Search Results - "Phylogenetics"

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers by Nkhata, Wilson, Shimelis, Hussein, Melis, Rob, Chirwa, Rowland, Mzengeza, Tenyson, Mathew, Isack, Shayanowako, Admire

“…The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.…”
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Incidence of RNA viruses infecting taro and tannia in East Africa and molecular characterisation of dasheen mosaic virusisolates by Kidanemariam, Dawit B., Sukal, A.C., Abraham, Adane D., Njuguna, Joyce N., Stomeo, Francesca, Dale, J.L., James, A.P., Harding, R.M.

“…The complete genomes of nine DsMV isolates from East Africa were cloned and sequenced. Phylogenetic analyses based on the amino acid sequence of the DsMV CP‐coding region revealed two distinct clades. …”
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Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates by Woldeyohannes, Aemiro Bezabih, Iohannes, Sessen Daniel, Miculan, Mara, Caproni, Leonardo, Ahmed, Jemal Seid, Sousa, Kauê de, Desta, Ermias Abate, Fadda, Carlo, Pè, Mario Enrico, Dell’Acqua, Matteo

“…Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. …”
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Distribution and genetic diversity of Tomato spotted wilt virus following an incursion into Kenya by Macharia, I., Backhouse, D., Ateka, Elijah Miinda, Wu, S.-B., Harvey, Jagger J.W., Njahira, Moses N., Skilton, Robert A.

“…Most of the positive samples came from Nakuru, where the virus was first detected, with only a single positive sample being obtained from Loitokitok and none from Bungoma or Kirinyaga. A phylogenetic analysis based on partial nucleocapsid (N) protein gene sequences suggested that the Kenyan isolates formed a single subgroup nested within a cluster of isolates that came predominantly from Europe. …”
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Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel by Zubair, Saima, Fischer, Anne, Liljander, Anne M., Meens, Jochen, Hegerman, Jan, Gourlé, Hadrien, Bishop, Richard P., Roebbelen, Ina, Younan, Mario, Mustafa, Mudassir Imran, Mushtaq, Mamoona, Bongcam-Rudloff, Erik, Jores, Joerg

“…This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. …”
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Taxonomic and Ecogeographic Predictors of Resistance Against Phthorimaea operculella Zeller in Wild Potato Tubers by Horgan, F.G., Portalanza, D., Pelletier, Y., Quiring, D.T.

“…The frequency of resistant accessions was similar across phylogenetic clades, but resistance was more frequent in accessions with an endosperm balance number (EBN) of 1 or 4 and a ploidy level of 4 × or 6 × . …”
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Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species by Bozan, I., Achakkagari, S.R., Anglin, Noelle L., Ellis, David, Tai, H.H., Stromvik, M.V.

“…Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. …”
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Characterization of Hoplolaimus seinhorsti and Hoplolaimus pararobustus (Tylenchina: Hoplolaimidae) from banana, with phylogeny and species delineation in the genus Hoplolaimus by Olajide, E., Singh, P.R., Kolombia, Y.A., Rumbarar, M.K., Couvreur, M., Bert, W.

“…The morphological and molecular characterisations of two lance nematode species isolated from the rhizosphere of banana, Hoplolaimus seinhorsti and H. pararobustus, are provided based on an integrative study that includes light and scanning electron microscopy, phylogenetic analysis and two tree-based molecular species delimitation methods (GMYC and bPTP). …”
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Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats by Belay, Shumuye, Belay, Gurja, Nigussie, Helen, Ahbara, Abulgasim, Tijjani, Abdulfatai, Dessie, Tadelle, Mekuriaw, Getinet, Han, Jian-Lin, Mor, Siobhan M., Woldekiros, H.S., Dobney, Kieth, Lebrasseur, Ophelie, Hanotte, Olivier H., Mwacharo, Joram M.

“…Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. …”
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Next generation sequencing and genetic analyses reveal factors driving evolution of sweetpotato viruses in Uganda by Adero, Joanne, Wokorach, G., Stomeo, Francesca, Yao, Nasser, Machuka, Eunice, Njuguna, Joyce, Byarugaba, D.K., Kreuze, J., Yencho, G.C., Otema, M.A., Yada, B., Kitavi, M.

“…Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. …”
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Overexpression of TdNACB improves the drought resistance of rice by Fangyi Gong, Tian Zhang, Yusen Lu, Velu, Govindan, Ruiqin Liu, Jia Liu, Xiangquan Wang, Dengcai Liu, Youliang Zheng, Lin Huang, Bihua Wu

“…The transcriptome analysis found 14,284, 22,383 and 21,451 genes had expression corresponding responsed to drought stress at 24h, 48h, 120h, respectively and significantly enriched in ‘Arginine and proline metabolism’ and ‘Peroxisome’ in BAd7-209. 1666 transcription factors (TFs) related responsed to drought stress in which TdNACB showed high expression at 24h, 48h and 120h and had the closest relationship with TaNAC48 and OsNAC6 in phylogenetic analysis. Overexpression of TdNACB significantly enhanced drought resistance in rice and overexpression lines had significantly higher CAT, POD and SOD activity, Pro content and lower MDA content than those of the WT under drought stress. …”
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High-quality genome resource of Ustilaginoidea virens (UV2_4G), causal agent of an emerging false smut disease in rice by Bashyal, Bishnu Maya, Yadav, Gaurav Kumar, Parmar, Pooja, Sunani, Sunil Kumar, Aggarwal, Shweta, Gopala Krishnan, S., Kumar, Atul, Zaidi, Najam Waris, Aggarwal, Rashmi

