ArticleBMC genomics2009
Analysis of the complement and molecular evolution of tRNA genes in cow.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
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- How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?Genome biology and evolution · 2026Article
- Sex-biased duplicates are rapidly generated duringbioRxiv : the preprint server for biology · 2025Article
- tRNA gene content, structure, and organization in the flowering plant lineage.Frontiers in plant science · 2024Article
- Identification of a tsRNA Contributor to Impaired Diabetic Wound Healing via High Glucose-Induced Endothelial Dysfunction.Diabetes, metabolic syndrome and obesity : targets and therapy · 2023Article
- Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus.G3 (Bethesda, Md.) · 2022Article
- Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds.Genome biology and evolution · 2021Article
- Gene transfer and nucleotide sequence evolution by Gossypium cytoplasmic genomes indicates novel evolutionary characteristics.Plant cell reports · 2020Article
- Transfer RNA genes experience exceptionally elevated mutation rates.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs.Frontiers in genetics · 2017Article
- Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.Nucleic acids research · 2015Article
- tRNA anticodon shifts in eukaryotic genomes.RNA (New York, N.Y.) · 2014Article
- Complete genome sequence of Riemerella anatipestifer reference strain.Journal of bacteriology · 2012Article
- Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae).BMC evolutionary biology · 2010Article
- The evolution of tRNA genes in Drosophila.Genome biology and evolution · 2010Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDetailed information regarding the number and organization of transfer RNA (tRNA) genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale.
resultsIn this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-GlyCCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-GlyGCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes.
conclusionThe use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a set of cow tRNA genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes.
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