There are several models of the branching order of bacterial phyla, one of these is the
Genome Taxonomy Database (GTDB).
The GTDB is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by an Australian Research Council Laureate Fellowship. The genomes used to construct the phylogeny are obtained from
RefSeq and
Genbank, and GTDB releases are indexed to
RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB.
The GTDB taxonomy is based on genome trees inferred with FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria, and with IQ-TREE from a concatenated set of 53 (since RS207; 122 before) marker proteins for Archaea. Additional marker sets are also used to cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes.
National Center for Biotechnology Information (NCBI) taxonomy was initially used to decorate the genome tree via tax2tree. The 16S rRNA-based
Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured representatives.
List of Prokaryotic names with Standing in Nomenclature (LPSN) is used as the primary taxonomic authority for establishing naming priorities. Taxonomic ranks are normalised using PhyloRank and the taxonomy manually curated to remove polyphyletic groups.
Phylogeny
Cladogram was taken from
GTDB
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to breaking up parap ...
release 07-RS207 (8th April 2022).
See also
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Branching order of bacterial phyla (Woese, 1987)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.
The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all p ...
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Branching order of bacterial phyla after ARB Silva Living Tree
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 ...
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Branching order of bacterial phyla (Ciccarelli et al., 2006)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli ''et al.'' for their iTOL project.
This tree is based on a concatenated set of conserved protein and not 16S rRNA (cf. Branchi ...
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Branching order of bacterial phyla (Battistuzzi et al.,2004)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2004 by Battistuzzi and Hedges, note the coinage of the taxa Terrabacteria and Hydrobacteria.
See also
* Branching order of bacterial phyla (Woes ...
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Branching order of bacterial phyla (Gupta, 2001)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic ex ...
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Branching order of bacterial phyla (Cavalier-Smith, 2002)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some mor ...
External links
Genome Taxonomy Database
References
{{DEFAULTSORT:Bacterial Phyla
Bacteria phyla
Bacteriology
Systems of bacterial taxonomy