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.
Highlights
Detailed information regarding the number and organization of transfer RNA genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes
We suggest that this subfamily originated from an ancestral tRNAGlyGCC gene via a point mutation prior to the radiation of the mammalian lineages
The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a set of cow transfer RNA (tRNA) genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes
Summary
Detailed 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. The tRNA multigene family usually comprises 20 amino acid accepting groups; each group may contain one or more tRNA members that recognize different codons commonly referred to as tRNA isoacceptors. In some cases tRNAs that charge different amino acids share higher sequence similarity than respective tRNAs in the same isoaccepting group [8]. This interesting observation may be explained by a phenomenon called "tRNA gene recruitment" where a tRNA from one amino acid family can be recruited to another family via a single point mutation [9]. A phylogenetic approach utilizing complete sets of tRNA genes from different genomes will allow us to trace a more complete history of tRNA genes and gain insight into the evolutionary processes that have shaped modern tRNA repertoires
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