“…Comparative analysis revealed isolate UV2_4G is distinct with 31 unique clusters and placed distantly in phylogenetic analysis. Taken together, this high-quality genome assembly and sequence annotation resource can give an improved insight for characterizing the biological and pathogenic mechanisms of U. virens.…”
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Rice heavy metal P-type ATPase OsHMA6 is likely a copper efflux protein by Wenli, Zou, Chang, Li, Yajun, Zhu, Jingguang, Chen, Haohua, He, Ye, Guoyou

“…We here reported the characterization of rice OsHMA6, a member of the P1B-type ATPase family. Phylogenetic tree analysis showed that OsHMA6 belonged to the Cu/Ag subgroup of the HMA family and had a close evolutionary relationship with OsHMA9. …”
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A pathovar of Xanthomonas oryzae infecting wild grasses provides insight into the evolution of pathogenicity in rice agroecosystems by Lang, Jillian M., Pérez-Quintero, Alvaro L., Koebnik, Ralf, DuCharme, Elysa, Sarra, Soungalo, Doucoure, Hinda, Keita, Ibrahim, Ziegle, Janet, Jacobs, Jonathan M., Oliva, Ricardo, Koita, Ousmane, Szurek, Boris, Verdier, Valérie, Leach, Jan E.

“…L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. …”
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Geographic and research center origins of rice resistance to Asian planthoppers and leafhoppers: implications for rice breeding and gene deployment by Horgan, Finbarr G., Srinivasan, Thanga, Bentur, Jagadish, Kumar, Ram, Bhanu, K., Sarao, Preetinder, Chien, Ho, Almazan, Maria, Bernal, Carmencita, Ramal, Angelee, Ferrater, Jedeliza, Huang, Shou-Horng

“…Virulence of the whitebacked planthopper, Sogatella furcifera, in Taiwan and the Philippines was also assessed. Phylogenetic analysis of the varieties using single-nucleotide polymorphisms (SNPs) indicated a clade of highly resistant varieties from South Asia with two further South Asian clades of moderate resistance. …”
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The 3,000 rice genomes project by Li, Z.K., Zhang, G.Y., McNally, K.L.

“…From our sequencing efforts, approximately 18.9 million single nucleotide polymorphisms (SNPs) in rice were discovered when aligned to the reference genome of the temperate japonica variety, Nipponbare. Phylogenetic analyses based on SNP data confirmed differentiation of the O. sativa gene pool into 5 varietal groups – indica, aus/boro, basmati/sadri, tropical japonica and temperate japonica.Here, we report an international resequencing effort of 3,000 rice genomes. …”
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Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice by Knauth, Stefan, Hurek, Thomas, Brar, Darshan, Reinhold-Hurek, Barbara

“…Application of N‐fertilizer at planting had a long‐term effect on the profile of expressed nitrogenase genes. Phylogenetic analysis of a clone library constructed for nifH fragments expressed in wild species of rice roots indicated that active diazotrophs were not related to cultured strains. …”
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Annotation and molecular characterisation of the TaIRO3 and TaHRZ iron homeostasis genes in bread wheat (Triticum aestivum L.) by Carey-Fung, Oscar, Beasley, Jesse T., Johnson, Alexander A. T.

“…Protein analysis revealed that TaIRO3 and TaHRZ proteins contain functionally conserved domains for DNA-binding, dimerisation, Fe binding, or polyubiquitination, and phylogenetic analysis revealed clustering of TaIRO3 and TaHRZ proteins with other monocot IRO3 and HRZ proteins, respectively. …”
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Diversity and Pathogenicity of Fusarium temperatum Scaufl. & Munaut causing Fusarium ear rot of maize (Zea mays L.) in major maize growing agroecosystems of Ethiopia by Deressa, Temesgen, Girma Adugna, Mahabaleswara, Suresh L., Zelalem Bekeko, Vaughan, Martha, Opoku, Joseph

“…The comparison of the sequence with established reference sequences; NRRL 13,291 and CBS 138,287 revealed 100% sequence identity with F. temperatum isolates. A phylogenetic tree was constructed with concatenated sequences of the two genes. …”
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Genomic characterization and population structure of indigenous cavies from the Democratic Republic of Congo: Implications for breeding and conservation by Ayagirwe, R., Kyallo, Martina, Meutchieye, F., Manjeli, Y., Mutwedu, V.B., Mugumaarhahama, Y., Baenyi, P., Wasso, S., Bisimwa, P., Yao, Nasser

“…The observed molecular variance suggests potential for selection within populations before crossbreeding, providing avenues for genetic enhancement. Phylogenetic analysis of the 343 individuals grouped them into three distinct clusters, indicating that DRC’s cavy populations consist of three gene pools. …”
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