Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach

Abstract

The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey's Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.Archaea, phylogeny, taxonomy, composition vector, alignment-free, CVTree, 16S rRNA analysis Citation:Sun J D, Xu Z, Hao B L. Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach.

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

“…Since the methodology and foundation of the CVTree approach has been demonstrated in numerous previous publications [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] as well as discussed by other authors [25] , [26] , we provide only a brief summary of the essentials in this paper.…”

“…Lineage modifications and taxonomic revisions are routine issues, leading to a convergent phylogeny-based classification of microbial organisms. Over the years, CVTree has been applied to viruses [33] , [34] , Archaea and Bacteria [13] , [14] , [15] , [16] , [17] , [18] , [20] , [21] , [22] , [24] , chloroplasts [35] , and fungi [36] with remarkable success. The powerful and parallelized CVTree3 web server will bring about many additional new applications.…”

“…However, effectively inferring phylogenetic trees from the genome sequences and comparing the branching orders with taxonomy at all ranks present challenges. To this end, the composition vector (CV) approach to prokaryotic phylogeny developed by our group in the last decade [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] has the potential to meet this challenge. In this paper, we describe the latest version (Version 3) of the CVTree web server and demonstrate its applications.…”

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

“…The CVTree results summarized above were a continuation and extension of a similar study [ 56 ] based on 62 Archaea genomes available at the beginning of 2010. The fact that, five years apart and with 117 more genomes added, the results remain consistent informs of the robustness of the CVTree approach.…”

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

“…Finally, although alignment-free approaches have recently been proposed to enable genome-scale phylogenetic inference, such as the average common subsequence [ 105 ], composition vector (CVTree) [ 106 ], k-mer [ 107 ] methods, to the best of our knowledge, they have not been used in the phylogenetic analysis of SARS-CoV-2.…”