 | This article needs to be updated. (October 2019) |
'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. [1] At one stage, 23S sequences were also collected, [2] but this has since stopped. [3]
Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.
Similar (and more recent) projects include the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which focused on whole genome sequencing of bacteria and archaea. [4] [5]
Tree
The tree was created by maximum likelihood analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis). This phylogeny is a summary of the 16S rRNA based LTP_08_2023 and contains all type species with validly published names up to August 2023. [6] [7] [8]
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
See also
- Branching order of bacterial phyla (Woese, 1987)
- Branching order of bacterial phyla (Gupta, 2001)
- Branching order of bacterial phyla (Cavalier-Smith, 2002)
- Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
- Branching order of bacterial phyla (Battistuzzi et al., 2004)
- Branching order of bacterial phyla (Ciccarelli et al., 2006)
- Branching order of bacterial phyla (Genome Taxonomy Database, 2018)
- Bacterial phyla
- List of Archaea genera
- List of bacteria genera
- List of bacterial orders
- LPSN, list of accepted bacterial and archaeal names
References
- ^ Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi: 10.1016/j.syapm.2008.07.001. hdl: 10261/103580. PMID 18692976.
- ^ Yarza, Pablo; Ludwig, Wolfgang; Euzéby, Jean; Amann, Rudolf; Schleifer, Karl-Heinz; Glöckner, Frank Oliver; Rosselló-Móra, Ramon (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi: 10.1016/j.syapm.2010.08.001. PMID 20817437.
- ^ Munoz, R. L.; Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Oliver Glöckner, F.; Rosselló-Móra, R. (2011). "Release LTPs104 of the All-Species Living Tree". Systematic and Applied Microbiology. 34 (3): 169–170. doi: 10.1016/j.syapm.2011.03.001. PMID 21497273.
- ^ Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D. (December 2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. Bibcode: 2009Natur.462.1056W. doi: 10.1038/nature08656. ISSN 0028-0836. PMC 3073058. PMID 20033048.
- ^ Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R. (5 August 2014). "Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains". PLOS Biology. 12 (8): e1001920. doi: 10.1371/journal.pbio.1001920. ISSN 1545-7885. PMC 4122341. PMID 25093819.
- ^ "The LTP". Retrieved 20 November 2023.
- ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
- ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
External links
| This article needs to be updated. (October 2019) |
'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. [1] At one stage, 23S sequences were also collected, [2] but this has since stopped. [3]
Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.
Similar (and more recent) projects include the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which focused on whole genome sequencing of bacteria and archaea. [4] [5]
Tree
The tree was created by maximum likelihood analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis). This phylogeny is a summary of the 16S rRNA based LTP_08_2023 and contains all type species with validly published names up to August 2023. [6] [7] [8]
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
See also
- Branching order of bacterial phyla (Woese, 1987)
- Branching order of bacterial phyla (Gupta, 2001)
- Branching order of bacterial phyla (Cavalier-Smith, 2002)
- Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
- Branching order of bacterial phyla (Battistuzzi et al., 2004)
- Branching order of bacterial phyla (Ciccarelli et al., 2006)
- Branching order of bacterial phyla (Genome Taxonomy Database, 2018)
- Bacterial phyla
- List of Archaea genera
- List of bacteria genera
- List of bacterial orders
- LPSN, list of accepted bacterial and archaeal names
References
- ^ Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi: 10.1016/j.syapm.2008.07.001. hdl: 10261/103580. PMID 18692976.
- ^ Yarza, Pablo; Ludwig, Wolfgang; Euzéby, Jean; Amann, Rudolf; Schleifer, Karl-Heinz; Glöckner, Frank Oliver; Rosselló-Móra, Ramon (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi: 10.1016/j.syapm.2010.08.001. PMID 20817437.
- ^ Munoz, R. L.; Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Oliver Glöckner, F.; Rosselló-Móra, R. (2011). "Release LTPs104 of the All-Species Living Tree". Systematic and Applied Microbiology. 34 (3): 169–170. doi: 10.1016/j.syapm.2011.03.001. PMID 21497273.
- ^ Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D. (December 2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. Bibcode: 2009Natur.462.1056W. doi: 10.1038/nature08656. ISSN 0028-0836. PMC 3073058. PMID 20033048.
- ^ Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R. (5 August 2014). "Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains". PLOS Biology. 12 (8): e1001920. doi: 10.1371/journal.pbio.1001920. ISSN 1545-7885. PMC 4122341. PMID 25093819.
- ^ "The LTP". Retrieved 20 November 2023.
- ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
- ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.