Analysis of the complement and molecular evolution of tRNA genes in cow

Tang, Dave T. P., Glazov, Evgeny A., McWilliam, Sean M., Barris, Wesley C. and Dalrymple, Brian P. (2009) Analysis of the complement and molecular evolution of tRNA genes in cow. BMC Genomics, 10 188.1-188.13. doi:10.1186/1471-2164-10-188


Author Tang, Dave T. P.
Glazov, Evgeny A.
McWilliam, Sean M.
Barris, Wesley C.
Dalrymple, Brian P.
Title Analysis of the complement and molecular evolution of tRNA genes in cow
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2009-04-24
Sub-type Article (original research)
DOI 10.1186/1471-2164-10-188
Open Access Status DOI
Volume 10
Start page 188.1
End page 188.13
Total pages 13
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Subject 0604 Genetics
Formatted 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.

Conclusion
: 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 188

Document type: Journal Article
Sub-type: Article (original research)
Collections: UQ Diamantina Institute - Open Access Collection
UQ Diamantina Institute Publications
 
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Created: Thu, 23 Sep 2010, 16:30:41 EST by Laura McTaggart on behalf of UQ Diamantina Institute