title: Functional genome annotation through phylogenomic mapping.
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.
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Balaji S
authors.initials: BS
authors.lastname: Srinivasan
authors.forename: Nora B
authors.initials: NB
authors.lastname: Caberoy
authors.forename: Garret
authors.initials: G
authors.lastname: Suen
authors.forename: Rion G
authors.initials: RG
authors.lastname: Taylor
authors.forename: Radhika
authors.initials: R
authors.lastname: Shah
authors.forename: Farah
authors.initials: F
authors.lastname: Tengra
authors.forename: Barry S
authors.initials: BS
authors.lastname: Goldman
authors.forename: Anthony G
authors.initials: AG
authors.lastname: Garza
authors.forename: Roy D
authors.initials: RD
authors.lastname: Welch
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D005075:Biological Evolution; D019295:Computational Biology; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D016941:Myxococcus xanthus / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny
chemical_list: D001426:Bacterial Proteins