Journal ArticleDOI
MEGA2 : Molecular evolutionary genetics analysis software
TLDR
MEGA2 vastly extends the capabilities of MEGA version 1 by facilitating analyses of large datasets, enabling creation and analyses of groups of sequences, and expanding the repertoire of statistical methods for molecular evolutionary studies.Abstract:
Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net.read more
Citations
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Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess ω-alicyclic fatty acids, and emended description of the genus Alicyclobacillus
TL;DR: Phylogenetic analyses based on both 16S rRNA and gyrB (DNA gyrase B subunit gene) gene sequences showed that strain 3A(T) falls into the Alicyclobacillus cluster, validated by significant bootstrap values and DNA-DNA hybridization values were under 13 %, indicating that strain3A (T) represents a distinct species.
Journal ArticleDOI
Identification and Characterization of a Phospholipase D–Superfamily Gene in Rickettsiae
TL;DR: A gene that encodes a putative phospholipase D (PLD) and that has been detected by Southern blotting in 11 analyzed strains of rickettsiae is identified and may be critical for the intracellular life of these bacteria.
Journal ArticleDOI
Change in Japanese encephalitis virus distribution, Thailand.
Narong Nitatpattana,Audrey Dubot-Pérès,Meriadeg Ar Gouilh,Marc Souris,Philippe Barbazan,Sutee Yoksan,Xavier de Lamballerie,Jean-Paul Gonzalez +7 more
TL;DR: Japanese encephalitis virus genotypes in Thailand were studied in pigs and mosquitoes collected near houses of confirmed human JEV cases in 2003–2005, which shows a switch from genotype III incidence that started during the 1980s.
Journal ArticleDOI
Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.
Shinyoung Lee,Joonyul Kim,Jun-Seock Son,Jongmin Nam,Dong-Hoon Jeong,Keunsub Lee,Seonghoe Jang,Jihye Yoo,Jinwon Lee,Dong-Yeon Lee,Hong-Gyu Kang,Gynheung An +11 more
TL;DR: The authors' PCR screening for T-DNA insertions within 12 MADS-box genes resulted in the identification of five insertions in four different genes, which will be valuable when isolating T- DNA insertional mutants in various rice genes.
Journal ArticleDOI
Microtubule Organization Requires Cell Cycle-dependent Nucleation at Dispersed Cytoplasmic Sites: Polar and Perinuclear Microtubule Organizing Centers in the Plant Pathogen Ustilago maydis
TL;DR: The data suggest that MT reorganization in U. maydis depends on cell cycle-specific nucleation at dispersed cytoplasmic sites, at a polar MTOC and the SPB, which supports the notion that polar growth requires polar MT nucleation.
References
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Book
Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
TL;DR: This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Journal ArticleDOI
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
TL;DR: In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included.
Book
Molecular Evolution: A Phylogenetic Approach
TL;DR: The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of molecular phylogenetics as mentioned in this paper.
Journal ArticleDOI
Phylogenetic test of the molecular clock and linearized trees.
TL;DR: To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Journal ArticleDOI
Molecular Evolution — A Phylogenetic Approach.
TL;DR: The authors set themselves the tasks of showing how evolutionary information is written into gene sequences and describing the methods by which such information can be recovered and succeed, providing a wealth of examples and setting many of them in a historical perspective.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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