title: Analysis of the complement and molecular evolution of tRNA genes in cow.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: CSIRO Livestock Industries, Queensland Biosciences Precinct, St Lucia, QLD, Australia. d.tang@imb.uq.edu.au
authors.forename: Dave T P
authors.initials: DT
authors.lastname: Tang
authors.forename: Evgeny A
authors.initials: EA
authors.lastname: Glazov
authors.forename: Sean M
authors.initials: SM
authors.lastname: McWilliam
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Barris
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002417:Cattle / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D012343:RNA, Transfer / Q000145:classification / Q000235:genetics*
chemical_list: D012343:RNA, Transfer