A phylum-level bacterial phylogenetic marker database.
Mol Biol Evol
; 30(6): 1258-62, 2013 Jun.
Article
in En
| MEDLINE
| ID: mdl-23519313
ABSTRACT
Large-scale, genome-level molecular phylogenetic analyses present both opportunities and challenges for bacterial evolutionary and ecological studies. We constructed a phylum-level bacterial phylogenetic marker database by surveying all complete bacterial genomes and identifying single-copy genes that were widely distributed in each of the 20 bacterial phyla. We showed that phylum trees made using these markers were highly resolved and were more robust than the bacterial genome tree based on 31 universal bacterial marker genes. In addition, using the Global Ocean Sampling data set as an example, we demonstrated that the expanded marker database greatly increased the power of metagenomic phylotyping. We incorporated the database into an automated phylogenomic inference application (Phyla-AMPHORA) and made it publicly available. We believe that this centralized resource should have broad applicability in bacterial systematics, phylogenetics, and metagenomic studies.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Bacteria
/
Genetic Markers
/
Computational Biology
/
Databases, Genetic
/
Genes, Bacterial
Language:
En
Journal:
Mol Biol Evol
Journal subject:
BIOLOGIA MOLECULAR
Year:
2013
Type:
Article
Affiliation country:
United States