CVTree3 Web Server for Whole-Genome-Based and Alignment-Free Prokaryotic Phylogeny and Taxonomy

Abstract

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

“…Additionally, the phylogenetic relationships between complete and draft genomes from A. caldus strains were estimated. We employed an online platform CVTree3 (Zuo and Hao, 2015) to construct the whole-genome based phylogenetic tree using a composition vector approach. This whole-genome-based and alignment-free prokaryotic phylogeny was validated by directly comparing our result with the taxonomy of these strains, as opposed to performing statistical resampling tests such as bootstrap or jackknife.…”

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

“…The web server CVTree3, which is an alignment- and parameter-free method that relies on the oligopeptide content ( K -tuple length) of conserved proteins to deduce evolutionary relatedness (Zuo and Hao 2015), was used for phylogenetic analysis. The web server constructs phylogenetic trees using the Neighbor-Joining method based on a dissimilarity matrix.…”

“…Trees constructed by the web server are not subjected to statistical re-sampling (bootstrap or jackknife analyses) because the underlying method emphasizes on the “objective” correctness of phylogeny with respect to taxonomy. The method also does not provide a “scale” for the length of the branches because it emphasizes on tree topology and not evolutionary time (Zuo and Hao 2015). …”

Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis

“…In fact, all these 11 genomes were discussed and three deposited by Sheridan et al (2016b). Uploading these genomes to the wholegenome-based web server CVTree3 (Zuo & Hao, 2015) together with 2755 archaeal and bacterial genomes, phylogenetic trees for K=3-9 (K denoting the peptide length in the alignment-free algorithm; see, for example, Zuo et al, 2014) are easily generated. The vicinity of E. rectale may be represented in shorthand notation as (Roseburia{6/7}, (R. faecis{1}, E. rectale {4})).…”

“…Detailed, interactively expandable and collapsible results may be inspected by inputting the Project Number 30160305_0739_16116 to the CVTree3 web server (Zuo & Hao, 2015) at http://tlife. fudan.edu.cn/cvtree3/.…”