.U., Deo, D., Ugbaa, M.S., Ezugwu, J., Ekeruo, G., Dughduh, P., Iyorkaa, N., Simon, M., Okoh, T.

“…As part of efforts to promote crop improvement, this study was carried out to determine the level of genetic polymorphism and phylogenetic relationship that exists among four selected improved varieties of cowpea (SAMPEA-14, SAMPEA-15, SAMPEA-17 and SAMPEA-18) using ten SSR molecular markers. …”
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Distribution and diversity of emergent Banana bunchy top virus infecting banana and plantain in Cameroon, Central Africa por Ngatat, S., Hanna, R., Doumtsop Fotio, A.R.P., Lienou, J.A., Nanga, S.N., Fotso Kaute, A., Osundahunsi, B., Fiaboe, K., Ndemba, B., Dossa, G.S., Alabi, T., Kumar, P.L.

“…The findings indicate BBTV expansion from the location of first detection in 2008 to about 4–25 km in all directions, with the virus spread range of about 700 km2, as of the last survey in 2022. Phylogenetic analysis using complete nucleotide sequences of the BBTV-R and BBTV-S gene aligned Cameroon isolates with the sub-Saharan Africa subgroup of the Pacific-Indian Oceans (PIO) group of BBTV isolates, suggesting a likely virus invasion from neighbouring central African countries where BBTV presence had been reported in the 1980s. …”
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Genomic epidemiology of Rift Valley fever virus involved in the 2018 and 2022 outbreaks in livestock in Rwanda por Nsengimana, I., Juma, John, Roesel, Kristina, Gasana, M.N., Ndayisenga, F., Muvunyi, C.M., Hakizimana, E., Hakizimana, J.N., Eastwood, G., Chengula, A.A., Bett, Bernard K., Kasanga, C.J., Oyola, Samuel O.

“…Both maximum likelihood and Bayesian-based phylogenetic analyses were performed. The findings showed that RVF viruses belonging to a single lineage, C, were circulating during the two outbreaks, and shared a recent common ancestor with RVF viruses isolated in Uganda between 2016 and 2019, and were also linked to the 2006/2007 largest East Africa RVF outbreak reported in Kenya, Tanzania, and Somalia. …”
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DArTseq-based genome-wide SNP markers reveal limited genetic diversity and highly structured population in assembled West African cowpea germplasm por Koura, A.A., Kena, A.W., Annor, B., Adejumobi, I.I., Maina, F., Sayadi Maazou, A.R., Razakou, I.B.Y., Attamah, P., Kusi, R., Boukar, O., Akromah, R.

“…Discriminant analysis and phylogenetic analysis supported this finding, indicating the presence of distinct groups within the cowpea population. …”
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Detection and prevalence of a novel Bandavirus related to Guertu virus in Amblyomma gemma ticks and human populations in Isiolo County, Kenya por Koka, H., Langat, S., Oyola, Samuel O., Cherop, F., Rotich, G., Mutisya, J., Ofula, V., Limbaso, K., Ongus, J.R., Lutomiah, J., Sang, R.

“…The virus genome is consistent with the described genomes of other members of the genus <i>Bandavirus</i>, with nucleotides lengths of 6403, 3332 and 1752 in the Large (L), Medium (M) and Small (S) segments respectively. Phylogenetic analysis showed that the virus clustered with Guertu virus although it formed a distinct and well supported branch. …”
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Evaluating genetic diversity and seed composition stability within Pan-African Soybean Variety Trials por de Meyer, M., Prenger, E., Mahmood, A., da Fonseca Santos, M, Chigeza, G., Song, O., Mwadzingeni, L., Mukoro, R., Chibanda, M., Mabuyaye, G., Diers, B., Scaboo, A.

“…We also evaluated genetic diversity of 19 PAT cultivars through phylogenetic analyses with 1059 USDA Germplasm Resources Information Network (GRIN) diversity panel accessions. …”
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Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding por Wang, Yulong, Jiang, Conghui, Zhang, Xingtan, Yan, Huimin, Yin, Zhigang, Sun, Xingming, Gao, Fenghua, Zhao, Yan, Liu, Wei, Han, Shichen, Zhang, Jingjing, Zhang, Yage, Zhang, Zhanying, Zhang, Hongliang, Li, Jinjie, Xie, Xianzhi, Zhao, Quanzhi, Wang, Xiaoning, Ye, Guoyou, Li, Junzhou, Ming, Ray, Li, Zichao

“…In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. …”
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Changes in insecticide resistance and host range performance of planthoppers artificially selected to feed on resistant rice por Horgan, Finbarr G., Garcia, Charle Patrick F., Haverkort, Fay, de Jong, Peter W., Ferrater, Jedeliza B.

