ArticleRNA (New York, N.Y.)2010
Stable tRNA-based phylogenies using only 76 nucleotides.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Investigations into the Diversity and Distribution of tRNA and Phylogenetics of Translation Factors in Amoebozoa-InfectingViruses · 2025Article
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
- tRNA modification profiles in obligate and moderate thermophilic bacilli.Extremophiles : life under extreme conditions · 2022Article
- Article
- Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.ISME communications · 2021Article
- Steller's sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans.Nature communications · 2021Article
- On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions?Frontiers in molecular biosciences · 2021Review
- The complete mitochondrial genome of a parasite at the animal-fungal boundary.Parasites & vectors · 2020Article
- Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtlesPeerJ · 2020Article
- Article
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis.Nature communications · 2018Article
- Rooted tRNAomes and evolution of the genetic code.Transcription · 2018Article
- MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination.Epigenetics & chromatin · 2017Article
- Evolution of initiator tRNAs and selection of methionine as the initiating amino acid.RNA biology · 2016Article
- Article
- A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes.Genome biology and evolution · 2015Article
- Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T.SpringerPlus · 2015Article
- tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria.PLoS computational biology · 2014Article
- Article
- Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes.Nucleic acids research · 2013Article
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Authors and funding
5 authors.
Funding
Abstract
tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.
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