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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 class, Halobacteria, expanded to the genus level.
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life-05-00949-f004: The class, Halobacteria, expanded to the genus level.

Mentions: The first line of Figure 2<F>Halobacteriaceae{28+1} informs that among the 29 genomes, there was one without proper lineage information. In fact, it was Halophilic_archaeon_DL31_uid72619, a name not validly published and not following the basic rule for a binomen. Its NCBI lineage from phylum down to genus was “unclassified”. However, by expanding this line, the strain is seen to be located deeply inside the class Halobacteria (see Figure 4). As at present, the class consists of only one order, which, in turn, is made of one family [33], it is safe to assign this strain to a yet unspecified genus. This modification would yield a monophyletic branch, Halobacteria{29}.


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 class, Halobacteria, expanded to the genus level.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00949-f004: The class, Halobacteria, expanded to the genus level.
Mentions: The first line of Figure 2<F>Halobacteriaceae{28+1} informs that among the 29 genomes, there was one without proper lineage information. In fact, it was Halophilic_archaeon_DL31_uid72619, a name not validly published and not following the basic rule for a binomen. Its NCBI lineage from phylum down to genus was “unclassified”. However, by expanding this line, the strain is seen to be located deeply inside the class Halobacteria (see Figure 4). As at present, the class consists of only one order, which, in turn, is made of one family [33], it is safe to assign this strain to a yet unspecified genus. This modification would yield a monophyletic branch, Halobacteria{29}.

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.