ArticleGenome research2000
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Protein folds as synapomorphies of the tree of life.Evolution; international journal of organic evolution · 2022Article
- Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families.Evolutionary bioinformatics online · 2020Article
- Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.Archaea (Vancouver, B.C.) · 2016Review
- Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants.BMC genomics · 2015Article
- Article
- A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.Genome biology and evolution · 2014Article
- Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes.PloS one · 2014Article
- Global patterns of protein domain gain and loss in superkingdoms.PLoS computational biology · 2014Article
- Article
- Exploring fold space preferences of new-born and ancient protein superfamilies.PLoS computational biology · 2013Article
- Metabolic classification of microbial genomes using functional probes.BMC genomics · 2012Article
- The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis.Journal of molecular evolution · 2012Article
- The rhizome of life: what about metazoa?Frontiers in cellular and infection microbiology · 2012Review
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
- Reconstructing phylogeny from metabolic substrate-product relationships.BMC bioinformatics · 2011Article
- Article
- Article
- ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.BMC bioinformatics · 2009Article
- Minimum contradiction matrices in whole genome phylogenies.Evolutionary bioinformatics online · 2008Article
- Phylogeny vs genome reshuffling: horizontal gene transfer.Indian journal of microbiology · 2008Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We built whole-genome trees based on the presence or absence of particular molecular features, either orthologs or folds, in the genomes of a number of recently sequenced microorganisms. To put these genomic trees into perspective, we compared them to the traditional ribosomal phylogeny and also to trees based on the sequence similarity of individual orthologous proteins. We found that our genomic trees based on the overall occurrence of orthologs did not agree well with the traditional tree. This discrepancy, however, vanished when one restricted the tree to proteins involved in transcription and translation, not including problematic proteins involved in metabolism. Protein folds unite superficially unrelated sequence families and represent a most fundamental molecular unit described by genomes. We found that our genomic occurrence tree based on folds agreed fairly well with the traditional ribosomal phylogeny. Surprisingly, despite this overall agreement, certain classes of folds, particularly all-beta ones, had a somewhat different phylogenetic distribution. We also compared our occurrence trees to whole-genome clusters based on the composition of amino acids and di-nucleotides. Finally, we analyzed some technical aspects of genomic trees-e.g., comparing parsimony versus distance-based approaches and examining the effects of increasing numbers of organisms. Additional information (e.g. clickable trees) is available from http://bioinfo.mbb.yale.edu/genome/trees.
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