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

Zuo G, Xu Z, Hao B - Life (Basel) (2015)

Bottom Line: 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.A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.

View Article: PubMed Central - PubMed

Affiliation: Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China. ghongzuo@gmail.com.

ABSTRACT
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.

No MeSH data available.


The 179-genome Archaea branch of CVTree obtained by using the CVTree3 web server [21] without making lineage modifications. It has been collapsed to the rank class where possible. The branching order is to be compared with taxonomy, but does not scale the branch lengths.
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life-05-00949-f002: The 179-genome Archaea branch of CVTree obtained by using the CVTree3 web server [21] without making lineage modifications. It has been collapsed to the rank class where possible. The branching order is to be compared with taxonomy, but does not scale the branch lengths.

Mentions: CVTrees based on 179 Archaea, 2850 Bacteria and eight Eukarya genomes were generated by using the improved version CVTree3 [21] of the web server [20]. We show the Archaea part of a big CVTree in Figure 2. When inspecting the figure, we pay more attention to the newly proposed phyla and those taxa with incomplete or suspicious lineage information.


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

Zuo G, Xu Z, Hao B - Life (Basel) (2015)

The 179-genome Archaea branch of CVTree obtained by using the CVTree3 web server [21] without making lineage modifications. It has been collapsed to the rank class where possible. The branching order is to be compared with taxonomy, but does not scale the branch lengths.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390887&req=5

life-05-00949-f002: The 179-genome Archaea branch of CVTree obtained by using the CVTree3 web server [21] without making lineage modifications. It has been collapsed to the rank class where possible. The branching order is to be compared with taxonomy, but does not scale the branch lengths.
Mentions: CVTrees based on 179 Archaea, 2850 Bacteria and eight Eukarya genomes were generated by using the improved version CVTree3 [21] of the web server [20]. We show the Archaea part of a big CVTree in Figure 2. When inspecting the figure, we pay more attention to the newly proposed phyla and those taxa with incomplete or suspicious lineage information.

Bottom Line: 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.A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.

View Article: PubMed Central - PubMed

Affiliation: Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China. ghongzuo@gmail.com.

ABSTRACT
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.

No MeSH data available.