Functional genome annotation through phylogenomic mapping

Balaji S. Srinivasan, Nora B. Caberoy, Garret Suen, Rion G. Taylor, Radhika Shah, Farah Tengra, Barry S. Goldman, Anthony G. Garza, Roy D. Welch

Research output: Contribution to journalReview article

19 Scopus citations

Abstract

Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation-phylogenomic mapping-that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. We have developed and applied it to more than 200 sequenced bacterial genomes. Proteins with similar evolutionary histories were grouped together, placed on a three dimensional map and visualized as a topographical landscape. The resulting phylogenomic maps display thousands of proteins clustered in mountains on the basis of coinheritance, a strong indicator of shared function. In addition to systematic computational validation, we have experimentally confirmed the ability of phylogenomic maps to predict both mutant phenotype and gene function in the delta proteobacterium Myxococcus xanthus.

Original languageEnglish (US)
Pages (from-to)691-698
Number of pages8
JournalNature Biotechnology
Volume23
Issue number6
DOIs
StatePublished - Dec 9 2005

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

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    Srinivasan, B. S., Caberoy, N. B., Suen, G., Taylor, R. G., Shah, R., Tengra, F., Goldman, B. S., Garza, A. G., & Welch, R. D. (2005). Functional genome annotation through phylogenomic mapping. Nature Biotechnology, 23(6), 691-698. https://doi.org/10.1038/nbt1098