Whole genome-based phylogenetic analysis of free-living microorganisms

Sorel T. Fitz-Gibbon, Christopher H. House

Research output: Contribution to journalArticle

212 Citations (Scopus)

Abstract

A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relationships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.

Original languageEnglish (US)
Pages (from-to)4218-4222
Number of pages5
JournalNucleic acids research
Volume27
Issue number21
DOIs
StatePublished - Nov 1 1999

Fingerprint

Genome
Archaeoglobus
Genes
Horizontal Gene Transfer
History
Proteins

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

@article{eb3d9df681e34f7eb6f4c37bf8071cef,
title = "Whole genome-based phylogenetic analysis of free-living microorganisms",
abstract = "A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relationships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.",
author = "Fitz-Gibbon, {Sorel T.} and House, {Christopher H.}",
year = "1999",
month = "11",
day = "1",
doi = "10.1093/nar/27.21.4218",
language = "English (US)",
volume = "27",
pages = "4218--4222",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "21",

}

Whole genome-based phylogenetic analysis of free-living microorganisms. / Fitz-Gibbon, Sorel T.; House, Christopher H.

In: Nucleic acids research, Vol. 27, No. 21, 01.11.1999, p. 4218-4222.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Whole genome-based phylogenetic analysis of free-living microorganisms

AU - Fitz-Gibbon, Sorel T.

AU - House, Christopher H.

PY - 1999/11/1

Y1 - 1999/11/1

N2 - A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relationships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.

AB - A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relationships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.

UR - http://www.scopus.com/inward/record.url?scp=0033231209&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0033231209&partnerID=8YFLogxK

U2 - 10.1093/nar/27.21.4218

DO - 10.1093/nar/27.21.4218

M3 - Article

C2 - 10518613

AN - SCOPUS:0033231209

VL - 27

SP - 4218

EP - 4222

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 21

ER -