skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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 » 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.« less

Authors:
 [1];  [1];  [1];  [2];  [3]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Biological Sciences
  3. 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 Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1286772
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: 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. doi: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. doi: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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007

  • Moriya, Y.; Itoh, M.; Okuda, S.
  • Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
  • DOI: 10.1093/nar/gkm321

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

Search and clustering orders of magnitude faster than BLAST
journal, August 2010