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

Life
Guanghong ZuoBailin Hao

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.

References

Nov 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·C R Woese, G E Fox
Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·C R WoeseM L Wheelis
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·S M BarnsN R Pace
Jun 17, 1998·Proceedings of the National Academy of Sciences of the United States of America·C Woese
Feb 12, 2002·International Journal of Systematic and Evolutionary Microbiology·T Cavalier-Smith
Oct 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth WatersMichiel Noordewier
Jun 25, 2004·Nucleic Acids Research·Ji QiBailin Hao
Jul 24, 2004·Journal of Bioinformatics and Computational Biology·Bailin Hao, Ji Qi
Sep 15, 2005·Journal of Bacteriology·Konstantinos T Konstantinidis, James M Tiedje
Oct 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·G E FoxC R Woese
Jul 28, 2006·Nature·Anna-Louise ReysenbachMary A Voytek
Feb 16, 2008·Nature Reviews. Microbiology·Céline Brochier-ArmanetPatrick Forterre
Aug 12, 2008·Systematic and Applied Microbiology·Pablo YarzaRamon Rosselló-Móra
Aug 30, 2008·Molecular Genetics and Genomics : MGG·Andreas Wagner, Nicole de la Chaux
Jul 28, 2009·Research in Microbiology·Simonetta Gribaldo, Celine Brochier
Oct 20, 2009·International Journal of Systematic and Evolutionary Microbiology·Anna A PerevalovaElizaveta A Bonch-Osmolovskaya
Apr 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Brett J BakerJillian F Banfield
Aug 17, 2010·Antonie van Leeuwenhoek·Radhey S Gupta, Ali Shami
Sep 8, 2010·Systematic and Applied Microbiology·Pablo YarzaRamon Rosselló-Móra
Dec 15, 2010·Extremophiles : Life Under Extreme Conditions·Thomas A AuchtungColleen M Cavanaugh
Mar 9, 2011·Genomics, Proteomics & Bioinformatics·Guanghong ZuoBailin Hao
May 7, 2011·Current Opinion in Microbiology·Michael PesterMichael Wagner
Jun 3, 2011·Current Opinion in Microbiology·Celine Brochier-ArmanetSimonetta Gribaldo
Oct 25, 2011·Trends in Microbiology·Lionel Guy, Thijs J G Ettema
May 9, 2012·International Journal of Systematic and Evolutionary Microbiology·Patricia P ChanTodd M Lowe
Sep 26, 2013·Frontiers in Microbiology·Scott ClingenpeelTimothy R McDermott
Nov 19, 2013·Nucleic Acids Research·Aidan C Parte
Dec 3, 2013·Nucleic Acids Research·Pelin YilmazFrank Oliver Glöckner
Sep 11, 2014·Computational Biology and Chemistry·Guanghong ZuoBailin Hao
Nov 14, 2015·Genomics, Proteomics & Bioinformatics·Guanghong Zuo, Bailin Hao
Jan 1, 2010·Chinese Science Bulletin = Kexue Tongbao·JianDong SunBaiLin Hao

❮ Previous
Next ❯

Citations

Jan 23, 2016·Microbial Ecology·Christoph ReitschulerPaul Illmer
Jun 24, 2016·PLoS Computational Biology·Raquel BrombergZbyszek Otwinowski
Jul 10, 2019·International Journal of Genomics·Kai ChenChao-An Long
Jul 16, 2019·The Science of the Total Environment·Chetan KeswaniHarikesh B Singh
Jun 23, 2021·Nature Microbiology·Christian RinkePhilip Hugenholtz

❮ Previous
Next ❯

Methods Mentioned

BETA
pull down

Software Mentioned

All
CVTree3
CVTrees
Species Living Tree Project ( LTP )
CVTree

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.