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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Supplementary Figure 4
H. P. Mohammad,W. Zhang,H. S. Prevas,B. R. Leadem,M. Zhang,J. G. Herman,Craig M. Hooker,D. N. Watkins,B. Karim,D. L. Huso,S. B. Baylin +10 more
TL;DR: Prion generation was performed as previously described, with plasmid pER63 in the indicated strains with the appearance of different [URE3] variants in all four strains tested.
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Comprehensive expression profiling of the pectin methylesterase gene family during silique development in Arabidopsis thaliana
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TL;DR: This study used real-time RT-PCR to gain an overview of the expression of the entire PME family at eight silique developmental stages, in flower buds and in vegetative tissue in the Arabidopsis to highlight the high diversity of PME expression profiles.
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Multilocus Sequence Typing Confirms the Close Genetic Interrelatedness of Three Distinct Flavescence Dorée Phytoplasma Strain Clusters and Group 16SrV Phytoplasmas Infecting Grapevine and Alder in Europe
Guillaume Arnaud,Sylvie Malembic-Maher,Pascal Salar,Patrick Bonnet,Michael Maixner,Carmine Marcone,Elisabeth Boudon-Padieu,Xavier Foissac +7 more
TL;DR: Molecular typing of phytoplasma strains and phylogenetic analyses concluded that FD, PGY, and AldY were members of the same phylogenetic subclade, which may have originated in Europe.
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Polar Localizing Class V Myosin Chitin Synthases Are Essential during Early Plant Infection in the Plant Pathogenic Fungus Ustilago maydis
TL;DR: The data show that the polar class IV CHSs are essential for morphogenesis ex planta, whereas the class V myosin-CHS is essential during plant infection.
Journal ArticleDOI
SodERF3, a Novel Sugarcane Ethylene Responsive Factor (ERF), Enhances Salt and Drought Tolerance when Overexpressed in Tobacco Plants
Luis E Trujillo,Mailin Sotolongo,Carmen Menéndez,M. E. Ochogavía,Yamilet Coll,Ingrid Hernández,Orlando Borrás-Hidalgo,Bart P. H. J. Thomma,P. Vera,Lázaro Hernández +9 more
TL;DR: SodERF3, a sugarcane cDNA that encodes a 201-amino acid DNA-binding protein that acts as a transcriptional regulator of the ethylene responsive factor (ERF) superfamily, is described and Northern and Western blot analysis showed that Sod ERF3 is induced by ethylene.
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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