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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 Archaea branch in the All-Species Living Tree based on 366 16S rRNA sequences. The tree has been collapsed to the rank class (<C>), and only one lineage modification has been made. Numerals in curly brackets indicate the number of sequences contained in a collapsed branch. The collapsing and lineage modification was performed by using a web server similar to CVTree3. This Living Tree Viewer is accessible to all users [51].
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life-05-00949-f001: The Archaea branch in the All-Species Living Tree based on 366 16S rRNA sequences. The tree has been collapsed to the rank class (<C>), and only one lineage modification has been made. Numerals in curly brackets indicate the number of sequences contained in a collapsed branch. The collapsing and lineage modification was performed by using a web server similar to CVTree3. This Living Tree Viewer is accessible to all users [51].

Mentions: After making the lineage modification, we get Figure 1. The branchings in Figure 1 fully agree with the taxonomy of Archaea, as outlined in Section 3, at the phylum and class ranks. In particular, the eight classes of Euryarchaeota all behave as well-defined monophyletic branches. Further more, if one expands the class Methanomicrobia, its three subordinate orders, Methanocellales{3}, Methanosarcinales{31} and Methanomicrobiales{37}, all appear as monophyletic branches (not shown in Figure 1). The definition of orders within Thermoprotei, the only class in Crenarchaeota, is somehow problematic (more on this point near the end of Subsection 4.2).


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 Archaea branch in the All-Species Living Tree based on 366 16S rRNA sequences. The tree has been collapsed to the rank class (<C>), and only one lineage modification has been made. Numerals in curly brackets indicate the number of sequences contained in a collapsed branch. The collapsing and lineage modification was performed by using a web server similar to CVTree3. This Living Tree Viewer is accessible to all users [51].
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00949-f001: The Archaea branch in the All-Species Living Tree based on 366 16S rRNA sequences. The tree has been collapsed to the rank class (<C>), and only one lineage modification has been made. Numerals in curly brackets indicate the number of sequences contained in a collapsed branch. The collapsing and lineage modification was performed by using a web server similar to CVTree3. This Living Tree Viewer is accessible to all users [51].
Mentions: After making the lineage modification, we get Figure 1. The branchings in Figure 1 fully agree with the taxonomy of Archaea, as outlined in Section 3, at the phylum and class ranks. In particular, the eight classes of Euryarchaeota all behave as well-defined monophyletic branches. Further more, if one expands the class Methanomicrobia, its three subordinate orders, Methanocellales{3}, Methanosarcinales{31} and Methanomicrobiales{37}, all appear as monophyletic branches (not shown in Figure 1). The definition of orders within Thermoprotei, the only class in Crenarchaeota, is somehow problematic (more on this point near the end of Subsection 4.2).

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.