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
More filters
Journal ArticleDOI
Genome‐guided investigation of plant natural product biosynthesis
Franziska Kellner,Jeongwoon Kim,Bernardo J. Clavijo,John P. Hamilton,Kevin L. Childs,Brieanne Vaillancourt,Jason Cepela,Marc Habermann,Burkhard Steuernagel,Leah Clissold,Kirsten McLay,Carol Robin Buell,Sarah E. O'Connor +12 more
TL;DR: A genome assembly for C. roseus is generated that provides a near-comprehensive representation of the genic space that revealed the genomic context of key points within the MIA biosynthetic pathway including physically clustered genes, tandem gene duplication, expression sub-functionalization, and putative neo- functionalization.
Journal ArticleDOI
The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols
Pedro J. Martínez-García,Marc W. Crepeau,Daniela Puiu,Daniel Gonzalez-Ibeas,Jeanne Whalen,Kristian Stevens,Robin Paul,Timothy Butterfield,Monica Britton,Russell L. Reagan,Sandeep Chakraborty,Sriema L. Walawage,Hans A. Vasquez-Gross,Charis Cardeno,Randi A. Famula,Kevin Pratt,Sowmya Kuruganti,Mallikarjuna K. Aradhya,Charles A. Leslie,Abhaya M. Dandekar,Steven L. Salzberg,Jill L. Wegrzyn,Charles H. Langley,David B. Neale +23 more
TL;DR: The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits, and provides meaningful insight into the complex pathways required for the synthesis of polyphenols.
Journal ArticleDOI
Primate-specific ORF0 contributes to retrotransposon-mediated diversity.
Ahmet M. Denli,Iñigo Narvaiza,Bilal E. Kerman,Monique Pena,Christopher Benner,Maria C. Marchetto,Jolene K. Diedrich,Aaron Aslanian,Jiao Ma,Jiao Ma,James J. Moresco,Lynne Moore,Tony Hunter,Alan Saghatelian,Fred H. Gage,Fred H. Gage +15 more
TL;DR: It is shown that the primate LINE-1 5'UTR contains a primate-specific open reading frame (ORF) in the antisense orientation that is named ORF0, which is present in more than 3,000 loci across human and chimpanzee genomes and has a promoter and a conserved strong Kozak sequence that supports translation.
Journal ArticleDOI
Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of ‘Micro Tom’ tomato plants
TL;DR: To identify an actinobacterial strain that can promote growth and alleviate salinity stress in tomato plants, scientists isolated a bacterium from tomato plants that secrete a substance that acts as a “spatially aggregating substance” to promote growth.
Journal ArticleDOI
MicroRNA167-Directed Regulation of the Auxin Response Factors GmARF8a and GmARF8b Is Required for Soybean Nodulation and Lateral Root Development
Youning Wang,Li Kexue,Liang Chen,Yanmin Zou,Haipei Liu,Yinping Tian,Dongxiao Li,Rui Wang,Fang Zhao,Brett J. Ferguson,Peter M. Gresshoff,Xia Li +11 more
TL;DR: It is shown in soybean that the microRNA miR167 acts as a positive regulator of lateral root organs, namely nodules and lateral roots, and a key role is established for the miR 167-GmARF8 module in auxin-mediated nodule and lateral root formation in soybeans.
References
More filters
Journal ArticleDOI
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.
Related Papers (5)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more