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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Journal ArticleDOI
The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice.
Jie Liu,Juan Huang,Huan Guo,Liu Lan,Hongze Wang,Yuancheng Xu,Xiaohong Yang,Wenqiang Li,Hao Tong,Yingjie Xiao,Qingchun Pan,Feng Qiao,Mohammad Sharif Raihan,Haijun Liu,Xuehai Zhang,Ning Yang,Xiaqing Wang,Min Deng,Minliang Jin,Lijun Zhao,Xin Luo,Yang Zhou,Xiang Li,Wei Zhan,Nannan Liu,Hong Wang,Gengshen Chen,Qing Li,Jianbing Yan +28 more
TL;DR: The results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis.
Journal ArticleDOI
A WRKY transcription factor from Withania somnifera regulates triterpenoid withanolide accumulation and biotic stress tolerance through modulation of phytosterol and defense pathways
Anup Kumar Singh,Sarma Rajeev Kumar,Varun Dwivedi,Avanish Rai,Shaifali Pal,Ajit Kumar Shasany,Dinesh A. Nagegowda +6 more
TL;DR: While WsWRKY1 silencing in W. somnifera compromised the tolerance to bacterial growth, fungal infection, and insect feeding, its overexpression in tobacco led to improved biotic stress tolerance, demonstrating its importance as a metabolic engineering tool for simultaneous improvement of triterpenoid biosynthesis and plant defense.
Journal ArticleDOI
Structure, Function, Regulation and Phylogenetic Relationship of ZIP Family Transporters of Plants.
T. P. Ajeesh Krishna,T. Maharajan,G. Victor Roch,Savarimuthu Ignacimuthu,Stanislaus Antony Ceasar +4 more
TL;DR: A detailed account on structure, function, regulations and phylogenetic relationships of plant ZIP transporters is presented and insight to structure of plant Zips is given through homology modeling and multiple sequence alignment with Bordetella bronchiseptica ZIP, whose crystal structure has been solved recently.
Book ChapterDOI
The genus Geobacillus and their biotechnological potential.
TL;DR: A number of genome-sequencing projects have been completed or are underway allowing comparative studies, which reveal a significant amount of genome rearrangement within the genus, the presence of large genomic islands encompassing all the hemicellulose utilization genes and a genomic island incorporating a set of long chain alkane monooxygenase genes.
Journal ArticleDOI
Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles.
TL;DR: Bcode‐based OTU‐picking is an efficient way to delimit putative species from large data sets where the use of more sophisticated methods based on multilocus or genomic data is not feasible.
References
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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.
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