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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RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis
Yoshihiro Handa,Hiroyo Nishide,Naoya Takeda,Yutaka Suzuki,Masayoshi Kawaguchi,Katsuharu Saito +5 more
TL;DR: The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscles symbiosis.
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Green Synthesis of Silver Nanoparticles Using Pseudoduganella eburnea MAHUQ-39 and Their Antimicrobial Mechanisms Investigation against Drug Resistant Human Pathogens.
TL;DR: Green, rapid, facile, cost-effective and ecofriendly synthesis of AgNPs using Pseudoduganella eburnea MAHUQ-39 shows strong antimicrobial activity against multidrug-resistant pathogenic microbes and can be used as a powerful antimicrobial agent for various therapeutic applications.
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Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes
TL;DR: The present study describes the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons.
Journal ArticleDOI
Genome and evolution of the shade-requiring medicinal herb Panax ginseng.
Nam-Hoon Kim,Murukarthick Jayakodi,Sang Choon Lee,Beom-Soon Choi,Woojong Jang,Junki Lee,Hyun Hee Kim,Nomar Espinosa Waminal,Nomar Espinosa Waminal,Meiyappan Lakshmanan,Binh van Nguyen,Yun Sun Lee,Hyun-Seung Park,Hyun Jo Koo,Jee Young Park,Sampath Perumal,Ho Jun Joh,Hana Lee,Jin-Kyung Kim,In Seo Kim,Kyung-Hee Kim,Lokanand Koduru,Kyo Bin Kang,Sang Hyun Sung,Yeisoo Yu,Daniel S. Park,Doil Choi,Eunyoung Seo,Seungill Kim,Young-Chang Kim,Dong Yun Hyun,Youn-Il Park,Changsoo Kim,Tae-Ho Lee,Hyun Uk Kim,Moon Soo Soh,Yi Lee,Jun Gyo In,Heui Soo Kim,Yong-Min Kim,Deok-Chun Yang,Rod A. Wing,Dong-Yup Lee,Dong-Yup Lee,Andrew H. Paterson,Tae-Jin Yang +45 more
TL;DR: Functional and evolutionary analyses suggest that production of pharmacologically important dammarane‐type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light.
Journal ArticleDOI
Brazilian Cerrado soil reveals an untapped microbial potential for unpretreated polyethylene biodegradation.
TL;DR: Nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado are isolated, indicating that these microbes are capable of degrading unpretreated PE of very high molecular weight and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers.
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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