“…We found that planthoppers with long-term exposure to resistant hosts (particularly IR62 with the Bph3(t) and BPH32 gene loci, and PTB33 with the Bph3(t), BPH32 and BPH26 gene loci) gained virulence against related varieties with the same and different resistance genes, but planthoppers adapted to the resistant host IR65482-4-136-2-2 (BPH10 locus) had reduced performance on phylogenetically distant plants with distinct resistant genes. …”
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Loss-of-function Alleles of Heading date 1 (Hd1) are Associated with Adaptation of Temperate Japonica Rice Plants to the Tropical Region por Kim, Sung-Ryul, Torollo, Gideon, Yoon, Mi-Ra, Kwak, Jieun, Lee, Choon-Ki, Prahalada, G.D., Choi, Il-Ryong, Yeo, Un-Sang, Jeong, O-Young, Jena, Kshirod K., Lee, Jeom-Sig

“…All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. …”
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Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution por Chen, Sunlu, Saito, Nozomi, Encabo, Jaymee R., Yamada, Kanae, Choi, Il-Ryong, Kishima, Yuji

“…In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41–15.00 million years old. …”
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Characterisation of the nicotianamine aminotransferase and deoxymugineic acid synthase genes essential to Strategy II iron uptake in bread wheat (Triticum aestivum L.) por Beasley, Jesse T., Bonneau, Julien P., Johnson, Alexander A. T.

“…The coding sequences of the three TaDMAS1 homeologs consist of three exons with ≥97.8% nucleotide sequence identity. Phylogenetic analysis revealed that the TaNAAT and TaDMAS1 proteins are most closely related to the HvNAAT and HvDMAS1 proteins of barley and that there are two distinct groups of TaNAAT proteins—TaNAAT1 and TaNAAT2 –that correspond to the HvNAATA and HvNAATB proteins, respectively. …”
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Genetic diversity and population structure of Fasciola gigantica isolated from cattle in Malawi por Mogha, L., Kainga, H., Kamanga, N., Kapalamula, T.F., Wood, C., Thomas, Lian F., Mutua, Florence K., Sargison, N., Hayashida, K., Tsutsumi, T., Hayashi, N., Nonaka, N., Nakao, R., Chatanga, E.

“…The sequences obtained were used to investigate genetic diversity through median-joining networks and phylogenetic analysis. Tajima’s D test and Fu’s Fs statistics were used to determine the population structure. …”
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Genome-wide association study and marker validation to enhance yellow color in durum wheat por Cabas-Lühmann, Patricia, Dreisigacker, Susanne, Ammar, Karim, Megerssa, Shitaye H., Schwember, Andrés Ricardo, Matus, Iván, Ibba, Maria Itria

“…Allelic variants were identified at the Psy1-A1 and Psy1-B1 loci using gene-based molecular markers, while both genes showed close phylogenetic relationships and low sequence diversity across Triticum species. …”
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Unveiling hepatitis E virus diversity in Sudan's internally displaced populations: a molecular epidemiology approach por Osman, H.A., Bakr, W.M.K., Hashish, M.H., Elkhidir, I.M., Bedri, S., Oyola, Samuel O., Norder, H., El-Wahab, E.W.A.

“…Eighteen high-quality RNA-positive samples were sequenced, and genotyping was performed based on the ORF2 region. Phylogenetic analysis was conducted using the HEV Genotyping Tool and Geneious Prime software. …”
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Antibodies against bovine herpesvirus 4 are highly prevalent in wild African buffaloes throughout eastern and southern Africa por Dewals, B., Gillet, L., Gerdes, T., Taracha, E.L.N., Thiry, E., Vanderplasschen, A.

“…Our data are discussed in the light of our recent phylogenetic study demonstrating that the BoHV-4 Bo17 gene has been acquired from a recent ancestor of the African buffalo. …”
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Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.) por Galeano Mendoza, CH, Fernández, A.C., Gómez, M., Blair, Matthew W.

“…The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes.The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. …”
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Extensive polymorphism of Ra86 genes in field populations of Rhipicephalus appendiculatus from Kenya por Kamau, L.M., Skilton, Robert A., Githaka, Naftaly W., Kiara, Henry K., Kabiru, E., Shah, Tushaar, Musoke, A.J., Bishop, Richard P.

“…Evidence that selection contributes to the observed sequence variation was provided by analysis of ratio of synonymous and non-synonymous substitutions and application of the selective neutrality and neutral evolution tests to the primary data. Phylogenetic analysis clustered sequences from all Ra86 size types and Bm86, into four major clades based on amino acid substitutions, but there was no evidence that these groupings correlated with geographical separation of R. appendiculatus populations…”
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