Search Results - "Phylogenetics"

Molecular characterization of Ralstonia solanacearum strains from Ethiopia and tracing potential source of bacterial wilt disease outbreak in seed potatoes by Abdurahman, A., Griffin, D., Elphinstone, J., Struik, P.C., Schulz, S., Schulte-Geldermann, Elmar, Sharma, K.

“…Multiplex PCR and phylogenetic analysis of partial endoglucanase gene sequences identified all of the isolates as phylotype IIB sequevar 1. …”
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Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics by Tarekegn, G.M., Xiao-yang Ji, Xue Bai, Bin Liu, Wenguang Zhang, Birungi, Josephine, Djikeng, Appolinaire, Tesfaye, K.

“…The overall average pair-wise distance (F ST) was 0.049539 with the highest (F ST = 0.1245) and the lowest (F ST = 0.011) F ST distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. …”
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Genome-wide identification and analysis of arabidopsis sodium proton antiporter (NHX) and human sodium proton exchanger (NHE) homologs in sorghum bicolor by Kumari, P.H., Kumar, S.A., Ramesh, K., Reddy, P.S., Nagaraju, M., Prakash, A.B., Shah, T., Henderson, A., Srivastava, R.K., Rajasheker, G., Chitikineni, A., Varshney, Rajeev K., Rathnagiri, P., Narasu, M.L., Kishor, P.B.K.

“…Chromosome 2 was found to be a hotspot region with five sodium transporters. Phylogenetic analysis inferred six ortholog and three paralog groups. …”
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Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis by Islam, M.Z., Khalequzzaman, M., Bashar, Khairul, Ivy, N.A., Mian, M.A.K., Pittendrigh, B.R., Haque, M.M., Ali, M.P.

“…Detecting 140 alleles, 11 were unique and suitable as a germplasm diagnostic tool. Phylogenetic cluster analysis using genotypic traits classified germplasm into three major groups. …”
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Identification and molecular characterisation of Taro bacilliform virus and Taro bacilliform CH virus from East Africa by Kidanemariam, Dawit B., Sukal, A.C., Abraham, Adane D., Stomeo, Francesca, Dale, J.L., James, A.P., Harding, R.M.

“…Full‐length sequences from representative TaBV and TaBCHV isolates showed that the genome organization of TaBV isolates from East Africa was consistent with previous reports while TaBCHV isolates from East Africa were found to encode only four ORFs, distinct from a previous report from China. Phylogenetic analysis showed that all East African TaBV isolates form a single subgroup within known TaBV isolates, while TaBCHV isolates form at least two distinct subgroups. …”
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Validation of a diagnostic tool for the diagnosis of lumpy skin disease by Mwanandota, J.J., Macharia, Mercy, Ngeleja, C.M., Sallu, R.S., Yongolo, M.G., Mayenga, C., Holton, Timothy A.

“…In AHA, the LAMP assay DR was 14.3% and 1.9% for LAMP 1 and 2, respectively. Phylogenetic tree analysis confirmed the identity of CaPV. …”
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An RNA-Seq-based reference transcriptome for Citrus by Terol, Javier, Tadeo, Francisco R., Ventimilla, Daniel, Talón, Manuel

“…In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C.medica, C.aurantifolia, C.limon, C.bergamia, C.clementina, C.deliciosa, C.reshni, C.maxima, C.paradisi, C.aurantium, C.sinensis and Poncirus trifoliata. …”
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The Complete Genome Sequence of Citrus Vein Enation Virus (CVEV) Obtained through Deep Sequencing of Small RNAs by Vives, María C., Velázquez, Karelia, Pina, José A., Moreno, Pedro, Guerri, José, Navarro, Luis

“…The CVEV genomic RNA has 5,983 nt organized in five open reading frames, resembling that of PEMV-1. Phylogenetic comparison of amino acid signatures in RNA-dependent RNA polymerases of the family Luteoviridae clearly grouped CVEV with PEMV-1. …”
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Identification of a New Enamovirus Associated with Citrus Vein Enation Disease by Deep Sequencing of Small RNAs by Vives, María C., Velázquez, Karelia, Pina, José A., Moreno, Pedro, Guerri, José, Navarro, Luis

“…The CVEV gRNA was found to be single-stranded, positive-sense, with a size of 5,983 nucleotides and five open reading frames. Phylogenetic comparisons based on amino acid signatures of the RNA polymerase and the coat protein clearly classifies CVEV within the genus Enamovirus. …”
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Identification and functional characterization of cation-chloride cotransporters in plants by Colmenero-Flores, José M., Martinez, German, Gamba, Gerardo, Vazquez, Norma, Iglesias, Domingo J., Brumos, Javier, Talón, Manuel

