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Open Access Research article

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

Dave TP Tang, Evgeny A Glazov, Sean M McWilliam, Wesley C Barris and Brian P Dalrymple*

Author Affiliations

CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia

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BMC Genomics 2009, 10:188  doi:10.1186/1471-2164-10-188

Published: 24 April 2009

Additional files

Additional file 1:

Figure S1 – Bioinformatics pipeline for prediction of functional cow tRNA genes. The pipeline shows the various stages of tRNA filtering for the cow genome using bioinformatics and comparative genomics. Each process is indicated by a rectangle and each data store by a slanted rectangle. For more details for each process please refer to the Methods section.

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Additional file 2:

Table S1 – Codon usage in Bos taurus genome compared against tRNA gene number. The number of cow tRNA genes was predicted using our comparative approach (see methods). Codons that have been highlighted in bold are generally decoded by a single tRNA species due to wobble. Codon frequencies were obtained from http://www.kazusa.or.jp/codon/ webcite.

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Additional file 3:

btau3.1_tRNA.fa – Fasta file of our confident set of cow tRNA genes. The fasta file is annotated in the same format as seen in [26].

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Additional file 4:

Figure S5 – Cluster relationships of cow serine tRNA genes. Relationships between cow serine tRNA genes and a histidine tRNA gene, which is used as an outgroup. Posterior probability scores are shown for each cluster to support the strength of the respective clusters.

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Additional file 5:

Figure S6 – Cluster relationships of cow valine tRNA genes. Relationships between cow valine tRNA genes and a histidine tRNA gene, which is used as an outgroup. Posterior probability scores are shown for each cluster to support the strength of the respective clusters.

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Additional file 6:

Figure S2 – Multiple sequence alignment of predicted cow glycine tRNA genes. Multiple sequence alignment of all glycine tRNA genes with 20 bp of flanking sequence identified in the cow genome. BoxA (corresponding to nt 8–19) and BoxB (corresponding to nt 52–62) sites constitute internal promoter sites for RNA polymerase III. Conserved nucleotides are highlighted and indicated by asterisks.

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Additional file 7:

Table S2 – Summary of BLASTn matches and number of tRNA gene matches at a 95% similarity threshold. Cow tRNA genes were blasted against the full set of tRNA genes from a respective genome. BLAST results were parsed using two different thresholds, an e-value of 0.0001 and using our comparative approach.

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Additional file 8:

Table S3 – Summary of most abundant phylogenetic profiles and the bovine tRNA genes constituting the profile. The number of cow tRNA genes that make up the most abundant phylogenetic profiles are shown. Cow tRNA genes are grouped according to their amino acid specificity and anticodon.

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Additional file 9:

Figure S3 – Predicted secondary structure of the consensus Bov-tA2 sequence (downloaded from RepBase). Repetitive elements derived from tRNA maintain sequence similarity as well as structural features. Here we observe the similar stem loop structure of Bov-tA2 to tRNAs. Prediction of the secondary structure was done using tools available at Genomic tRNA database website [26].

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Additional file 10:

Figure S4 – Phylogenetic relationships of human, chimpanzee, rat, mouse, dog, horse, cow, opossum, platypus, chicken, lizard, tetraodon, fugu, stickleback, medaka, zebrafish, lamprey, lancelet, sea squirt and sea urchin. Phylogenetic relationships of many vertebrate genomes based on NCBI taxonomy.

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