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Open AccessArticle

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

by Guanghong Zuo 1, Zhao Xu 2 and Bailin Hao 1,*
1
Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
2
Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA
*
Author to whom correspondence should be addressed.
Life 2015, 5(1), 949-968; https://doi.org/10.3390/life5010949
Received: 9 December 2014 / Revised: 6 March 2015 / Accepted: 9 March 2015 / Published: 17 March 2015
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation. View Full-Text
Keywords: Archaea; phylogeny and taxonomy; 16S rRNA analysis; whole-genome comparison; alignment free; CVTree Archaea; phylogeny and taxonomy; 16S rRNA analysis; whole-genome comparison; alignment free; CVTree
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Zuo, G.; Xu, Z.; Hao, B. Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis. Life 2015, 5, 949-968.

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