MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TLDR
An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.Abstract:
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.read more
Citations
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Biosynthesis and Metabolic Fate of Phenylalanine in Conifers
María Belén Pascual,Jorge El-Azaz,Fernando de la Torre,Rafael A. Cañas,Concepción Ávila,Francisco M. Cánovas +5 more
TL;DR: Recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees are reviewed and the relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed.
Journal ArticleDOI
Cyclic Lipopeptide Biosynthetic Genes and Products, and Inhibitory Activity of Plant-Associated Bacillus against Phytopathogenic Bacteria
TL;DR: It is demonstrated that the antagonistic capacity of plant-associated Bacillus against plant pathogenic bacteria is related to the presence of cLP genes and to the production of the corresponding cLPs, and it is mainly associated to the species B. subtilis and B. amyloliquefaciens.
Journal ArticleDOI
Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.
TL;DR: The gene structure and motif distribution analysis of the GRAS members in G. hirsutum revealed that many genes of the SHR subfamily have more than one intron, which indicated these genes may have effect on the development and breeding of cotton.
Journal ArticleDOI
The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling
TL;DR: The key SWEET genes for technological improvement of sorghum in the production of biofuels are determined: SbSWEET8-1 for efflux of sucrose from the leaf; SbsWEET4-3 for unloading suc rose from the phloem in the stem; and Sb sWEET2-1 and S bSWEet7-1 in the same clade as seed development and AtS WEET8/RPG1 that
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The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization.
Christin Zachow,Ghazaleh Jahanshah,Irene de Bruijn,Chunxu Song,Federica Ianni,Zoltán Pataj,Heike Gerhardt,Isabelle Pianet,Michael Lämmerhofer,Gabriele Berg,Harald Gross,Jos M. Raaijmakers +11 more
TL;DR: Results indicate that Pseudomonas poae RE*1-1-14 produces a structurally new LP that is relevant for its antagonistic activity against soilborne plant pathogens and for colonization of sugar beet roots.
References
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
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