Phylogenetics
Phylogenetics analysis of SARS-CoV-2 spike glycoproteins
A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China [1]. This virus belongs to the coronavirus family from which previous outbreaks have emerged (SARS and MERS). They have been a great threat to public health causing many deaths including SARS-CoV-2. There is no proper treatment available to cure this coronavirus disease (covid19). Scientists and researchers are trying really hard to develop a drug or a vaccine or a proper way to cure covid19.
In this essence, Bioinformatics Review has built up a team of worldwide researchers to work on covid19. We will be updating all findings we get during this project. The first study we conducted on SARS-CoV-2 is explained as follows.
Phylogenetics analysis of SARS-CoV-2
The phylogenetic tree is shown below. This tree was created using the IQTREE tool [2] and the best model was found using ModelFinder [3].
Fig. 1 Phylogenetic tree of SARS-CoV-2 spike sequences with SARS-CoV spike sequences as an outgroup. The red color denotes SARS-CoV-2 spike sequences and green color denotes SARS-CoV spike sequences. The best model was VT+F4 as selected by the ModelFinder and the tree was constructed with 1000 replications.
The branch lengths of spike sequences suggest the divergence of SARS-CoV from SARS-CoV-2. The multiple sequence alignment (MSA) (Fig. 2) of these sequences shows several conserved regions across the entire alignment (File 1).
Further, experiments are being performed for a complete phylogeny and evolutionary study of these sequences. For all updates regarding Covid19 work being done by our research group, visit this page.
References
- Zhu, N., Zhang, D., & Wang, W. China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019 [published January 24, 2020]. N Engl J Med.
- Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution, 32(1), 268-274.
- Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature methods, 14(6), 587.
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MEGAX is a bioinformatics software/tool used for phylogenetic tree construction. In this article, we will construct a maximum likelihood (ML) tree for a number of protein sequences using MEGA7 [1]. (more…)
Covid19 has created a great threat to human health. As you are aware, in this coronavirus outbreak, Bioinformatics Review has created a group, BiR-nCov19 Drug Development Team, to work on finding prevention to this disease. This research group consists of researchers from all over the world. (more…)
Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criteria: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. (more…)
If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program [2] to calculate the dN/dS substitutions rate. Here is how you can do it. (more…)
Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the available online servers mess your file and the output format is also not supported by the other programs. Additionally, it is quite difficult to perform other customizations on the phylogeny tree. (more…)
Understanding evolution is critical for understanding biology. As the preeminent scientist Theodosius Dobzhansky stated, “Nothing in biology makes sense except in the light of evolution.” Evolution is the only scientific explanation for the diversity of life. It explains the striking similarities among vastly different forms of life, the changes that occur within populations, and the development of new life forms. Excluding evolution from the science curricula or compromising its treatment deprives students of this fundamental and unifying scientific concept to explain the natural world. (more…)
MEGA: Molecular Evolutionary Genetic Analysis
It is important to know the basic molecular relationship between two living organisms as one begins performing comparative studies for knowing the evolutionary aspects and for contributing to knowledge base. Several tools and soft ware have been introduced for meeting the task of such analysis. Each tool has different algorithm and method to perform molecular phylogeny. Examples include; ClustalW, Dendroscope, Hyphy, PAUP and Phylip etc. Among them is the most efficient tool, MEGA, Molecular evolutionary phylogenetic analysis which performs both sequence analysis and phylogenetic analysis in a very sophisticated manner.
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Estimation of present day diversity of organism and understanding their diversity forms new cornerstones of conservation biology, evolutionary biology and ecology. Maintaining the totality of all texa from past to present and classifying into groups reflect how they have changed over the period of times. Necessarily, phylogenetics and evolutionary study of a particular group help out in knowing pattern of occurrence and relationships between two distantly related class or families and their descendents. (more…)
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