Search Results - "Phylogenetics"

Phylogeny of Epilachna, Henosepilachna, and some minor genera of phytophagous ladybird beetles (Coleoptera: Coccinellidae: Coccinellinae: Epilachnini), with an analysis of ancestra... by Katoh, T., Koji, S., Ishida, A., Matsubayashi, K.W., Kahono, S., Kobayashi, N., Furukawa, K., Viet, B.T., Vasconcellos Neto, J., Lange, C.N., Goergen, Georg E., Nakano, S., Li, N., Yu, G., Katakura, H.

“…From a combined dataset of mitochondrial (ND2) and nuclear (28S) DNA sequences, we reconstructed the phylogeny of 46 species of Epilachnini from Asia, Africa, America, and the Australian region: 16 species in Epilachna, 24 species in Henosepilachna, and one species each in Adira, Afidenta, Afidentula, Afissula, Chnootriba, and Epiverta. In our phylogenetic trees, both Epilachna and Henosepilachna were reciprocally polyphyletic. …”
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Morphological and molecular characterisation and diagnostics of some species of Scutellonema Andrassy, 1958 (Tylenchida: Hoplolaimidae) with a molecular phylogeny of the genus by Berg, E. van den, Tiedt, L.R., Coyne, Danny L., Ploeg, A.T., Navas-Cortes, J.A., Roberts, P.A., Yeates, G.W., Subbotin, S.A.

“…Multivariate analyses determined that S. brachyurus from the USA and Taiwan (type A) differed from that from South Africa (type B) mainly in body, tail and DGO lengths, and ratios b , c , c and V. Phylogenetic relationships within Scutellonema are given as inferred from the analyses of the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences. …”
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Pratylenchus speijeri n. sp. (Nematoda: Pratylenchidae), a new rootlesion nematode pest of plantain in West Africa by Luca, F. de, Troccoli, A., Duncan, L.W., Subbotin, S.A., Waeyenberge, L., Coyne, Danny L., Brentu, F.C., Inserra, R.N.

“…An extensive comparison of the morphological and molecular characteristics of this new species with those of P. coffeae and other related amphimictic species did not result in an unambiguous separation of this species from P. coffeae because only a few morphological features of diagnostic value were found. Sequence and phylogenetic analyses of the D2-D3 expansion segments of the 28S rRNA gene, the ITS rRNA gene and a portion of the hsp90 gene of P. speijeri n. sp. and P. coffeae species complex populations from different sources generated majority consensus BI trees with three major clades: P. speijeri n. sp. from Musa spp. roots in Ghana; unidentified or putative new Pratylenchus sp. …”
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Assessment of the virulence spectrum and its association with genetic diversity in Magnaporthe oryzae populations from sub-Saharan Africa by Mutiga, Samuel K., Rotich, F., Ganeshan, V.D., Mwongera, D.T., Mgonja, Emmanuel M., Were, Vincent M., Harvey, Jagger J.W., Zhou, B., Wasilwa, L., Feng, C., Ouédraogo, I., Wang, G.L., Mitchell, T.K., Talbot, N.J., Correll, James C.

“…Genetic relatedness of isolates was assessed by single nucleotide polymorphisms derived from genotyping-by-sequencing and by vegetative compatibility tests. Phylogenetic analysis of SNPs of a subset of isolates (n = 78) revealed seven distinct clades that differed in virulence. …”
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Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia by Onyango, M.G., Aitken, N.C., Jack, C., Chuah, A., Oguya, J., Djikeng, Appolinaire, Kemp, Stephen J., Bellis, G.A., Nicholas, A., Walker, P.J., Duchemin, J.B.

“…We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. …”
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Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia by Sisay, Z., Djikeng, Appolinaire, Berhe, N., Belay, G., Gebreyes, W., Abegaz, W.E., Njahira, Moses N., Wang, Q.H., Saif, L.J.

“…The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. …”
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High genetic diversity and population differentiation in Clarias gariepinus of Yala Swamp: Evidence from mitochondrial DNA sequences by Barasa, J.E., Abila, R., Grobler, J.P., Agaba, Morris, Chemoiwa, E.J., Kaunda-Arara, B.

“…Two clusters were inferred both from the maximum likelihood tree and the spanning networks of phylogenetic relationships of haplotypes. Mismatch distribution for total sample was multi-modal but individually, distributions were uni-modal in LKG, but multimodal in LNG. …”
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A nomadic subtelomeric disease resistance gene cluster in common bean by David, Perrine, Chen, Nicolas W.G., Pedrosa Harand, Andrea, Thareau, Vincent, Sévignac, Mireille, Cannon, Steven B., Debouck, Daniel G., Langin, Thierry, Geffroy, Valerie

“…The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). …”
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Widespread occurrence and diversity of cassava brown streak virus (Potyviridae:Ipomovirus) in Tanzania by Rwegasira, G.M., Momanyi, G., Rey, M.E.C., Kahwa, G., Legg, James P.

