Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam
Abstract
To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. Inmore »
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Biological Sciences
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
- Sponsoring Org.:
- USDOE Office of Science (SC); USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1286772
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Evolutionary Biology (Online)
- Additional Journal Information:
- Journal Name: BMC Evolutionary Biology (Online); Journal Volume: 14; Journal Issue: 1; Journal ID: ISSN 1471-2148
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Prokaryotes; Cellular function; Pathway; Genomes; Evolution; Phylogenomics
Citation Formats
Chai, Juanjuan, Kora, Guruprasad, Ahn, Tae-Hyuk, Hyatt, Doug, and Pan, Chongle. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. United States: N. p., 2014.
Web. doi:10.1186/s12862-014-0207-y.
Chai, Juanjuan, Kora, Guruprasad, Ahn, Tae-Hyuk, Hyatt, Doug, & Pan, Chongle. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. United States. https://doi.org/10.1186/s12862-014-0207-y
Chai, Juanjuan, Kora, Guruprasad, Ahn, Tae-Hyuk, Hyatt, Doug, and Pan, Chongle. Thu .
"Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam". United States. https://doi.org/10.1186/s12862-014-0207-y. https://www.osti.gov/servlets/purl/1286772.
@article{osti_1286772,
title = {Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam},
author = {Chai, Juanjuan and Kora, Guruprasad and Ahn, Tae-Hyuk and Hyatt, Doug and Pan, Chongle},
abstractNote = {To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.},
doi = {10.1186/s12862-014-0207-y},
journal = {BMC Evolutionary Biology (Online)},
number = 1,
volume = 14,
place = {United States},
year = {Thu Oct 09 00:00:00 EDT 2014},
month = {Thu Oct 09 00:00:00 EDT 2014}
}
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