“…Deduced plant CCC proteins are highly conserved, and phylogenetic analyses revealed their relationships to the sub-family of animal K+:Cl- cotransporters. …”
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Complete sequence of three different biotypes of tomato spotted wilt virus (wild type, tomato Sw-5 resistance-breaking and pepper Tsw resistance-breaking) from Spain by Debreczeni, Diana E., Lopez, Carmelo, Aramburu, Jose, Daros, José A., Soler, Salvador, Galipienso, Luis, Falk, Bryce W., Rubio, Luis

“…Variations in nucleotide sequences and genomic RNA lengths among the different virus biotypes are reported here. Phylogenetic analysis of the five TSWV open reading frames showed evidence of reassortment between genomic segments of LL-N.05 and Pujol1TL3, which was supported by analysis with different recombination-detecting algorithms.…”
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Identification and genetic characterization of an ethylene-dependent polygalacturonase from apricot fruit by Leida, Carmen, Ríos, Gabino, Soriano, J. M., Pérez-Gago, María B., Llácer, Gerardo, Crisosto, Carlos H., Badenes, María L.

“…Protein sequence comparison with known polygalacturonases (PGs) revealed that multiple features as conserved domains and functional residues and a predicted signal peptide were present in PaPG. Moreover, a phylogenetic analysis of this and other plant PGs placed PaPG into a clade containing endoPGs expressed in fruit, abscission and dehiscence zones without a propeptide sequence, very close to PRF5 from peach (Prunus persica L Batsch). …”
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Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms by López, María M., Roselló, Montserrat, Llop, Pablo, Ferrer, Sergi, Christen, Richard, Gardan, Louis

“…Rep-PCR profiles, PCR products obtained with different pairs of primers and plasmid contents determined by restriction analysis showed differences between the novel strains and reference strains of E. amylovora and E. pyrifoliae. Phylogenetic analysis of 16S rRNA, gpd and recA gene sequences showed that the eight novel strains could not be assigned to any recognized species. …”
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Molecular analysis of the genomic RNAs 1 and 2 of the first Arabis mosaic virus isolate detected in Spanish grapevines. Short communication. by López-Fabuel, Irene, Olmos, Antonio, Bassler, Alexandra, Dupuis-Maguiraga, L., Torres, Luis B., Bertolini, Edson, Wetzel, Thierry

“…Interestingly, the VPg genes were identical between the two grapevine isolates ArMV-Du13 and -NW, suggesting a possible implication of the host. The phylogenetic analysis of the RNA 2 showed that the Spanish isolate was close to Grapevine fanleaf virus isolates. …”
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Host range testing of Tamarixia dryi (Hymenoptera: Eulophidae) sourced from South Africa for classical biological control of Trioza erytreae (Hemiptera: Psyllidae) in Europe by Urbaneja-Bernat, Pablo, Pérez-Rodríguez, Jésica, Krüger, Kerstin, Catalán, José, Rossita, Rizza, Hernández-Suárez, Estrella, Urbaneja, Alberto, Tena, Alejandro

“…The psyllids were selected based on phylogenetic and ecological criteria. Tamarixia dryi exhibited a high host specificity. …”
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Analysis of genetic diversity among a set of accessions from the IVIA's persimmon collection by Gil-Muñoz, Francisco, Zuriaga, Elena, Badenes, María L., Naval, María M.

“…Genetic structures were estimated using a Bayesian-based model clustering method, while a Neighbor-Joining phylogenetic tree was constructed to visualize the genetic relationships among the samples. …”
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Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome by Parfitt, Dan E., Badenes, María L.

“…Molecular genetic tools (PCR amplification followed by restriction analysis of a 3.2-kb region of variable chloroplast DNA, and restriction fragment length polymorphism analysis of the Pistacia cpDNA with tobacco chloroplast DNA probes) provided a new set of variables to study the phylogenetic relationships of 10 Pistacia species. Both parsimony and cluster analyses were used to divide the genus into two major groups. …”
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Embryological studies in Coffea arabica L by Vishveshwara, S., Chinnappa, C.C.

“…The significance of the multiovular condition in C. arabica from the phylogenetic point of view in Rubiaceae and from the genetics and breeding of plants in experimental selections is also discussed.…”
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Characterization of MITF gene in crayfish and their possible role in innate immunity by Wen, Yaru

“…In the secondary and tertiary structure of the deduced amino acid sequence, a conserved functional structure of bHLH-LZ was shown, which could bind to E-box. In the phylogenetic analysis, this obtained MITF-like gene showed a lager evolutionary distance to all the vertebrates and some invertebrates like lancelet (Branchiostoma belcheri), starfish (Acanthaster planci), sea urchin (Paracentrotus lividus) and (Lytechinus variegatus), but is closer than worms (Caenorhabditis elegans). …”

A minor study on avian metapneumovirus by Atterby, Clara

“…The sequencing of the RNA was unsuccessful and no phylogenetic tree comparing this strain to other known viral strains of aMPV could be designed. …”