In our last article, we mentioned the selection pressure analysis of SARS-CoV-2 spike glycoproteins. Now, we have analyzed spike glycoprotein sequences of SARS-CoV. No single purifying selection site was found in SARS-CoV spike glycoproteins as was revealed from our last analysis of SARS-CoV-2 spike glycoproteins.
The analysis was performed using Hyphy  on the Datamonkey server . BUSTED , MEME , and FUBAR  methods were used. MEME  and FUBAR  found 6 and 2 sites respectively under positive selection. The threshold was set to 0.05 (p-value) for MEME and 0.9 (posterior probability) for FUBAR. Additionally, unlike SARS-CoV-2, BUSTED  found evidence of selection on the tested branches of the phylogeny of SARS-CoV spike glycoproteins. It implies that there is at least one site on one branch that has experienced gene-wide episodic positive selection.
Interestingly, negative selection has not been found in both SARS-CoV and SARS-CoV-2 spike glycoproteins. Besides, only a small number of sites have been found to be experienced positive selection. These sites of SARS-CoV spike proteins under selection are being analyzed further.
- Pond, S. L. K., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. In Statistical methods in molecular evolution (pp. 125-181). Springer, New York, NY.
- Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Kosakovsky Pond, S. L. (2018). Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Molecular biology and evolution, 35(3), 773-777.
- Murrell, B., Weaver, S., Smith, M. D., Wertheim, J. O., Murrell, S., Aylward, A., … & Scheffler, K. (2015). Gene-wide identification of episodic selection. Molecular biology and evolution, 32(5), 1365-1371.
- Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Pond, S. L. K. (2012). Detecting individual sites subject to episodic diversifying selection. PLoS genetics, 8(7).
- Murrell, B., Moola, S., Mabona, A., Weighill, T., Sheward, D., Kosakovsky Pond, S. L., & Scheffler, K. (2013). FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Molecular biology and evolution, 30(5), 1196-1205.
Tutorial-II: Functional Divergence Analysis using DIVERGE 3.0 software
This is a continuation article of our previous post: Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software. In our last tutorial, we explained Type-II functional divergence. In this article, we will explain the rest of the evolutionary analysis using DIVERGE 3.0 software . (more…)
Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software
DIVERGE is a tool to detect functional divergence between member genes of a protein family based on (site-specific) shifted evolutionary rates after gene duplication or speciation . Since this tool contains several steps and offers a lot to discover, therefore, we are going to split its tutorial into parts. In this article, we will perform some initial steps in this software and will explain their significance. (more…)
Update: Selection analysis on spike glycoprotein of SARS-CoV-2
We have recently conducted a selection pressure analysis on SARS-CoV-2 spike glycoprotein sequences. The analysis revealed not even a single site showing evidence of purifying selection but episodic diversifying selection on three sites. Out of these three sites, two sites are potentially relevant (Fig. 3). (more…)