“…Forty-three amplicons were sequenced, and phylogenetic comparisons with nucleotide sequences from GenBank (National Center for Biotechnology Information database) suggested that one major clade of CBSV primarily exists in Tanzania. …”
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Unravelling the genetic diversity among cassava Bemisia tabaci whiteflies using NextRAD Sequencing by Wosula, Everlyne N., Chen, W., Fei, Z., Legg, James P.

“…Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. …”
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Genetic diversity of tartary buckwheat based on the sequence analysis of PAL by Li, M., Zhang, Z., Wu, B., Gao, J., Li, Y.

“…The Nucleotide polymorphism( p) value in samples from Sichuan was the highest( 0. 0148) . From the phylogenetic tree, it indicated that the 67 samples from the different province could be clustered into seven categories. …”
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Genomics of yams, a common source of food and medicine in the tropics by Mignouna, Hodeba D., Abang, Mathew M., Asiedu, Robert

“…Nevertheless, progress has been made recently towards understanding Dioscorea phylogeny and phylogenetic relationships within the genus. Also, improved molecular technologies have been developed for genome analysis, including germplasm characterization, cytogenetics, genetic mapping and tagging, and functional genomics. …”
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Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya by Wamaitha, M. Jane, Nigam, Deepti, Maina, Solomon, Stomeo, Francesca, Wangai, Anne, Njuguna, Joyce N., Holton, Timothy A., Wanjala, Bramwel W., Wamalwa, Mark, Lucas, Tanui, Djikeng, Appolinaire, García Ruiz, H.

“…A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. …”
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Molecular taxonomic, epidemiological and population genetic approaches to understanding yam anthracnose disease by Abang, Mathew M., Winter, S., Mignouna, Hodeba D., Green, K.R., Asiedu, Robert

“…Four forms of Colletotrichum are now known to be associated with foliar anthracnose of yam: the slow-growing grey (SGG), the fast-growing salmon (FGS), the fast-growing olive (FGO), and the fast-growing grey (FGG) forms. The close phylogenetic relationship of the first three forms to reference isolates of Colletotrichum gloeosporioides, and the fact that only strains of these forms have been observed to induce typical anthracnose symptoms on D. alata, recently confirmed that C. gloeosporioides is the causal agent of yam anthracnose disease. …”
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Prevalence and genome characterization of field isolates of sugarcane mosaic virus (SCMV) in Nigeria by Yayaya, A., Dangora, D.B., Kumar, P. Lava, Alegbejo, M.D., Gregg, L., Alabi, O.J.

“…Cloning and sequencing of gene-specific DNA amplicons from a subset of 45 samples (sugarcane = 33, maize = 9, itch grass = 3) confirmed their specificities to SCMV. Phylogenetic analysis of the partial gene sequences showed that they all belong to a single monophyletic clade of SCMV. …”
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Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana) by Rouard, M., Droc, Gaëtan, Martin, G., Hueber, Y., Sardos, J., Guignon, Valentin, Cenci, A., Geigle, B., Hibbins, M., Yahiaoui, N., Baurens, F.C., Berry, V., Hahn, M., D’Hont, Angélique, Roux, N.

“…These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. …”
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Characterization of Sour Cherry Isolates of Plum pox virus from the Volga Basin in Russia Reveals a New Cherry Strain of the Virus by Glasa, Miroslav, Prikhodko, Yuri, Predajna, Lukas, Nagyova, Alzbeta, Shneyder, Yuri, Zhivaeva, Tatiana, Subr, Zdeno, Cambra, Mariano, Candresse, Thierry

“…The comparison of complete genome sequences has shown that the nucleotide identity values with other PPV isolates reached only 77.5 to 83.5%. Phylogenetic analyses clearly assigned the RU-17sc, RU-18sc, and RU-30sc isolates from cherry to a distinct cluster, most closely related to PPV-C and, to a lesser extent, PPV-W. …”
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Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis by Sabbione, Agustin, Daurelio, Lucas D., Vegetti, Abelardo, Talón, Manuel, Tadeo, Francisco R., Dotto, Marcela

“…While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet.Results: Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. …”
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Minimally Invasive Embryo Transfer and Embryo Vitrification at the Optimal Embryo Stage in 3 Rabbit Model by García-Domínguez, Ximo, Marco-Jiménez, Francisco, Viudes-De-Castro, María P., Vicente, José Salvador

“…In addition to its phylogenetic proximity to the human species and its small size and low maintenance cost, it has important reproductive characteristics such as induced ovulation, a chronology of early embryonic development similar to humans and a short gestation that allow us to study the consequences of ARTs application easily. …”
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Genetic diversity of North Ethiopian indigenous sheep populations using mitochondrial DNA by Adhena, Mulata H.

“…The AMOVA analysis indicates 29.78% variation explain variations among the 4 populations. The phylogenetic network analysis clustered the detected haplotypes into two haplogroups, haplogroup A and B which are separated by 13 mutational sites. …”
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